5V00 | pdb_00005v00

Structure of HutD from Pseudomonas fluorescens SBW25 (Formate condition)

PDB DOI: https://doi.org/10.2210/pdb5V00/pdb
Entry: 5V00 supersedes: 3ESG

Classification: UNKNOWN FUNCTION
Organism(s): Pseudomonas [fluorescens] SBW25
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-02-27 Released: 2017-03-15
Deposition Author(s): Liu, Y., Johnston, J.M., Gerth, M.L., Baker, E.N., Lott, J.S., Rainey, P.B.
Funding Organization(s): Foundation for Research Science and Technology, Health Research Council (HRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.196 (Depositor), 0.199 (DCC)
R-Value Work:
0.167 (Depositor), 0.176 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a bicupin protein HutD involved in histidine utilization in Pseudomonas.

Gerth, M.L., Liu, Y., Jiao, W., Zhang, X.X., Baker, E.N., Lott, J.S., Rainey, P.B., Johnston, J.M.

(2017) Proteins 85: 1580-1588

PubMed: 28383128 Search on PubMed
DOI: https://doi.org/10.1002/prot.25303
Primary Citation Related Structures:
5V00

PubMed Abstract:
Cupins form one of the most functionally diverse superfamilies of proteins, with members performing a wide range of catalytic, non-catalytic, and regulatory functions. HutD is a predicted bicupin protein that is involved in histidine utilization (Hut) in Pseudomonas species. Previous genetic analyses have suggested that it limits the upper level of Hut pathway expression, but its mechanism of action is unknown. Here, we have determined the structure of PfluHutD at 1.74 Å resolution in several crystallization conditions, and identified N-formyl-l-glutamate (FG, a Hut pathway intermediate) as a potential ligand in vivo. Proteins 2017; 85:1580-1588. © 2017 Wiley Periodicals, Inc.

Organizational Affiliation

New Zealand Institute for Advanced Study, Massey University Albany, Auckland, New Zealand.

Macromolecule Content

Total Structure Weight: 43.14 kDa
Atom Count: 3,339
Modeled Residue Count: 369
Deposited Residue Count: 386
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	193	Pseudomonas [fluorescens] SBW25	Mutation(s): 0 Gene Names: PFLU_0360
UniProt
Find proteins for C3K802 (Pseudomonas fluorescens (strain SBW25)) Explore C3K802 Go to UniProtKB: C3K802
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C3K802
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain C [auth A] MOL2 format, chain N [auth B] MOL2 format, chain C [auth A] mmCIF format, chain N [auth B] mmCIF format, chain C [auth A]	C [auth A], N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.196 (Depositor), 0.199 (DCC)
R-Value Work: 0.167 (Depositor), 0.176 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.863	α = 90
b = 82.863	β = 90
c = 174.419	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-03-15

Deposition Author(s):

This entry supersedes: 3ESG

Funding Organization	Location	Grant Number
Foundation for Research Science and Technology	New Zealand	--
Health Research Council (HRC)	New Zealand	--

Revision History (Full details and data files)

Version 1.0: 2017-03-15
Type: Initial release
Version 1.1: 2017-04-19
Changes: Database references
Version 1.2: 2017-08-02
Changes: Database references
Version 1.3: 2020-01-01
Changes: Author supporting evidence
Version 1.4: 2023-10-04
Changes: Data collection, Database references, Refinement description