6K8C | pdb_00006k8c

Crystal structure of Helicobacter pylori folylpolyglutamate synthetase

PDB DOI: https://doi.org/10.2210/pdb6K8C/pdb

Classification: LIGASE
Organism(s): Helicobacter pylori 26695
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-06-11 Released: 2019-11-06
Deposition Author(s): Park, J.S., Han, B.W.
Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.219 (Depositor), 0.246 (DCC)
R-Value Work:
0.184 (Depositor)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6K8C

This is version 1.1 of the entry. See complete history.

Literature

Structural Analyses of Helicobacter Pylori FolC Conducting Glutamation in Folate Metabolism.

Park, J.S., Kim, H.S., Park, S.H., Park, M.S., Kang, S.-M., Kim, H.-J., Han, B.W.

(2019) Crystals (Basel)

DOI: https://doi.org/10.3390/cryst9080429

Macromolecule Content

Total Structure Weight: 46.3 kDa
Atom Count: 3,362
Modeled Residue Count: 378
Deposited Residue Count: 402
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Folylpolyglutamate synthase (FolC)	A	402	Helicobacter pylori 26695	Mutation(s): 0 Gene Names: HP_1545 EC: 6.3.2.17 (PDB Primary Data), 6.3.2.12 (UniProt)
UniProt
Find proteins for O26070 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O26070 Go to UniProtKB: O26070
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O26070
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT 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]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.219 (Depositor), 0.246 (DCC)
R-Value Work: 0.184 (Depositor)
R-Value Observed: 0.186 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.454	α = 90
b = 61.637	β = 115.962
c = 69.743	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-11-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	2013M3A6A4043695

Revision History (Full details and data files)

Version 1.0: 2019-11-06
Type: Initial release
Version 1.1: 2024-11-06
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.