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

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Basic information

Entry
Database: PDB / ID: 6zxu
TitleCatabolic reductive dehalogenase NpRdhA, N-terminally tagged.
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 / IRON/SULFUR CLUSTER / Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
Similarity search - Component
Biological speciesNitratireductor pacificus pht-3B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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)245,44418
Polymers239,1683
Non-polymers6,27615
Water31,7601763
1
A: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8156
Polymers79,7231
Non-polymers2,0925
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)81,8156
Polymers79,7231
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)81,8156
Polymers79,7231
Non-polymers2,0925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.110, 170.958, 107.873
Angle α, β, γ (deg.)90.00, 98.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1197-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A-4 - 697
2010B-2 - 697
1020A-4 - 695
2020C-2 - 695
1030B-2 - 695
2030C-2 - 695

NCS ensembles :
ID
1
2
3

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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, 1778 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1763 / 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: 3.49 Å3/Da / Density % sol: 64.71 %
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: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Nov 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.73→121.7 Å / Num. obs: 201357 / % possible obs: 93 % / Redundancy: 3.3 % / CC1/2: 1 / Rrim(I) all: 0.104 / Net I/σ(I): 8.7
Reflection shellResolution: 1.73→1.91 Å / Redundancy: 2.3 % / Num. unique obs: 10067 / CC1/2: 0.5 / Rrim(I) all: 0.873 / % possible all: 58

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RAS

4ras


Resolution: 1.73→121.69 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.222 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19384 9978 5 %RANDOM
Rwork0.16305 ---
obs0.16458 191391 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.921 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.02 Å2
2---0.08 Å20 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.73→121.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15666 0 327 1763 17756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.01916418
X-RAY DIFFRACTIONr_bond_other_d0.010.0215447
X-RAY DIFFRACTIONr_angle_refined_deg2.181.99822391
X-RAY DIFFRACTIONr_angle_other_deg1.895335372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41352090
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20922.388691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.668152536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.16515174
X-RAY DIFFRACTIONr_chiral_restr0.1630.22416
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02118842
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023776
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A40905
12B40905
21A40471
22C40471
31B39784
32C39784
LS refinement shellResolution: 1.73→1.758 Å
RfactorNum. reflection% reflection
Rfree0.327 12 -
Rwork0.32 231 -
obs--58 %

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