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- PDB-1ahj: NITRILE HYDRATASE -

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Basic information

Entry
Database: PDB / ID: 1ahj
TitleNITRILE HYDRATASE
Components
  • NITRILE HYDRATASE (SUBUNIT ALPHA)
  • NITRILE HYDRATASE (SUBUNIT BETA)
KeywordsLYASE / NITRILE HYDRATASE / IRON CENTER / NON-HEME IRON
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
: / Nitrile hydratase subunit alpha / Nitrile hydratase subunit beta
Similarity search - Component
Biological speciesRhodococcus sp. R312 (bacteria)
MethodX-RAY DIFFRACTION / MIRAS AVERAGING / Resolution: 2.65 Å
AuthorsHuang, W. / Schneider, G. / Lindqvist, Y.
CitationJournal: Structure / Year: 1997
Title: Crystal structure of nitrile hydratase reveals a novel iron centre in a novel fold.
Authors: Huang, W. / Jia, J. / Cummings, J. / Nelson, M. / Schneider, G. / Lindqvist, Y.
History
DepositionApr 5, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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)
C: NITRILE HYDRATASE (SUBUNIT ALPHA)
D: NITRILE HYDRATASE (SUBUNIT BETA)
E: NITRILE HYDRATASE (SUBUNIT ALPHA)
F: NITRILE HYDRATASE (SUBUNIT BETA)
G: NITRILE HYDRATASE (SUBUNIT ALPHA)
H: NITRILE HYDRATASE (SUBUNIT BETA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,24912
Polymers186,0258
Non-polymers2234
Water0
1
A: NITRILE HYDRATASE (SUBUNIT ALPHA)
B: NITRILE HYDRATASE (SUBUNIT BETA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5623
Polymers46,5062
Non-polymers561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-63 kcal/mol
Surface area17020 Å2
MethodPISA
2
E: NITRILE HYDRATASE (SUBUNIT ALPHA)
F: NITRILE HYDRATASE (SUBUNIT BETA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5623
Polymers46,5062
Non-polymers561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-61 kcal/mol
Surface area17130 Å2
MethodPISA
3
C: NITRILE HYDRATASE (SUBUNIT ALPHA)
D: NITRILE HYDRATASE (SUBUNIT BETA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5623
Polymers46,5062
Non-polymers561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-64 kcal/mol
Surface area17100 Å2
MethodPISA
4
G: NITRILE HYDRATASE (SUBUNIT ALPHA)
H: NITRILE HYDRATASE (SUBUNIT BETA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5623
Polymers46,5062
Non-polymers561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-61 kcal/mol
Surface area16940 Å2
MethodPISA
5
A: NITRILE HYDRATASE (SUBUNIT ALPHA)
B: NITRILE HYDRATASE (SUBUNIT BETA)
hetero molecules

E: NITRILE HYDRATASE (SUBUNIT ALPHA)
F: NITRILE HYDRATASE (SUBUNIT BETA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1246
Polymers93,0134
Non-polymers1122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
Buried area18660 Å2
ΔGint-125 kcal/mol
Surface area30620 Å2
MethodPISA
6
C: NITRILE HYDRATASE (SUBUNIT ALPHA)
D: NITRILE HYDRATASE (SUBUNIT BETA)
hetero molecules

G: NITRILE HYDRATASE (SUBUNIT ALPHA)
H: NITRILE HYDRATASE (SUBUNIT BETA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1246
Polymers93,0134
Non-polymers1122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area18600 Å2
ΔGint-125 kcal/mol
Surface area30460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.854, 144.239, 159.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.997023, 0.062616, -0.044983), (0.052612, 0.126072, -0.990625), (-0.056358, -0.990043, -0.128991)65.27081, 100.62289, 118.43628
2given(-0.993863, 0.058979, -0.093579), (-0.059558, 0.427564, 0.902021), (0.093211, 0.902059, -0.421427)42.26377, 23.38027, -36.27829
3given(0.99262, 0.022209, 0.119216), (-0.01441, -0.954517, 0.297809), (0.120408, -0.297329, -0.947152)20.35925, 145.01817, 86.93984

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Components

#1: Protein
NITRILE HYDRATASE (SUBUNIT ALPHA)


Mass: 22991.031 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rhodococcus sp. R312 (bacteria) / References: UniProt: P13448, nitrile hydratase
#2: Protein
NITRILE HYDRATASE (SUBUNIT BETA)


Mass: 23515.289 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rhodococcus sp. R312 (bacteria) / References: UniProt: P13449, nitrile hydratase
#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe

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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: 2.8 Å3/Da / Density % sol: 53 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlenzyme1drop
220 mMHEPES1drop
340 mMbutyrate1drop
427 %PEG80001reservoir
50.3 M1reservoirMgCl2
60.1 MTris1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 56428 / % possible obs: 93.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 45.4 Å2 / Rsym value: 0.068 / Net I/σ(I): 20.3
Reflection shellResolution: 2.65→2.71 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.26 / % possible all: 75.7
Reflection
*PLUS
Num. measured all: 347098 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 75.7 % / Rmerge(I) obs: 0.26

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SQUASHphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MIRAS AVERAGING / Resolution: 2.65→7.5 Å / Isotropic thermal model: GROUPED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1783 3.5 %RANDOM
Rwork0.264 ---
obs0.264 50428 89 %-
Displacement parametersBiso mean: 24.7 Å2
Refinement stepCycle: LAST / Resolution: 2.65→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12828 0 4 0 12832
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.53
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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