3FNN | pdb_00003fnn

Biochemical and structural analysis of an atypical ThyX: Corynebacterium glutamicum NCHU 87078 depends on ThyA for thymidine biosynthesis

PDB DOI: https://doi.org/10.2210/pdb3FNN/pdb

Classification: TRANSFERASE
Organism(s): Corynebacterium glutamicum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-12-26 Released: 2009-12-29
Deposition Author(s): Wang, W.-C., Liu, J.-S., Chang, C.-M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.260 (Depositor), 0.228 (DCC)
R-Value Work:
0.223 (Depositor), 0.225 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Biochemical and structural analysis of an atypical ThyX: Corynebacterium glutamicum NCHU 87078 depends on ThyA for thymidine biosynthesis

Wang, W.-C., Liu, J.-S., Chang, C.-M.

To be published.

Macromolecule Content

Total Structure Weight: 29.71 kDa
Atom Count: 1,921
Modeled Residue Count: 227
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase thyX	A	256	Corynebacterium glutamicum	Mutation(s): 0 EC: 2.1.1.148
UniProt
Find proteins for P40111 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore P40111 Go to UniProtKB: P40111
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40111
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.260 (Depositor), 0.228 (DCC)
R-Value Work: 0.223 (Depositor), 0.225 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.806	α = 90
b = 95.806	β = 90
c = 64.637	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-12-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, 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.