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- PDB-9d5u: Nitrile hydratase S112A mutant -

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Basic information

Entry
Database: PDB / ID: 9d5u
TitleNitrile hydratase S112A 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: 1.35 Å
AuthorsMiller, C.G. / Holz, R.C. / Liu, D.
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

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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)49,4183
Polymers49,3262
Non-polymers921
Water4,522251
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)98,8366
Polymers98,6514
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area21760 Å2
ΔGint-115 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.837, 65.837, 185.637
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-403-

HOH

21B-437-

HOH

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Components

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


Mass: 23155.592 Da / Num. of mol.: 1 / Mutation: S112A
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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.35 Å3/Da / Density % sol: 47.76 %
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: 1.35→35.99 Å / Num. obs: 100941 / % possible obs: 97.6 % / Redundancy: 2 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 7.5
Reflection shellResolution: 1.35→1.38 Å / Rmerge(I) obs: 0.47 / Num. unique obs: 8715 / % possible all: 85.2

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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: 1.35→35.99 Å / SU ML: 0.01 / Cross valid method: FREE R-VALUE / σ(F): 18.59 / Phase error: 32.85 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.259 2044 2.02 %
Rwork0.2392 --
obs0.2521 100941 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→35.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 6 251 3721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02
X-RAY DIFFRACTIONf_angle_d2.048
X-RAY DIFFRACTIONf_dihedral_angle_d8.207482
X-RAY DIFFRACTIONf_chiral_restr0.08503
X-RAY DIFFRACTIONf_plane_restr0.009640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.31521200.31525841X-RAY DIFFRACTION80
1.38-1.420.31261420.31196724X-RAY DIFFRACTION92
1.42-1.460.29541360.29546958X-RAY DIFFRACTION94
1.46-1.510.28111360.28116861X-RAY DIFFRACTION95
1.51-1.560.30531460.30537112X-RAY DIFFRACTION97
1.56-1.630.28921460.28927145X-RAY DIFFRACTION98
1.63-1.70.35171460.32517164X-RAY DIFFRACTION98
1.7-1.790.30231420.30237182X-RAY DIFFRACTION98
1.79-1.90.30381480.30387186X-RAY DIFFRACTION98
1.9-2.050.3031470.2837240X-RAY DIFFRACTION98
2.05-2.260.29771440.26357221X-RAY DIFFRACTION98
2.26-2.580.2611490.24977289X-RAY DIFFRACTION98
2.58-3.250.27141520.23317372X-RAY DIFFRACTION98
3.25-100.24631580.19457634X-RAY DIFFRACTION98

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