4WR2 | pdb_00004wr2

Crystal structure of a putative pyrimidine-specific ribonucleoside hydrolase (RihA) Protein from Shewanella loihica PV-4 (SHEW_0697, Target PSI-029635) with divalent cation and PEG 400 bound at the active site

• PDB DOI: https://doi.org/10.2210/pdb4WR2/pdb

• Classification: HYDROLASE
• Organism(s): Shewanella loihica PV-4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-22 Released: 2014-11-12 
• Deposition Author(s): Himmel, D.M., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Seidel, R.D., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.171 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

Crystal structure of a putative pyrimidine-specific ribonucleoside hydrolase (RihA) Protein from Shewanella loihica PV-4 (SHEW_0697, Target PSI-029635) with divalent cation and PEG 400 bound at the active site

Himmel, D.M., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Seidel, R.D., Bonanno, J.B., 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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.81 kDa 
• Atom Count: 2,662 
• Modeled Residue Count: 308 
• Deposited Residue Count: 335 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrimidine-specific ribonucleoside hydrolase RihA	A	335	Shewanella loihica PV-4	Mutation(s): 0  Gene Names: rihA, Shew_0697 EC: 3.2
UniProt
Find proteins for A3QAS1 (Shewanella loihica (strain ATCC BAA-1088 / PV-4)) Explore A3QAS1  Go to UniProtKB:  A3QAS1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	C [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 1.70 Å
• R-Value Free:  0.171 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.078	α = 90
b = 115.047	β = 90
c = 141.64	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-12 
Deposition Author(s): Himmel, D.M., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Seidel, R.D., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-10-30
  Changes: Structure summary