9P8Z | pdb_00009p8z

Crystal Structure of GTP cyclohydrolase 1 (FolE) from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb9P8Z/pdb

Classification: HYDROLASE
Organism(s): Plasmodium vivax Sal-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-06-23 Released: 2025-07-02
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free:
0.259 (Depositor), 0.262 (DCC)
R-Value Work:
0.210 (Depositor), 0.215 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of GTP cyclohydrolase 1 (FolE) from Mycobacterium tuberculosis

Seibold, S., Liu, L., Lovell, S., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 495.76 kDa
Atom Count: 29,166
Modeled Residue Count: 3,759
Deposited Residue Count: 4,460
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP cyclohydrolase 1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	223	Plasmodium vivax Sal-1	Mutation(s): 0 Gene Names: folE, gchA, Rv3609c, MTCY07H7B.13 EC: 3.5.4.16
UniProt
Find proteins for P9WN57 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WN57 Go to UniProtKB: P9WN57
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WN57
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain Y [auth E] SDF format, chain X [auth D] SDF format, chain W [auth C] SDF format, chain V [auth B] SDF format, chain U [auth A] SDF format, chain QA [auth T] SDF format, chain PA [auth S] SDF format, chain OA [auth R] SDF format, chain NA [auth Q] SDF format, chain MA [auth P] SDF format, chain LA [auth O] SDF format, chain KA [auth N] SDF format, chain JA [auth M] SDF format, chain IA [auth L] SDF format, chain HA [auth K] SDF format, chain FA [auth J] SDF format, chain EA [auth I] SDF format, chain DA [auth H] SDF format, chain BA [auth G] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth D] MOL2 format, chain W [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth A] MOL2 format, chain QA [auth T] MOL2 format, chain PA [auth S] MOL2 format, chain OA [auth R] MOL2 format, chain NA [auth Q] MOL2 format, chain MA [auth P] MOL2 format, chain LA [auth O] MOL2 format, chain KA [auth N] MOL2 format, chain JA [auth M] MOL2 format, chain IA [auth L] MOL2 format, chain HA [auth K] MOL2 format, chain FA [auth J] MOL2 format, chain EA [auth I] MOL2 format, chain DA [auth H] MOL2 format, chain BA [auth G] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth D] mmCIF format, chain W [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth A] mmCIF format, chain QA [auth T] mmCIF format, chain PA [auth S] mmCIF format, chain OA [auth R] mmCIF format, chain NA [auth Q] mmCIF format, chain MA [auth P] mmCIF format, chain LA [auth O] mmCIF format, chain KA [auth N] mmCIF format, chain JA [auth M] mmCIF format, chain IA [auth L] mmCIF format, chain HA [auth K] mmCIF format, chain FA [auth J] mmCIF format, chain EA [auth I] mmCIF format, chain DA [auth H] mmCIF format, chain BA [auth G]	BA [auth G] DA [auth H] EA [auth I] FA [auth J] HA [auth K] BA [auth G], DA [auth H], EA [auth I], FA [auth J], HA [auth K], IA [auth L], JA [auth M], KA [auth N], LA [auth O], MA [auth P], NA [auth Q], OA [auth R], PA [auth S], QA [auth T], U [auth A], V [auth B], W [auth C], X [auth D], Y [auth E], Z [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain IA [auth L] Focus chain JA [auth M] Focus chain KA [auth N] Focus chain LA [auth O] Focus chain MA [auth P] Focus chain NA [auth Q] Focus chain OA [auth R] Focus chain PA [auth S] Focus chain QA [auth T] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain IA [auth L] Focus chain JA [auth M] Focus chain KA [auth N] Focus chain LA [auth O] Focus chain MA [auth P] Focus chain NA [auth Q] Focus chain OA [auth R] Focus chain PA [auth S] Focus chain QA [auth T] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain GA [auth J] SDF format, chain CA [auth G] SDF format, chain AA [auth F] MOL2 format, chain GA [auth J] MOL2 format, chain CA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain GA [auth J] mmCIF format, chain CA [auth G] mmCIF format, chain AA [auth F]	AA [auth F], CA [auth G], GA [auth J]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain GA [auth J] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain GA [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.259 (Depositor), 0.262 (DCC)
R-Value Work: 0.210 (Depositor), 0.215 (DCC)
R-Value Observed: 0.213 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.547	α = 89.11
b = 109.121	β = 88.12
c = 122.548	γ = 77.95

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-02

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394