5TRQ | pdb_00005trq

WELO5 SMALL MOLECULE HALOGENASE WITH NI(II) AND SUCCINATE

PDB DOI: https://doi.org/10.2210/pdb5TRQ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Hapalosiphon welwitschii UTEX B 1830
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-10-27 Released: 2017-11-29
Deposition Author(s): McDonough, M.A., Gallimore, E., Clifton, I.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.207 (Depositor), 0.200 (DCC)
R-Value Work:
0.188 (Depositor), 0.199 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

WELO5 SMALL MOLECULE HALOGENASE WITH NI(II) AND SUCCINATE

Gallimore, E.O., McDonough, M.A., Clifton, I.J., Schofield, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 66.15 kDa
Atom Count: 5,172
Modeled Residue Count: 566
Deposited Residue Count: 582
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WelO5	A, B	291	Hapalosiphon welwitschii UTEX B 1830	Mutation(s): 0
UniProt
Find proteins for A0A067YX61 (Hapalosiphon welwitschii UTEX B 1830) Explore A0A067YX61 Go to UniProtKB: A0A067YX61
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A067YX61
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIN Query on SIN Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	E [auth A], L [auth B]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], M [auth B], N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B]	O [auth B], P [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain O [auth B] Focus chain P [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], J [auth B], K [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.207 (Depositor), 0.200 (DCC)
R-Value Work: 0.188 (Depositor), 0.199 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.063	α = 91.77
b = 46.066	β = 90.54
c = 74.437	γ = 108.71

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
xia2	data reduction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-11-29

Deposition Author(s):

McDonough, M.A.

Gallimore, E.

Clifton, I.J.

Revision History (Full details and data files)

Version 1.0: 2017-11-29
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description