2YJ4 | pdb_00002yj4

Conformational changes in the catalytic domain of the CPx-ATPase CopB- B upon nucleotide binding

PDB DOI: https://doi.org/10.2210/pdb2YJ4/pdb

Classification: HYDROLASE
Organism(s): Saccharolobus solfataricus P2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-05-18 Released: 2012-05-30
Deposition Author(s): Voellmecke, C., Schlicker, C., Luebben, M., Hofmann, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.273 (Depositor), 0.270 (DCC)
R-Value Work:
0.220 (Depositor), 0.220 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Conformational Changes in the Catalytic Domain of the Cpx-ATPase Copb-B Upon Nucleotide Binding

Voellmecke, C., Schlicker, C., Luebben, M., Hofmann, E.

To be published.

Macromolecule Content

Total Structure Weight: 58.6 kDa
Atom Count: 3,799
Modeled Residue Count: 500
Deposited Residue Count: 526
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COPPER-TRANSPORTING ATPASE	A, B	263	Saccharolobus solfataricus P2	Mutation(s): 1 EC: 3.6.3.10
UniProt
Find proteins for Q97UU7 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97UU7 Go to UniProtKB: Q97UU7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q97UU7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.273 (Depositor), 0.270 (DCC)
R-Value Work: 0.220 (Depositor), 0.220 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.12	α = 90
b = 75.15	β = 90
c = 133.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-05-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-30
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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Conformational changes in the catalytic domain of the CPx-ATPase CopB- B upon nucleotide binding

Conformational Changes in the Catalytic Domain of the Cpx-ATPase Copb-B Upon Nucleotide Binding

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations