2GHS | pdb_00002ghs

CRYSTAL STRUCTURE OF A CALCIUM-BINDING PROTEIN, REGUCALCIN (AGR_C_1268) FROM AGROBACTERIUM TUMEFACIENS STR. C58 AT 1.55 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb2GHS/pdb

Classification: Calcium-BINDING PROTEIN
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-03-27 Released: 2006-04-11
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.176 (Depositor), 0.185 (DCC)
R-Value Work:
0.137 (Depositor), 0.150 (DCC)
R-Value Observed:
0.139 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Calcium-binding protein, regucalcin (15155668) from AGROBACTERIUM TUMEFACIENS at 1.55 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 36.1 kDa
Atom Count: 2,657
Modeled Residue Count: 295
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AGR_C_1268p	A	326	Agrobacterium fabrum str. C58	Mutation(s): 9 Gene Names: 15155668
UniProt
Find proteins for Q7D0W3 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7D0W3 Go to UniProtKB: Q7D0W3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7D0W3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.176 (Depositor), 0.185 (DCC)
R-Value Work: 0.137 (Depositor), 0.150 (DCC)
R-Value Observed: 0.139 (Depositor)

Diffraction Data: https://doi.org/10.18430/M32GHS

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.258	α = 90
b = 75.703	β = 90
c = 81.538	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-04-11

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2006-04-11
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-01-25
Changes: Database references, Derived calculations
Version 1.4: 2024-11-20
Changes: Data collection, Structure summary

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.