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- PDB-6zy0: Catabolic reductive dehalogenase NpRdhA, N-terminally tagged, K48... -

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Basic information

Entry
Database: PDB / ID: 6zy0
TitleCatabolic reductive dehalogenase NpRdhA, N-terminally tagged, K488Q variant
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
Similarity search - Function
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 / 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: 2.13 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

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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)245,40517
Polymers239,1653
Non-polymers6,24114
Water5,963331
1
A: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7785
Polymers79,7221
Non-polymers2,0574
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)81,8146
Polymers79,7221
Non-polymers2,0925
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)81,8146
Polymers79,7221
Non-polymers2,0925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.346, 169.569, 107.799
Angle α, β, γ (deg.)90.000, 98.330, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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: 79721.516 Da / Num. of mol.: 3 / Mutation: K488Q
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, 345 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 63.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting 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: May 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.13→106.66 Å / Num. obs: 84101 / % possible obs: 94.5 % / Redundancy: 7 % / Biso Wilson estimate: 34.23 Å2 / CC1/2: 1 / Rrim(I) all: 0.196 / Net I/σ(I): 8.2
Reflection shellResolution: 2.13→2.44 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4206 / CC1/2: 0.6 / Rrim(I) all: 1.238 / % possible all: 74.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6ZXU

6zxu


Resolution: 2.13→106.66 Å / SU ML: 0.2083 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 4269 5.08 %
Rwork0.1855 79828 -
obs0.1874 84097 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.27 Å2
Refinement stepCycle: LAST / Resolution: 2.13→106.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15846 0 326 331 16503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005516564
X-RAY DIFFRACTIONf_angle_d1.321122576
X-RAY DIFFRACTIONf_chiral_restr0.12622422
X-RAY DIFFRACTIONf_plane_restr0.00683003
X-RAY DIFFRACTIONf_dihedral_angle_d19.44952469
LS refinement shellResolution: 2.13→2.44 Å
RfactorNum. reflection% reflection
Rfree0.35 1 -
Rwork0.3434 --
obs--74.6 %

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