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- PDB-1ugq: Crystal structure of apoenzyme of Co-type nitrile hydratase -

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Basic information

Entry
Database: PDB / ID: 1ugq
TitleCrystal structure of apoenzyme of Co-type nitrile hydratase
Components
  • Nitrile Hydratase alpha subunit
  • Nitrile Hydratase beta subunit
KeywordsLYASE / APOENZYME / NON-CORRIN COBALT / NITRILE / HYDRATION
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, alpha subunit / Nitrile hydratase, beta subunit / Nitrile hydratase, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / 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, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / 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: 2 Å
AuthorsMiyanaga, A. / Fushinobu, S. / Ito, K. / Shoun, H. / Wakagi, T.
CitationJournal: Eur.J.Biochem. / Year: 2004
Title: Mutational and structural analysis of cobalt-containing nitrile hydratase on substrate and metal binding
Authors: Miyanaga, A. / Fushinobu, S. / Ito, K. / Shoun, H. / Wakagi, T.
History
DepositionJun 17, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrile Hydratase alpha subunit
B: Nitrile Hydratase beta subunit


Theoretical massNumber of molelcules
Total (without water)49,2112
Polymers49,2112
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-51 kcal/mol
Surface area18530 Å2
MethodPISA
2
A: Nitrile Hydratase alpha subunit
B: Nitrile Hydratase beta subunit

A: Nitrile Hydratase alpha subunit
B: Nitrile Hydratase beta subunit


Theoretical massNumber of molelcules
Total (without water)98,4214
Polymers98,4214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area21140 Å2
ΔGint-113 kcal/mol
Surface area32660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.362, 65.362, 184.099
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 Nitrile Hydratase alpha subunit


Mass: 23040.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Strain: JCM 3095 / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SID2, nitrile hydratase
#2: Protein Nitrile Hydratase beta subunit


Mass: 26170.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Strain: JCM 3095 / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SID3, nitrile hydratase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2003
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→19.389 Å / Num. all: 31332 / Num. obs: 31332 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.9 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.389 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2282674.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1561 5 %RANDOM
Rwork0.184 ---
all0.186 31328 --
obs0.184 31328 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.4289 Å2 / ksol: 0.404744 e/Å3
Displacement parametersBiso mean: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å21.5 Å20 Å2
2--1.57 Å20 Å2
3----3.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 2→19.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 0 268 3734
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it3.271.5
X-RAY DIFFRACTIONc_mcangle_it3.712
X-RAY DIFFRACTIONc_scbond_it4.812
X-RAY DIFFRACTIONc_scangle_it5.762.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 246 4.8 %
Rwork0.181 4849 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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