1X7I | pdb_00001x7i

Crystal structure of the native copper homeostasis protein (cutCm) with calcium binding from Shigella flexneri 2a str. 301

PDB DOI: https://doi.org/10.2210/pdb1X7I/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Shigella flexneri 2a str. 301
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2004-08-14 Released: 2005-03-01
Deposition Author(s): Zhu, D.Y., Zhu, Y.Q., Huang, R.H., Xiang, Y., Wang, D.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.226 (Depositor), 0.224 (DCC)
R-Value Work:
0.198 (Depositor), 0.196 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1X7I

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the copper homeostasis protein (CutCm) from Shigella flexneri at 1.7 A resolution: The first structure of a new sequence family of TIM barrels

Zhu, D.Y., Zhu, Y.Q., Huang, R.H., Xiang, Y., Yang, N., Lu, H.X., Li, G.P., Jin, Q., Wang, D.C.

(2004) Proteins 58: 764-768

PubMed: 15624211 Search on PubMed
DOI: https://doi.org/10.1002/prot.20362
Primary Citation Related Structures:
1X7I, 1X8C

Organizational Affiliation

Center for Structural and Molecular Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China.

Macromolecule Content

Total Structure Weight: 55.77 kDa
Atom Count: 4,129
Modeled Residue Count: 474
Deposited Residue Count: 512
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper homeostasis protein cutC	A, B	256	Shigella flexneri 2a str. 301	Mutation(s): 0
UniProt
Find proteins for P67825 (Shigella flexneri) Explore P67825 Go to UniProtKB: P67825
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P67825
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.226 (Depositor), 0.224 (DCC)
R-Value Work: 0.198 (Depositor), 0.196 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.327	α = 90
b = 97.672	β = 90
c = 132.691	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CCP4	data scaling
SHELXD	phasing
SHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-03-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-03-01
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.