3DZB | pdb_00003dzb

Crystal structure of Prephenate dehydrogenase from Streptococcus thermophilus

PDB DOI: https://doi.org/10.2210/pdb3DZB/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptococcus thermophilus LMG 18311
Expression System: Escherichia coli
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free:
0.278 (Depositor), 0.276 (DCC)
R-Value Work:
0.234 (Depositor), 0.233 (DCC)
R-Value Observed:
0.271 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Prephenate dehydrogenase from Streptococcus thermophilus

Zhang, Z., Eswaramoorthy, S., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 71.56 kDa
Atom Count: 4,499
Modeled Residue Count: 567
Deposited Residue Count: 634
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prephenate dehydrogenase	A, B	317	Streptococcus thermophilus LMG 18311	Mutation(s): 0 Gene Names: tyrA, stu0642 EC: 1.3.1.12
UniProt
Find proteins for Q5M554 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M554 Go to UniProtKB: Q5M554
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5M554
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.278 (Depositor), 0.276 (DCC)
R-Value Work: 0.234 (Depositor), 0.233 (DCC)
R-Value Observed: 0.271 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.906	α = 90
b = 145.005	β = 90
c = 56.227	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):

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: 2012-05-02
Changes: Structure summary
Version 1.3: 2017-10-25
Changes: Refinement description
Version 1.4: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-10-16
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.