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- PDB-3vyh: Crystal structure of aW116R mutant of nitrile hydratase from Pseu... -

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Basic information

Entry
Database: PDB / ID: 3vyh
TitleCrystal structure of aW116R mutant of nitrile hydratase from Pseudonocardia thermophilla
Components
  • Cobalt-containing nitrile hydratase subunit alpha
  • Cobalt-containing nitrile hydratase subunit beta
KeywordsLYASE / nitrile hydratase / metalloenzyme / hydration
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; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, beta subunit / 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; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, beta subunit / 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 / 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
: / 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: 1.63 Å
AuthorsYamanaka, Y. / Sato, M. / Arakawa, T. / Namima, S. / Hori, S. / Ohtaki, A. / Noguchi, K. / Katayama, Y. / Yohda, M. / Odaka, M.
CitationJournal: To be published
Title: Effects of argnine residue around the substrate pocket on the substrate specificity of thiocyanate hydrolase
Authors: Yamanaka, Y. / Sato, M. / Arakawa, T. / Namima, S. / Hori, S. / Ohtaki, A. / Noguchi, K. / Katayama, Y. / Yohda, M. / Odaka, M.
History
DepositionSep 25, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)49,8333
Polymers49,7742
Non-polymers591
Water6,630368
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)99,6666
Polymers99,5484
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area21230 Å2
ΔGint-107 kcal/mol
Surface area33000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.683, 65.683, 184.796
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 23190.576 Da / Num. of mol.: 1 / Mutation: W116R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SID2, nitrile hydratase
#2: Protein Cobalt-containing nitrile hydratase subunit beta / L-NHase / L-nitrilase


Mass: 26583.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Production host: Escherichia coli (E. coli) / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES-NaOH pH7.5, 1.4M sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 17, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 61652 / % possible obs: 99.4 %
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 7.7 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IRE

1ire


Resolution: 1.63→48.44 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.471 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20271 2962 5.1 %RANDOM
Rwork0.1736 ---
obs0.17508 55668 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.944 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.63→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 1 368 3818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0223534
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2021.964798
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.3035.047429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68723.584173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65815580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2261528
X-RAY DIFFRACTIONr_chiral_restr0.1740.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212758
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3071.52139
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.05523462
X-RAY DIFFRACTIONr_scbond_it3.16231395
X-RAY DIFFRACTIONr_scangle_it4.9234.51336
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.631→1.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 212 -
Rwork0.186 4062 -
obs--99.88 %

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