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- PDB-4ob0: Crystal Structure of Nitrile Hydratase from Pseudonocardia thermo... -

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Basic information

Entry
Database: PDB / ID: 4ob0
TitleCrystal Structure of Nitrile Hydratase from Pseudonocardia thermophila bound to Phenyl Boronic Acid
Components
  • Cobalt-containing nitrile hydratase subunit alpha
  • Cobalt-containing nitrile hydratase subunit beta
KeywordsLYASE / Nitrile Hydratase / nucleophile
Function / homology
Function and homology information


nitrile catabolic process / nitrile hydratase activity / nitrile hydratase / indole-3-acetonitrile nitrile hydratase activity / cobalt ion binding / transition metal ion binding
Similarity search - Function
Nitrile hydratase, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / 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, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / 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
: / PHENYL BORONIC ACID / 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: 1.2 Å
AuthorsRui, W. / Salette, M. / Ruslan, S. / Richard, H. / Dali, L.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: The active site sulfenic acid ligand in nitrile hydratases can function as a nucleophile.
Authors: Martinez, S. / Wu, R. / Sanishvili, R. / Liu, D. / Holz, R.
History
DepositionJan 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cobalt-containing nitrile hydratase subunit alpha
B: Cobalt-containing nitrile hydratase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7974
Polymers50,6162
Non-polymers1812
Water11,331629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-58 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.680, 65.680, 185.691
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
11B-612-

HOH

21B-622-

HOH

31B-623-

HOH

41B-653-

HOH

51B-656-

HOH

DetailsHeterodimer of alpha subunit and beta subunit.

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Components

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


Mass: 24032.475 Da / Num. of mol.: 1 / Fragment: Nitrile hydratase alpha subunit
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 / Fragment: Nitrile hydratase beta subunit
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: Chemical ChemComp-PBC / PHENYL BORONIC ACID


Mass: 121.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7BO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 276 K / Method: evaporation / pH: 7.5
Details: 1.4 M sodium citrate tribasic, 0.1 M HEPES, 20 mM Phenyl Boronic Acid, pH 7.5, EVAPORATION, temperature 276K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2012
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→30.96 Å / Num. all: 859631 / Num. obs: 139129 / % possible obs: 95.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1.4 / Redundancy: 6.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.4
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 1.4 / Num. unique all: 14875 / % possible all: 71

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→30.96 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 18.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 6751 5.01 %Random
Rwork0.1525 ---
obs0.1541 139067 95.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→30.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 10 629 4101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063649
X-RAY DIFFRACTIONf_angle_d1.0794975
X-RAY DIFFRACTIONf_dihedral_angle_d13.0651387
X-RAY DIFFRACTIONf_chiral_restr0.046517
X-RAY DIFFRACTIONf_plane_restr0.006657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.21360.37271030.34122599X-RAY DIFFRACTION55
1.2136-1.22790.37291380.33392986X-RAY DIFFRACTION66
1.2279-1.24290.35631610.323314X-RAY DIFFRACTION73
1.2429-1.25860.33851850.3163773X-RAY DIFFRACTION82
1.2586-1.27520.32292270.30244014X-RAY DIFFRACTION89
1.2752-1.29270.32882160.28264429X-RAY DIFFRACTION96
1.2927-1.31110.34332490.26264503X-RAY DIFFRACTION99
1.3111-1.33070.28352420.24264561X-RAY DIFFRACTION100
1.3307-1.35150.24862510.22044556X-RAY DIFFRACTION100
1.3515-1.37360.26012360.20374562X-RAY DIFFRACTION100
1.3736-1.39730.25192450.18344666X-RAY DIFFRACTION100
1.3973-1.42270.21892690.17684489X-RAY DIFFRACTION100
1.4227-1.45010.20572420.16814560X-RAY DIFFRACTION100
1.4501-1.47970.22022300.15884596X-RAY DIFFRACTION100
1.4797-1.51190.1912360.14624599X-RAY DIFFRACTION100
1.5119-1.5470.18542370.1364599X-RAY DIFFRACTION100
1.547-1.58570.16612600.12734564X-RAY DIFFRACTION100
1.5857-1.62860.17342440.12114616X-RAY DIFFRACTION100
1.6286-1.67650.15772380.12114599X-RAY DIFFRACTION100
1.6765-1.73060.15782380.12144659X-RAY DIFFRACTION100
1.7306-1.79250.15692630.11884547X-RAY DIFFRACTION100
1.7925-1.86420.16272670.12354627X-RAY DIFFRACTION100
1.8642-1.94910.15272560.12584584X-RAY DIFFRACTION100
1.9491-2.05180.16762590.11654671X-RAY DIFFRACTION100
2.0518-2.18030.14872560.12154624X-RAY DIFFRACTION100
2.1803-2.34860.17772360.1294668X-RAY DIFFRACTION100
2.3486-2.58490.16242440.13584685X-RAY DIFFRACTION100
2.5849-2.95860.17432440.14854703X-RAY DIFFRACTION100
2.9586-3.72660.17082340.13614778X-RAY DIFFRACTION100
3.7266-30.97050.14972640.144966X-RAY DIFFRACTION99

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