5KSW | pdb_00005ksw

DHODB-I74D mutant

PDB DOI: https://doi.org/10.2210/pdb5KSW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lactococcus lactis, Lactococcus lactis subsp. lactis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-07-10 Released: 2016-08-03
Deposition Author(s): Pompeu, Y.A., Stewart, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free:
0.244 (Depositor), 0.245 (DCC)
R-Value Work:
0.176 (Depositor), 0.178 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Isoleucine 74 Plays a Key Role in Controlling Electron Transfer Between Lactococcus lactis Dihydroorotate Dehydrogenase 1B Subunits

Pompeu, Y.A., Stewart, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 125.44 kDa
Atom Count: 9,054
Modeled Residue Count: 1,135
Deposited Residue Count: 1,136
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase	A, D [auth C]	306	Lactococcus lactis	Mutation(s): 1 Gene Names: pyrD, LG36_1039 EC: 1.3.1.14
UniProt
Find proteins for Q9CFW8 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CFW8 Go to UniProtKB: Q9CFW8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9CFW8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit	B, C [auth D]	262	Lactococcus lactis subsp. lactis	Mutation(s): 0 Gene Names: pyrK, NCDO895_2366
UniProt
Find proteins for Q9CFW7 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CFW7 Go to UniProtKB: Q9CFW7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9CFW7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth D] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D] mmCIF format, chain H [auth B] mmCIF format, chain K [auth D]	H [auth B], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain H [auth B] Focus chain K [auth D] Interactions & Density Focus chain H [auth B] Focus chain K [auth D]
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain M [auth C] mmCIF format, chain E [auth A] mmCIF format, chain M [auth C]	E [auth A], M [auth C]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain M [auth C]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth D] MOL2 format, chain I [auth B] MOL2 format, chain L [auth D] mmCIF format, chain I [auth B] mmCIF format, chain L [auth D]	I [auth B], L [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth C] MOL2 format, chain G [auth A] MOL2 format, chain N [auth C] mmCIF format, chain G [auth A] mmCIF format, chain N [auth C]	G [auth A], N [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth C] Interactions & Density Focus chain G [auth A] Focus chain N [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free: 0.244 (Depositor), 0.245 (DCC)
R-Value Work: 0.176 (Depositor), 0.178 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.99	α = 90
b = 151.72	β = 90
c = 214.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-08-03

Deposition Author(s):

Pompeu, Y.A.

Stewart, J.D.

Revision History (Full details and data files)

Version 1.0: 2016-08-03
Type: Initial release
Version 1.1: 2016-08-10
Changes: Data collection
Version 1.2: 2017-04-26
Changes: Structure summary
Version 1.3: 2017-09-27
Changes: Author supporting evidence
Version 1.4: 2017-11-01
Changes: Author supporting evidence
Version 1.5: 2023-10-04
Changes: Data collection, Database references, Refinement description

5KSW | pdb_00005ksw

DHODB-I74D mutant

Literature

Isoleucine 74 Plays a Key Role in Controlling Electron Transfer Between Lactococcus lactis Dihydroorotate Dehydrogenase 1B Subunits

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2