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- PDB-9d6k: Nitrile hydratase BR157A mutant -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9d6k
TitleNitrile hydratase BR157A mutant
Components
  • Cobalt-containing nitrile hydratase subunit alpha
  • Cobalt-containing nitrile hydratase subunit beta
KeywordsLYASE / nitrile hydratase
Function / homology
Function and homology information


nitrile catabolic process / nitrile hydratase / nitrile hydratase activity / cobalt ion binding / transition metal ion binding
Similarity search - Function
Nitrile hydratase, alpha subunit / Nitrile hydratase, beta subunit / Nitrile hydratase beta subunit domain / Nitrile hydratase beta subunit, N-terminal / : / Nitrile hydratase beta subunit, C-terminal / Nitrile hydratase beta subunit, N-terminal / Nitrile hydratase alpha subunit /Thiocyanate hydrolase gamma subunit / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, alpha chain ...Nitrile hydratase, alpha subunit / Nitrile hydratase, beta subunit / Nitrile hydratase beta subunit domain / Nitrile hydratase beta subunit, N-terminal / : / Nitrile hydratase beta subunit, C-terminal / Nitrile hydratase beta subunit, N-terminal / Nitrile hydratase alpha subunit /Thiocyanate hydrolase gamma subunit / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, alpha chain / Nitrile hydratase alpha /Thiocyanate hydrolase gamma superfamily / Electron transport accessory-like domain superfamily
Similarity search - Domain/homology
OXYGEN ATOM / Cobalt-containing nitrile hydratase subunit alpha / Cobalt-containing nitrile hydratase subunit beta
Similarity search - Component
Biological speciesPseudonocardia thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsMiller, C.G. / Holz, R.C. / Liu, D. / Kaley, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J Inorg Biochem / Year: 2024
Title: Role of second-sphere arginine residues in metal binding and metallocentre assembly in nitrile hydratases.
Authors: Miller, C. / Huntoon, D. / Kaley, N. / Ogutu, I. / Fiedler, A.T. / Bennett, B. / Liu, D. / Holz, R.
History
DepositionAug 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cobalt-containing nitrile hydratase subunit alpha
B: Cobalt-containing nitrile hydratase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1723
Polymers49,1562
Non-polymers161
Water11,656647
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.176, 66.176, 185.671
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-672-

HOH

21B-627-

HOH

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Components

#1: Protein Cobalt-containing nitrile hydratase subunit alpha / L-NHase / L-nitrilase


Mass: 23072.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7SID2, nitrile hydratase
#2: Protein Cobalt-containing nitrile hydratase subunit beta / L-NHase / L-nitrilase


Mass: 26084.033 Da / Num. of mol.: 1 / Mutation: R157A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7SID3, nitrile hydratase
#3: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1.2 M sodium citrate tribasic in 0.1 M HEPES at pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Nov 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.29→19.47 Å / Num. obs: 120019 / % possible obs: 99.9 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.023 / Rrim(I) all: 0.074 / Net I/σ(I): 15.7
Reflection shellResolution: 1.29→1.31 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.491 / Num. unique obs: 5805 / Rpim(I) all: 0.262 / Rrim(I) all: 0.558

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.29→19.47 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1911 5983 4.99 %
Rwork0.1546 --
obs0.1564 120018 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.29→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3457 0 1 647 4105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063635
X-RAY DIFFRACTIONf_angle_d1.0024955
X-RAY DIFFRACTIONf_dihedral_angle_d9.095499
X-RAY DIFFRACTIONf_chiral_restr0.085514
X-RAY DIFFRACTIONf_plane_restr0.009658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.30.27921830.23793675X-RAY DIFFRACTION98
1.3-1.320.31841970.21533741X-RAY DIFFRACTION99
1.32-1.330.25962340.20413688X-RAY DIFFRACTION100
1.33-1.350.24832010.19493813X-RAY DIFFRACTION100
1.35-1.370.24432170.1813684X-RAY DIFFRACTION100
1.37-1.390.23081870.17693797X-RAY DIFFRACTION100
1.39-1.410.22652190.17713759X-RAY DIFFRACTION100
1.41-1.430.23221880.17683725X-RAY DIFFRACTION100
1.43-1.450.26212000.17083762X-RAY DIFFRACTION100
1.45-1.470.21682190.17273791X-RAY DIFFRACTION100
1.47-1.50.21691690.16713770X-RAY DIFFRACTION100
1.5-1.530.22521980.15673775X-RAY DIFFRACTION100
1.53-1.560.19792050.15493749X-RAY DIFFRACTION100
1.56-1.590.20492100.15223782X-RAY DIFFRACTION100
1.59-1.620.19472000.14623774X-RAY DIFFRACTION100
1.62-1.660.19372150.1543778X-RAY DIFFRACTION100
1.66-1.70.20951680.15033830X-RAY DIFFRACTION100
1.7-1.750.23031770.15863800X-RAY DIFFRACTION100
1.75-1.80.19962250.15943759X-RAY DIFFRACTION100
1.8-1.860.1941850.15713793X-RAY DIFFRACTION100
1.86-1.920.22040.15343810X-RAY DIFFRACTION100
1.92-20.21352090.15673790X-RAY DIFFRACTION100
2-2.090.17982010.1553824X-RAY DIFFRACTION100
2.09-2.20.18551660.1463884X-RAY DIFFRACTION100
2.2-2.340.192250.14953782X-RAY DIFFRACTION100
2.34-2.520.17051990.15193837X-RAY DIFFRACTION100
2.52-2.770.18091790.15633909X-RAY DIFFRACTION100
2.77-3.170.18821850.16073920X-RAY DIFFRACTION100
3.17-3.990.17082140.13693914X-RAY DIFFRACTION100
3.99-100.15532040.14534120X-RAY DIFFRACTION100

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