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- PDB-7w8m: Crystal structure of Co-type nitrile hydratase mutant from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 7w8m
TitleCrystal structure of Co-type nitrile hydratase mutant from Pseudomonas thermophila - A129R
Components
  • Cobalt-containing nitrile hydratase subunit beta
  • Nitrile hydratase
KeywordsLYASE / hydratase / catalyze the hydration of nitriles to form amides
Function / homology
Function and homology information


nitrile catabolic process / nitrile hydratase / nitrile hydratase activity / 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
: / nitrile hydratase / Cobalt-containing nitrile hydratase subunit beta
Similarity search - Component
Biological speciesPseudonocardia thermophila DSM 43832 (bacteria)
Pseudonocardia thermophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMa, D. / Cheng, Z.Y. / Hou, X.D. / Peplowski, L. / Lai, Q.P. / Fu, K. / Yin, D.J. / Rao, Y.J. / Zhou, Z.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Citation
Journal: Chem Sci / Year: 2022
Title: Insight into the broadened substrate scope of nitrile hydratase by static and dynamic structure analysis.
Authors: Ma, D. / Cheng, Z. / Peplowski, L. / Han, L. / Xia, Y. / Hou, X. / Guo, J. / Yin, D. / Rao, Y. / Zhou, Z.
#1: Journal: Biochem Biophys Res Commun / Year: 2001
Title: Crystal structure of cobalt-containing nitrile hydratase.
Authors: Miyanaga, A. / Fushinobu, S. / Ito, K. / Wakagi, T.
History
DepositionDec 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,0193
Polymers49,9602
Non-polymers591
Water1,856103
1
A: Nitrile hydratase
B: Cobalt-containing nitrile hydratase subunit beta
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)100,0396
Polymers99,9214
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area21490 Å2
ΔGint-130 kcal/mol
Surface area32890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.517, 65.517, 183.754
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Nitrile hydratase


Mass: 23290.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila DSM 43832 (bacteria)
Gene: SAMN05443637_10361 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1M6Q338, nitrile hydratase
#2: Protein Cobalt-containing nitrile hydratase subunit beta / L-NHase / L-nitrilase


Mass: 26669.760 Da / Num. of mol.: 1 / Mutation: A129R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Gene: SAMN05443637_10360 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7SID3, nitrile hydratase
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: sodium citrate, HEPES-NaOH, pH 7.5

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Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.542 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Apr 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.598→22.37 Å / Num. obs: 14569 / % possible obs: 96.94 % / Redundancy: 1.82 % / Rsym value: 0.077 / Net I/av σ(I): 12.087 / Net I/σ(I): 12.27
Reflection shell
Resolution (Å)Num. unique obsRsym valueDiffraction-ID
2.598-2.69262260.2091
2.69-2.798237490.1771
2.798-2.925211460.161
2.925-3.079185070.1291
3.079-3.271158460.1051
3.271-3.523131850.0791
3.523-3.876105570.0691
3.876-4.43379100.0581
4.433-5.57152470.0631

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
SAINTV8.38Adata scaling
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IRE

1ire


Resolution: 2.6→22.37 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 721 4.95 %
Rwork0.1774 13848 -
obs0.1805 14569 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.8 Å2 / Biso mean: 17.4282 Å2 / Biso min: 4.42 Å2
Refinement stepCycle: final / Resolution: 2.6→22.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 1 103 3577
Biso mean--24.76 20.25 -
Num. residues----431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.80.25821550.19582693284899
2.8-3.080.26211640.196827222886100
3.08-3.520.22751240.17072778290299
3.52-4.430.21741420.15592787292999
4.44-22.370.24781360.18642868300497

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