3SC3 | pdb_00003sc3

Crystal structure of a Putative DNA replication regulator Hda (Sama_1916) from SHEWANELLA AMAZONENSIS SB2B at 3.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3SC3/pdb

• Classification: HYDROLASE REGULATOR, DNA BINDING PROTEIN
• Organism(s): Shewanella amazonensis SB2B
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-06 Released: 2011-07-13 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal structure of a Putative DNA replication regulator Hda (Sama_1916) from SHEWANELLA AMAZONENSIS SB2B at 3.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 51.5 kDa 
• Atom Count: 3,335 
• Modeled Residue Count: 423 
• Deposited Residue Count: 450 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative DNA replication regulator Hda	A, B	225	Shewanella amazonensis SB2B	Mutation(s): 0  Gene Names: SAMA_14OCT04_CONTIG53_REVISED_GENE1514, Sama_1916
UniProt
Find proteins for A1S6W5 (Shewanella amazonensis (strain ATCC BAA-1098 / SB2B)) Explore A1S6W5  Go to UniProtKB:  A1S6W5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33SC3

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.44	α = 90
b = 162.44	β = 90
c = 162.44	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary