4GYP | pdb_00004gyp

Crystal structure of the heterotetrameric complex of GlucD and GlucDRP from E. coli K-12 MG1655 (EFI TARGET EFI-506058)

PDB DOI: https://doi.org/10.2210/pdb4GYP/pdb

Classification: LYASE/LYASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-09-05 Released: 2012-09-12
Deposition Author(s): Lukk, T., Ghasempur, S., Imker, H.J., Gerlt, J.A., Nair, S.K., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.186 (Depositor), 0.190 (DCC)
R-Value Work:
0.149 (Depositor), 0.150 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Glucarate dehydratase and its related protein from Escherichia coli form a heterotetrameric complex.

Lukk, T., Ghasempur, S., Imker, H.J., Nair, S.K., Gerlt, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 200.79 kDa
Atom Count: 15,174
Modeled Residue Count: 1,754
Deposited Residue Count: 1,808
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucarate dehydratase	A, B	446	Escherichia coli K-12	Mutation(s): 0 Gene Names: b2787, gudD, JW2758, ygcX EC: 4.2.1.40
UniProt
Find proteins for P0AES2 (Escherichia coli (strain K12)) Explore P0AES2 Go to UniProtKB: P0AES2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AES2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucarate dehydratase-related protein	C, D	458	Escherichia coli K-12	Mutation(s): 0 Gene Names: b2788, gudX, JW2759, ygcY EC: 4.2.1
UniProt
Find proteins for Q46915 (Escherichia coli (strain K12)) Explore Q46915 Go to UniProtKB: Q46915
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q46915
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain O [auth D] MOL2 format, chain O [auth D] mmCIF format, chain O [auth D]	O [auth D]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain O [auth D] Interactions & Density Focus chain O [auth D]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	K [auth C], N [auth D]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain K [auth C] Focus chain N [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth C] SDF format, chain R [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth C] MOL2 format, chain R [auth D] mmCIF format, chain H [auth A] mmCIF format, chain M [auth C] mmCIF format, chain R [auth D]	H [auth A], M [auth C], R [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth C] Focus chain R [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	G [auth A], L [auth C], P [auth D], Q [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth C] Focus chain P [auth D] Focus chain Q [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.186 (Depositor), 0.190 (DCC)
R-Value Work: 0.149 (Depositor), 0.150 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.47	α = 90
b = 113.02	β = 105.89
c = 128.59	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-09-12

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-09-12
Type: Initial release
Version 1.1: 2012-09-19
Changes: Structure summary
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description