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- PDB-2d0q: Complex of Fe-type NHase with Cyclohexyl isocyanide, photo-activa... -

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Basic information

Entry
Database: PDB / ID: 2d0q
TitleComplex of Fe-type NHase with Cyclohexyl isocyanide, photo-activated for 1hr at 277K
Components(Nitrile hydratase subunit ...) x 2
KeywordsLYASE / cysteine-sulfinic acid / cysteine-sulfenic acid / photo-reactive / nitrile / hydration / substrate analogue / complex / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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, 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
CYCLOHEXYL ISOCYANIDE / : / Nitrile hydratase subunit alpha / Nitrile hydratase subunit beta
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNojiri, M. / Kawano, Y. / Hashimoto, K. / Kamiya, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: X-ray snap shots of Inhibitor Binding Process in Photo-reactive Nitrile Hydratase
Authors: Nojiri, M. / Kawano, Y. / Hashimoto, K. / Kamiya, N.
History
DepositionAug 5, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)46,74310
Polymers46,4322
Non-polymers3118
Water10,485582
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-71 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.352, 60.201, 81.585
Angle α, β, γ (deg.)90.00, 125.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1832-

HOH

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Components

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

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


Mass: 22917.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodococcus erythropolis (bacteria) / Strain: N771 / References: UniProt: P13448, nitrile hydratase
#2: Protein Nitrile hydratase subunit beta / / Nitrilase / NHase


Mass: 23514.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodococcus erythropolis (bacteria) / Strain: N771 / References: UniProt: P13449, nitrile hydratase

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Non-polymers , 4 types, 590 molecules

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


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.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CYI / CYCLOHEXYL ISOCYANIDE


Mass: 109.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.5 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8000, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 17, 2001
RadiationMonochromator: diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.65→40.22 Å / Num. all: 53428 / Num. obs: 53428 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.65→1.71 Å / % possible all: 83.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→40.22 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.94 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.16455 5373 10.1 %RANDOM
Rwork0.15439 ---
all0.1554 48097 --
obs0.15439 48097 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.455 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20.24 Å2
2--0.75 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 15 585 3833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223329
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.9654532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3735401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73422.987154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4515532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4571529
X-RAY DIFFRACTIONr_chiral_restr0.0790.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022552
X-RAY DIFFRACTIONr_nbd_refined0.2180.21763
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22298
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2404
X-RAY DIFFRACTIONr_metal_ion_refined0.0890.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.233
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0860.24
X-RAY DIFFRACTIONr_mcbond_it0.9341.52081
X-RAY DIFFRACTIONr_mcangle_it1.13323305
X-RAY DIFFRACTIONr_scbond_it1.66631416
X-RAY DIFFRACTIONr_scangle_it2.7014.51227
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 296 -
Rwork0.198 2166 -
obs-2951 80.85 %

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