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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.266 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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), 0.250 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33DI5

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

Entry History 

Deposition Data

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

Revision History  

• 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