3BVC | pdb_00003bvc

Crystal structure of uncharacterized protein Ism_01780 from Roseovarius nubinhibens ISM

• PDB DOI: https://doi.org/10.2210/pdb3BVC/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Roseovarius nubinhibens ISM
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-06 Released: 2008-02-12 
• Deposition Author(s): Patskovsky, Y., Toro, R., Meyer, A.J., Rutter, M., Iizuka, M., Maletic, M., Smith, D., Wasserman, S., 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: 2.75 Å
• R-Value Free: 
  0.298 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Literature

Crystal structure of an uncharacterized protein Ism_01780 from Roseovarius nubinhibens.

Patskovsky, Y., Toro, R., Meyer, A.J., Rutter, M., Iizuka, M., Maletic, M., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.1 kDa 
• Atom Count: 3,214 
• Modeled Residue Count: 406 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein Ism_01780	A, B	212	Roseovarius nubinhibens ISM	Mutation(s): 0  Gene Names: ISM_01780
UniProt
Find proteins for A3SHZ8 (Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM)) Explore A3SHZ8  Go to UniProtKB:  A3SHZ8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	E [auth A], H [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CA	C [auth A], D [auth A], F [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.298 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.405	α = 90
b = 101.973	β = 90
c = 76.506	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-12 
Deposition Author(s): Patskovsky, Y., Toro, R., Meyer, A.J., Rutter, M., Iizuka, M., Maletic, M., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-02-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, 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: 2024-02-21
  Changes: Data collection, Database references, Refinement description