5NHS | pdb_00005nhs

The crystal structure of Xanthomonas albilineans N5, N10-methylenetetrahydrofolate dehydrogenase-cyclohydrolase (FolD)

PDB DOI: https://doi.org/10.2210/pdb5NHS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Xanthomonas albilineans GPE PC73
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-03-22 Released: 2018-05-16
Deposition Author(s): Bueno, R.V., Guido, R.V.C., Maluf, F.V., Lima, G.M.A., Oliveira, A.A.
Funding Organization(s): Sao Paulo Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.241 (Depositor), 0.244 (DCC)
R-Value Work:
0.191 (Depositor), 0.198 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of Xanthomonas albilineans N5, N10-methylenetetrahydrofolate dehydrogenase-cyclohydrolase (FolD)

Bueno, R.V., Guido, R.V.C., Maluf, F.V., Lima, G.M.A., Oliveira, A.A.

To be published.

Macromolecule Content

Total Structure Weight: 62.98 kDa
Atom Count: 4,445
Modeled Residue Count: 561
Deposited Residue Count: 592
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional protein FolD	A, B	296	Xanthomonas albilineans GPE PC73	Mutation(s): 0 Gene Names: folD, XALc_1581 EC: 3.5.4.9 (PDB Primary Data), 1.5.1.5 (PDB Primary Data)
UniProt
Find proteins for D2UAL4 (Xanthomonas albilineans (strain GPE PC73 / CFBP 7063)) Explore D2UAL4 Go to UniProtKB: D2UAL4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2UAL4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.241 (Depositor), 0.244 (DCC)
R-Value Work: 0.191 (Depositor), 0.198 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.295	α = 90
b = 76.404	β = 90
c = 66.641	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation	Brazil	2013/04737-8
Sao Paulo Research Foundation	Brazil	2016/16038-5
Sao Paulo Research Foundation	Brazil	11/08042-9

Revision History (Full details and data files)

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: 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.