3IVD | pdb_00003ivd

Putative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Uridine

• PDB DOI: https://doi.org/10.2210/pdb3IVD/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli O6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-31 Released: 2009-09-29 
• Deposition Author(s): Ramagopal, U.A., Toro, R., 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: 1.90 Å
• R-Value Free: 
  0.210 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Putative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Uridine

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.

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 2  

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

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

Macromolecule Content 

• Total Structure Weight: 113.38 kDa 
• Atom Count: 8,223 
• Modeled Residue Count: 998 
• Deposited Residue Count: 1,018 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotidase	A, B	509	Escherichia coli O6	Mutation(s): 0  Gene Names: c4898
UniProt
Find proteins for A0A0H2VD83 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) Explore A0A0H2VD83  Go to UniProtKB:  A0A0H2VD83

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URI	E [auth A], I [auth B]	URIDINE C9 H12 N2 O6 DRTQHJPVMGBUCF-XVFCMESISA-N
FE	C [auth A], G [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
MN	D [auth A], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	F [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.90 Å
• R-Value Free:  0.210 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.597	α = 74.04
b = 67.281	β = 77.55
c = 86.417	γ = 83.76

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-29 
Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary