4IOL | pdb_00004iol

N10-formyltetrahydrofolate synthetase from Moorella thermoacetica with ADP/ZD9 and XPO

PDB DOI: https://doi.org/10.2210/pdb4IOL/pdb

Classification: LIGASE/LIGASE INHIBITOR
Organism(s): Moorella thermoacetica ATCC 39073
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-01-08 Released: 2013-04-10
Deposition Author(s): Stec, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free:
0.279 (Depositor), 0.275 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Time passes yet errors remain: Comments on the structure of N(10) -formyltetrahydrofolate synthetase.

Stec, B.

(2013) Protein Sci 22: 671-674

PubMed: 23533144 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.2252
Primary Citation Related Structures:
4IOJ, 4IOK, 4IOL, 4IOM

Macromolecule Content

Total Structure Weight: 121.63 kDa
Atom Count: 8,654
Modeled Residue Count: 1,114
Deposited Residue Count: 1,118
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate--tetrahydrofolate ligase	A, B	559	Moorella thermoacetica ATCC 39073	Mutation(s): 0 Gene Names: fhs, Moth_0109 EC: 6.3.4.3
UniProt
Find proteins for Q2RM91 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320)) Explore Q2RM91 Go to UniProtKB: Q2RM91
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2RM91
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
ZD9 Query on ZD9 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2,7-dimethyl-6-[(prop-1-yn-1-ylamino)methyl]quinazolin-4(3H)-one C₁₄ H₁₅ N₃ O VHJQNTIPWBTKDM-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
XPO Query on XPO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	formyl phosphate C H₃ O₅ P TVISEJUYYBUVNV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B]	C [auth A], G [auth A], H [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.279 (Depositor), 0.275 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.37	α = 90
b = 160.37	β = 90
c = 258.074	γ = 120

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-04-10

Deposition Author(s):

Stec, B.

Revision History (Full details and data files)

Version 1.0: 2013-04-10
Type: Initial release
Version 1.1: 2013-06-12
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

4IOL | pdb_00004iol

N10-formyltetrahydrofolate synthetase from Moorella thermoacetica with ADP/ZD9 and XPO

Literature

Time passes yet errors remain: Comments on the structure of N(10) -formyltetrahydrofolate synthetase.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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