3RHF | pdb_00003rhf

Crystal structure of Polyphosphate Kinase 2 from Arthrobacter aurescens TC1

PDB DOI: https://doi.org/10.2210/pdb3RHF/pdb

Classification: TRANSFERASE
Organism(s): Paenarthrobacter aurescens TC1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-04-11 Released: 2011-06-01
Deposition Author(s): Nocek, B., Hatzos-Skintges, C., Feldmann, B., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.235 (Depositor), 0.232 (DCC)
R-Value Work:
0.184 (Depositor), 0.183 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Polyphosphate Kinase 2 from Arthrobacter aurescens TC1

Nocek, B., Hatzos-Skintges, C., Feldmann, B., Babnigg, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 132.25 kDa
Atom Count: 9,424
Modeled Residue Count: 1,124
Deposited Residue Count: 1,156
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative polyphosphate kinase 2 family protein	A, B, C, D	289	Paenarthrobacter aurescens TC1	Mutation(s): 0 Gene Names: AAur_2811
UniProt
Find proteins for A1R8G0 (Paenarthrobacter aurescens (strain TC1)) Explore A1R8G0 Go to UniProtKB: A1R8G0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1R8G0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain J [auth B] MOL2 format, chain V [auth D] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth B] mmCIF format, chain V [auth D] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth B]	J [auth B], L [auth B], P [auth C], V [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain V [auth D] Interactions & Density Focus chain J [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain V [auth D]
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain R [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain X [auth D] MOL2 format, chain R [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain X [auth D] mmCIF format, chain R [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], R [auth C], X [auth D]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain X [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain W [auth D] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain W [auth D] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain W [auth D] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], W [auth D], Z [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain W [auth D] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain W [auth D] Focus chain Z [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain AA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain AA [auth D]	AA [auth D] H [auth A] I [auth A] M [auth B] N [auth B] AA [auth D], H [auth A], I [auth A], M [auth B], N [auth B], S [auth C], T [auth C], U [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain Q [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Q [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Q [auth C]	Q [auth C], Y [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Focus chain Y [auth D] Interactions & Density Focus chain Q [auth C] Focus chain Y [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.235 (Depositor), 0.232 (DCC)
R-Value Work: 0.184 (Depositor), 0.183 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.353	α = 90
b = 126.353	β = 90
c = 199.064	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
PHENIX	model building
SHELX	model building
ARP/wARP	model building
MLPHARE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
SHELX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-06-01

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2011-06-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary