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- PDB-6zy1: Catabolic reductive dehalogenase NpRdhA, N-terminally tagged in c... -

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Basic information

Entry
Database: PDB / ID: 6zy1
TitleCatabolic reductive dehalogenase NpRdhA, N-terminally tagged in complex with 3-bromo-4-hydroxybenzoic acid
ComponentsOxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
KeywordsOXIDOREDUCTASE / reductive dehalogenase / B12 / iron-sulfur
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / metal ion binding / plasma membrane
Similarity search - Function
Reductive dehalogenase domain / Reductive dehalogenase subunit / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
COBALAMIN / 3 bromo 4 hydroxybenzoic acid / IRON/SULFUR CLUSTER / Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
Similarity search - Component
Biological speciesNitratireductor pacificus pht-3B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.99 Å
AuthorsLeys, D. / Halliwell, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M007316/1 United Kingdom
CitationJournal: Microorganisms / Year: 2020
Title: Catabolic Reductive Dehalogenase Substrate Complex Structures Underpin Rational Repurposing of Substrate Scope.
Authors: Halliwell, T. / Fisher, K. / Payne, K.A.P. / Rigby, S.E.J. / Leys, D.
History
DepositionJul 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
B: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
C: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,98918
Polymers239,1683
Non-polymers6,82115
Water20,9871165
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A: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9966
Polymers79,7231
Non-polymers2,2745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9966
Polymers79,7231
Non-polymers2,2745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9966
Polymers79,7231
Non-polymers2,2745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.871, 170.104, 107.651
Angle α, β, γ (deg.)90, 98.35, 90
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein /


Mass: 79722.570 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratireductor pacificus pht-3B (bacteria)
Gene: NA2_14372 / Production host: Bacillus megaterium (bacteria) / References: UniProt: K2MB66

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Non-polymers , 5 types, 1180 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-QSB / 3 bromo 4 hydroxybenzoic acid / 3-bromanyl-4-oxidanyl-benzoic acid


Mass: 217.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H5BrO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1165 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris propane (pH 8.5), 0.2 M sodium nitrate and 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.99→106.5 Å / Num. obs: 112327 / % possible obs: 94 % / Redundancy: 3.5 % / CC1/2: 1 / Rrim(I) all: 0.181 / Net I/σ(I): 6.8
Reflection shellResolution: 1.99→2.21 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5617 / CC1/2: 0.6 / Rrim(I) all: 0.827 / % possible all: 78.5

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Processing

Software
NameVersionClassification
PHENIX1refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6ZXU

6zxu


Resolution: 1.99→106 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.211 --
Rwork0.177 --
obs-112327 94 %
Refinement stepCycle: LAST / Resolution: 1.99→106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15836 0 357 1165 17358

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