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- PDB-2cz0: photo-activation state of Fe-type NHase in aerobic condition -

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Basic information

Entry
Database: PDB / ID: 2cz0
Titlephoto-activation state of Fe-type NHase in aerobic condition
Components
  • Nitrile hydratase subunit alpha
  • Nitrile hydratase subunit beta
KeywordsLYASE / CYSTEINE-SULFINIC ACID / CYSTEINE-SULFENIC ACID / POST-TRANSLATIONAL MODIFICATION / NITRILE / HYDRATION / NON-HEM IRON / photo-reactive / over-oxidization / 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
butanoic acid / : / Nitrile hydratase subunit alpha / Nitrile hydratase subunit beta
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKawano, Y. / Hashimoto, K. / Odaka, M. / Nakayama, H. / Takio, K. / Endo, I. / Kamiya, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: photo-activation state of Fe-type NHase in aerobic condition
Authors: Kawano, Y. / Hashimoto, K. / Odaka, M. / Nakayama, H. / Takio, K. / Endo, I. / Kamiya, N.
History
DepositionJul 9, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 9, 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

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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)46,6084
Polymers46,4642
Non-polymers1442
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-48 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.016, 60.182, 81.573
Angle α, β, γ (deg.)90.00, 125.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1468-

HOH

21B-400-

HOH

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Components

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


Mass: 22949.871 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
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-BUA / BUTANOIC ACID


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8000, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 30, 1999
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 1.5→100 Å / Num. all: 64041 / Num. obs: 64041 / % possible obs: 88.7 %
Reflection shellResolution: 1.5→1.55 Å / % possible all: 89.1

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50 Å / Num. parameters: 14533 / Num. restraintsaints: 13368 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 6457 11.2 %RANDOM
Rwork0.1728 ---
all0.1736 57547 --
obs0.1728 57547 79.5 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3613
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 13 391 3603
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0255
X-RAY DIFFRACTIONs_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.056
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.107
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.062
X-RAY DIFFRACTIONs_approx_iso_adps0.035

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