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- PDB-3wvd: Crystal structure of Nitrile Hydratase mutant bR56K complexed wit... -

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Basic information

Entry
Database: PDB / ID: 3wvd
TitleCrystal structure of Nitrile Hydratase mutant bR56K complexed with Trimethylacetonitrile, photo-activated for 50 min
Components(Nitrile hydratase subunit ...) x 2
KeywordsLYASE / cysteine sulfinic acid / Cys-SO2H / Cys-SOH
Function / homology
Function and homology information


nitrile hydratase / indole-3-acetonitrile nitrile hydratase activity / transition metal ion binding
Similarity search - Function
Nitrile hydratase, alpha subunit / Nitrile hydratase, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / 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 / Nitrile hydratase, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / 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 / SH3 type barrels. - #50 / Electron transport accessory-like domain superfamily / Cyclin A; domain 1 / SH3 type barrels. / Roll / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / 2,2-dimethylpropanenitrile / Nitrile hydratase subunit alpha / Nitrile hydratase subunit beta
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsYamanaka, Y. / Hashimoto, K. / Noguchi, K. / Yohda, M. / Odaka, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile.
Authors: Yamanaka, Y. / Kato, Y. / Hashimoto, K. / Iida, K. / Nagasawa, K. / Nakayama, H. / Dohmae, N. / Noguchi, K. / Noguchi, T. / Yohda, M. / Odaka, M.
History
DepositionMay 17, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrile hydratase subunit alpha
B: Nitrile hydratase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7637
Polymers46,5512
Non-polymers2125
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-47 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.084, 59.965, 81.720
Angle α, β, γ (deg.)90.00, 125.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Nitrile hydratase subunit ... , 2 types, 2 molecules AB

#1: Protein Nitrile hydratase subunit alpha / NHase / Nitrilase


Mass: 23065.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: nthA / Production host: Escherichia coli (E. coli) / References: UniProt: P13448, nitrile hydratase
#2: Protein Nitrile hydratase subunit beta / NHase / Nitrilase


Mass: 23486.289 Da / Num. of mol.: 1 / Mutation: R56K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: nthB, nha2 / Production host: Escherichia coli (E. coli) / References: UniProt: P13449, nitrile hydratase

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Non-polymers , 4 types, 383 molecules

#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TAN / 2,2-dimethylpropanenitrile / Trimethylacetonitrile


Mass: 83.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG8000, 0.3M magnesium chloride, 0.1M Tris-HCl pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 1, 2012
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 149669 / % possible obs: 99 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→18.19 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.755 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16318 7079 5 %RANDOM
Rwork0.14194 ---
obs0.14299 133677 95.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.019 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.17 Å2
2---0.24 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.18→18.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 10 378 3580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0193337
X-RAY DIFFRACTIONr_bond_other_d0.0020.023093
X-RAY DIFFRACTIONr_angle_refined_deg2.2371.9634562
X-RAY DIFFRACTIONr_angle_other_deg1.02637132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1835422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58623.113151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.10415510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2931527
X-RAY DIFFRACTIONr_chiral_restr0.1480.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213810
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02759
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.37736430
X-RAY DIFFRACTIONr_sphericity_free18.815118
X-RAY DIFFRACTIONr_sphericity_bonded9.41656599
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 400 -
Rwork0.204 8012 -
obs--76.7 %

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