2V4I | pdb_00002v4i

Structure of a novel N-acyl-enzyme intermediate of an N-terminal nucleophile (Ntn) hydrolase, OAT2

PDB DOI: https://doi.org/10.2210/pdb2V4I/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces clavuligerus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2008-09-22 Released: 2008-10-07
Deposition Author(s): Iqbal, A., Clifton, I.J., Schofield, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.247 (Depositor), 0.242 (DCC)
R-Value Work:
0.214 (Depositor), 0.213 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Structure of a Novel N-Acyl-Enzyme Intermediate of an N-Terminal Nucleophile (Ntn) Hydrolase, Oat2

Iqbal, A., Schofield, C.J., Clifton, I.J.

To be published.

Macromolecule Content

Total Structure Weight: 163.74 kDa
Atom Count: 11,153
Modeled Residue Count: 1,504
Deposited Residue Count: 1,544
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN	A, C, E, G	173	Streptomyces clavuligerus	Mutation(s): 0 EC: 2.3.1.35
UniProt
Find proteins for P0DJQ5 (Streptomyces clavuligerus) Explore P0DJQ5 Go to UniProtKB: P0DJQ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DJQ5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN	B, D, F, H	213	Streptomyces clavuligerus	Mutation(s): 1 EC: 2.3.1.35
UniProt
Find proteins for P0DJQ5 (Streptomyces clavuligerus) Explore P0DJQ5 Go to UniProtKB: P0DJQ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DJQ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AYA Query on AYA	B, D, F, H	L-PEPTIDE LINKING	C₅ H₉ N O₃		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.247 (Depositor), 0.242 (DCC)
R-Value Work: 0.214 (Depositor), 0.213 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.455	α = 90
b = 180.163	β = 90
c = 60.962	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
RIGID-BODY	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-10-07

Deposition Author(s):

Schofield, C.J.

Revision History (Full details and data files)

Version 1.0: 2008-10-07
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.