1U3F

Structural and Functional Characterization of a 5,10-Methenyltetrahydrofolate Synthetase from Mycoplasma pneumoniae (GI: 13508087)

PDB DOI: https://doi.org/10.2210/pdb1U3F/pdb

Classification: LIGASE
Organism(s): Mycoplasmoides pneumoniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-07-21 Released: 2004-12-07
Deposition Author(s): Chen, S., Yakunin, A.F., Proudfoot, M., Kim, R., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.268
R-Value Work: 0.223
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087) at 2.2 A resolution

Chen, S., Shin, D.H., Pufan, R., Kim, R., Kim, S.-H.

(2004) Proteins 56: 839-843

PubMed: 15281135 Search on PubMed
DOI: https://doi.org/10.1002/prot.20214
Primary Citation of Related Structures:
1SBQ, 1U3F, 1U3G

Organizational Affiliation

Department of Chemistry, University of California, Berkeley, California.

Macromolecule Content

Total Structure Weight: 45.64 kDa
Atom Count: 3,033
Modelled Residue Count: 328
Deposited Residue Count: 378
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5,10-Methenyltetrahydrofolate Synthetase	A, B	189	Mycoplasmoides pneumoniae	Mutation(s): 0 EC: 6.3.3.2
UniProt
Find proteins for P75430 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75430 Go to UniProtKB: P75430
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P75430
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.268
R-Value Work: 0.223
R-Value Observed: 0.223
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.135	α = 90
b = 74.369	β = 90
c = 110.614	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-12-07

Deposition Author(s):

Berkeley Structural Genomics Center (BSGC)

Revision History (Full details and data files)

Version 1.0: 2004-12-07
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-03-06
Changes: Data collection, Database references, Derived calculations

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1U3F

Structural and Functional Characterization of a 5,10-Methenyltetrahydrofolate Synthetase from Mycoplasma pneumoniae (GI: 13508087)

Crystal structure of methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087) at 2.2 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)