3B5M | pdb_00003b5m

Crystal structure of conserved uncharacterized protein from Rhodopirellula baltica

• PDB DOI: https://doi.org/10.2210/pdb3B5M/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Rhodopirellula baltica SH 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-10-26 Released: 2007-11-13 
• Deposition Author(s): Patskovsky, Y., Bonanno, J.B., Sridhar, V., Rutter, M., Powell, A., Maletic, M., Rodgers, R., Wasserman, S., Smith, D., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 
  0.202 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Conserved Uncharacterized Protein from Rhodopirellula baltica.

Patskovsky, Y., Bonanno, J.B., Sridhar, V., Rutter, M., Powell, A., Maletic, M., Rodgers, R., Wasserman, S., Smith, D., Sauder, J.M., Burley, S.K., Almo, S.C.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.68 kDa 
• Atom Count: 7,588 
• Modeled Residue Count: 776 
• Deposited Residue Count: 820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	205	Rhodopirellula baltica SH 1	Mutation(s): 0  Gene Names: RB3938
UniProt
Find proteins for Q7UTD8 (Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)) Explore Q7UTD8  Go to UniProtKB:  Q7UTD8

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free:  0.202 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.268	α = 93.89
b = 58.315	β = 91.12
c = 73.799	γ = 90.1

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-13 
Deposition Author(s): Patskovsky, Y., Bonanno, J.B., Sridhar, V., Rutter, M., Powell, A., Maletic, M., Rodgers, R., Wasserman, S., Smith, D., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Refinement description