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- PDB-9d65: Nitrile hydratase BR52A mutant -

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Basic information

Entry
Database: PDB / ID: 9d65
TitleNitrile hydratase BR52A 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
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: 1.45 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 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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


Theoretical massNumber of molelcules
Total (without water)49,2722
Polymers49,2722
Non-polymers00
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-49 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.964, 65.964, 186.400
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-328-

HOH

21B-310-

HOH

31B-490-

HOH

41B-510-

HOH

51B-517-

HOH

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Components

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


Mass: 23187.592 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: 26084.031 Da / Num. of mol.: 1 / Mutation: R52A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
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: Oct 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.45→31.22 Å / Num. obs: 84526 / % possible obs: 99.37 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 8.8
Reflection shellResolution: 1.45→3.925 Å / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8359 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5156: ???)refinement
SCALAdata scaling
PHASERphasing
Adxvdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→31.22 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2789 4306 5.09 %
Rwork0.2399 --
obs0.2419 84526 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→31.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 0 468 3928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.82
X-RAY DIFFRACTIONf_dihedral_angle_d20.3111370
X-RAY DIFFRACTIONf_chiral_restr0.077514
X-RAY DIFFRACTIONf_plane_restr0.007660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.460.32421050.29952673X-RAY DIFFRACTION100
1.46-1.480.34751730.27862611X-RAY DIFFRACTION100
1.48-1.50.29871330.25642693X-RAY DIFFRACTION100
1.5-1.520.31811490.24832606X-RAY DIFFRACTION100
1.52-1.540.33011490.26452685X-RAY DIFFRACTION100
1.54-1.560.35951080.2392688X-RAY DIFFRACTION100
1.56-1.580.29011270.22342631X-RAY DIFFRACTION100
1.58-1.60.28091520.2232681X-RAY DIFFRACTION100
1.6-1.630.30081200.22212660X-RAY DIFFRACTION100
1.63-1.660.28861670.22662668X-RAY DIFFRACTION100
1.66-1.680.29371780.22392612X-RAY DIFFRACTION100
1.68-1.710.27831410.22972668X-RAY DIFFRACTION100
1.71-1.750.31821440.21722669X-RAY DIFFRACTION100
1.75-1.780.27181590.23392689X-RAY DIFFRACTION100
1.78-1.820.30071280.21992649X-RAY DIFFRACTION100
1.82-1.860.24531470.24262659X-RAY DIFFRACTION100
1.86-1.910.30511280.22892671X-RAY DIFFRACTION100
1.91-1.960.32461220.25192726X-RAY DIFFRACTION100
1.96-2.020.2931370.24152680X-RAY DIFFRACTION100
2.02-2.090.28471420.23652685X-RAY DIFFRACTION100
2.09-2.160.27421400.24292685X-RAY DIFFRACTION100
2.16-2.250.27271580.24322681X-RAY DIFFRACTION100
2.25-2.350.28351740.24322669X-RAY DIFFRACTION100
2.35-2.470.26571480.24492703X-RAY DIFFRACTION100
2.47-2.630.33491550.24732707X-RAY DIFFRACTION100
2.63-2.830.32841140.25462238X-RAY DIFFRACTION82
2.83-3.110.26011450.25092763X-RAY DIFFRACTION100
3.11-3.560.23881570.23882722X-RAY DIFFRACTION100
3.57-4.490.26961520.21892800X-RAY DIFFRACTION100
4.49-100.24241540.24242948X-RAY DIFFRACTION100

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