3DI5 | pdb_00003di5

Crystal structure of a dinb-like protein (bce_4655) from bacillus cereus atcc 10987 at 2.01 A resolution

PDB DOI: https://doi.org/10.2210/pdb3DI5/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Bacillus cereus ATCC 10987
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-19 Released: 2008-08-19
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.266 (Depositor), 0.254 (DCC)
R-Value Work:
0.229 (Depositor), 0.226 (DCC)
R-Value Observed:
0.231 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3DI5

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a DinB-like Protein (NP_980948.1) from BACILLUS CEREUS ATCC 10987 at 2.01 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 19.22 kDa
Atom Count: 1,210
Modeled Residue Count: 150
Deposited Residue Count: 168
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DinB-like Protein	A	168	Bacillus cereus ATCC 10987	Mutation(s): 0 Gene Names: NP_980948.1, BCE_4655
UniProt
Find proteins for Q72ZL3 (Bacillus cereus (strain ATCC 10987 / NRS 248)) Explore Q72ZL3 Go to UniProtKB: Q72ZL3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72ZL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI 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]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [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: 2.01 Å
R-Value Free: 0.266 (Depositor), 0.254 (DCC)
R-Value Work: 0.229 (Depositor), 0.226 (DCC)
R-Value Observed: 0.231 (Depositor)

Diffraction Data:

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.12	α = 90
b = 84.19	β = 90
c = 50.32	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-08-19

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-08-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-13
Changes: Data collection, 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.