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- PDB-2cyz: photo-activation state of Fe-type NHase in anaerobic condition -

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Basic information

Entry
Database: PDB / ID: 2cyz
Titlephoto-activation state of Fe-type NHase in anaerobic 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 / 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; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / 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 / Nitrile hydratase, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / 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
: / Nitrile hydratase subunit alpha / Nitrile hydratase subunit beta
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 anaerobic 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)46,5284
Polymers46,4482
Non-polymers802
Water12,737707
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-58 kcal/mol
Surface area16440 Å2
MethodPISA
2
A: Nitrile hydratase subunit alpha
B: Nitrile hydratase subunit beta
hetero molecules

A: Nitrile hydratase subunit alpha
B: Nitrile hydratase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0578
Polymers92,8964
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area18750 Å2
ΔGint-125 kcal/mol
Surface area29180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.052, 60.587, 82.007
Angle α, β, γ (deg.)90.00, 124.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1302-

HOH

21B-1548-

HOH

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Components

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


Mass: 22933.873 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
#3: Chemical ChemComp-FE / FE (III) ION


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.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 707 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
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: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 13, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 66078 / Num. obs: 66078 / % possible obs: 98.5 %
Reflection shellResolution: 1.55→1.61 Å / % possible all: 97.3

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→20 Å / Num. parameters: 15757 / Num. restraintsaints: 13423 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 6523 11.2 %RANDOM
Rwork0.1489 ---
obs0.1489 58022 86.4 %-
all-58022 --
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3908
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3213 0 2 709 3924
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0258
X-RAY DIFFRACTIONs_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.053
X-RAY DIFFRACTIONs_approx_iso_adps0.039

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