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- PDB-9d5v: Nitrile hydratase S112D mutant -

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Basic information

Entry
Database: PDB / ID: 9d5v
TitleNitrile hydratase S112D 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: 1.26 Å
AuthorsMiller, C.G. / Liu, D. / Holz, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2204024 United States
CitationJournal: J.Inorg.Biochem. / Year: 2024
Title: Catalytic and post-translational maturation roles of a conserved active site serine residue in nitrile hydratases.
Authors: Miller, C. / Knutson, K. / Liu, D. / Bennett, B. / Holz, R.C.
History
DepositionAug 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)49,4623
Polymers49,3702
Non-polymers921
Water6,035335
1
A: Cobalt-containing nitrile hydratase subunit alpha
B: Cobalt-containing nitrile hydratase subunit beta
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)98,9246
Polymers98,7404
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area21900 Å2
ΔGint-112 kcal/mol
Surface area32540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.682, 65.682, 185.144
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-406-

HOH

21B-465-

HOH

31B-480-

HOH

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Components

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


Mass: 23199.602 Da / Num. of mol.: 1 / Mutation: S112D
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: 26170.148 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: Q7SID3, nitrile hydratase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.34 Å3/Da / Density % sol: 47.33 %
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: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.26→35.9 Å / Num. obs: 125649 / % possible obs: 99.91 % / Redundancy: 2 % / Rmerge(I) obs: 0.011 / Net I/σ(I): 18.86
Reflection shellResolution: 1.26→10 Å / Rmerge(I) obs: 0.258 / Num. unique obs: 12297

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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: 1.26→35.9 Å / Cross valid method: FREE R-VALUE / σ(F): 16.24 / Phase error: 26.98 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.23 2016 1.6 %
Rwork0.2125 --
obs0.2193 125649 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.26→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 6 335 3808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.976
X-RAY DIFFRACTIONf_dihedral_angle_d7.82479
X-RAY DIFFRACTIONf_chiral_restr0.076502
X-RAY DIFFRACTIONf_plane_restr0.008639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.290.27341360.27348433X-RAY DIFFRACTION95
1.29-1.330.29551440.28698687X-RAY DIFFRACTION98
1.33-1.360.28021430.28028739X-RAY DIFFRACTION98
1.36-1.410.31481420.27748702X-RAY DIFFRACTION98
1.41-1.460.28621450.27038833X-RAY DIFFRACTION98
1.46-1.520.23051420.23058729X-RAY DIFFRACTION98
1.52-1.590.26411420.25068804X-RAY DIFFRACTION98
1.59-1.670.26341440.24758822X-RAY DIFFRACTION98
1.67-1.770.26451450.24878856X-RAY DIFFRACTION98
1.77-1.910.2321450.2328818X-RAY DIFFRACTION98
1.91-2.10.22981440.22948893X-RAY DIFFRACTION98
2.1-2.410.21881450.21718927X-RAY DIFFRACTION98
2.41-3.030.241450.21729020X-RAY DIFFRACTION98
3.03-100.20141510.17349373X-RAY DIFFRACTION98

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