3DZ1 | pdb_00003dz1

Crystal structure of Dihydrodipicolinate Synthase from Rhodopseudomonas palustris at 1.87A resolution

PDB DOI: https://doi.org/10.2210/pdb3DZ1/pdb

Classification: LYASE
Organism(s): Rhodopseudomonas palustris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-29 Released: 2008-08-12
Deposition Author(s): Satyanarayana, L., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.215 (Depositor), 0.213 (DCC)
R-Value Work:
0.190 (Depositor), 0.185 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Dihydrodipicolinate Synthase from Rhodopseudomonas palustris at 1.87A resolution

Satyanarayana, L., Eswaramoorthy, S., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 34.76 kDa
Atom Count: 2,625
Modeled Residue Count: 301
Deposited Residue Count: 313
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A	313	Rhodopseudomonas palustris	Mutation(s): 0 Gene Names: RPA3190 EC: 4.2.1.52
UniProt
Find proteins for Q6N4Z3 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N4Z3 Go to UniProtKB: Q6N4Z3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6N4Z3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.215 (Depositor), 0.213 (DCC)
R-Value Work: 0.190 (Depositor), 0.185 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.463	α = 90
b = 84.264	β = 90
c = 114.821	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXCD	phasing
SHARP	phasing
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-08-12

Deposition Author(s):

Satyanarayana, L.

Eswaramoorthy, S.

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-08-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Structure summary

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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.