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- PDB-2ahj: NITRILE HYDRATASE COMPLEXED WITH NITRIC OXIDE -

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Basic information

Entry
Database: PDB / ID: 2ahj
TitleNITRILE HYDRATASE COMPLEXED WITH NITRIC OXIDE
Components(NITRILE HYDRATASE) x 2
KeywordsLYASE / PHOTOREACTIVE ENZYME / NITRIC OXIDE BINDING ENZYME / NON-HEME IRON CENTER / POST-TRANSLATIONAL MODIFICATION OF CYSTEINE RESIDUES / HYDRATASE
Function / homology
Function and homology information


nitrile hydratase / nitrile hydratase activity / transition metal ion binding
Similarity search - Function
Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, beta subunit / Nitrile hydratase, alpha subunit / 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; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, beta subunit / Nitrile hydratase, alpha subunit / 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
1,4-DIETHYLENE DIOXIDE / : / NITRIC OXIDE / Nitrile hydratase subunit alpha / Nitrile hydratase subunit beta
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsNagashima, S. / Nakasako, M. / Dohmae, N. / Tsujimura, M. / Takio, K. / Odaka, M. / Yohda, M. / Kamiya, N. / Endo, I.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms.
Authors: Nagashima, S. / Nakasako, M. / Dohmae, N. / Tsujimura, M. / Takio, K. / Odaka, M. / Yohda, M. / Kamiya, N. / Endo, I.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization of a Photosensitive Nitrile Hydratase from Rhodococcus Sp. N-771
Authors: Nagamune, T. / Honda, J. / Cho, W.D. / Kamiya, N. / Teratani, Y. / Hirata, A. / Sasabe, H. / Endo, I.
History
DepositionDec 24, 1997Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 21, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NITRILE HYDRATASE
B: NITRILE HYDRATASE
C: NITRILE HYDRATASE
D: NITRILE HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,66315
Polymers92,8964
Non-polymers76711
Water12,412689
1
A: NITRILE HYDRATASE
B: NITRILE HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8808
Polymers46,4482
Non-polymers4316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-85 kcal/mol
Surface area16450 Å2
MethodPISA
2
C: NITRILE HYDRATASE
D: NITRILE HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7847
Polymers46,4482
Non-polymers3355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-77 kcal/mol
Surface area16630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.400, 145.600, 52.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.171143, -0.985246, 0.000639), (-0.985224, -0.171143, -0.00664), (0.006651, 0.000507, -0.999978)
Vector: 120.364, 143.50349, 98.6977)

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein NITRILE HYDRATASE / NHASE


Mass: 22933.873 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: IN NITROSYLATED STATE (INACTIVE FORM) / Source: (natural) Rhodococcus erythropolis (bacteria) / Strain: SP. N-771 / References: UniProt: P13448, nitrile hydratase
#2: Protein NITRILE HYDRATASE / NHASE


Mass: 23514.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: IN NITROSYLATED STATE (INACTIVE FORM) / Source: (natural) Rhodococcus erythropolis (bacteria) / Strain: SP. N-771 / References: UniProt: P13449, nitrile hydratase

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Non-polymers , 6 types, 700 molecules

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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO
#7: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE NON-HEME IRON CENTER IS LOCATED AT THE INTERFACE BETWEEN THE A AND B SUBUNIT. THREE CYSTEINE ...THE NON-HEME IRON CENTER IS LOCATED AT THE INTERFACE BETWEEN THE A AND B SUBUNIT. THREE CYSTEINE RESIDUES, ONE SERINE RESIDUE IN THE A SUBUNIT ARE COORDINATED TO THE NON-HEME IRON ATOM. TWO OF THE THREE CYSTEINE RESIDUES (CYS 112 AND CYS 114) ARE POST-TRANSLATIONALLY MODIFIED TO CYSTEINE SULFINIC (112 CYS-SO2H) AND CYSTEINE SULFENIC (114 CYS-SOH) ACIDS. THE SIXTH LIGAND IS AN ENDOGENOUS NO MOLECULE.
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 49 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.6 Mammonium sulfate1reservoir
250 mMHepes-NaOH1reservoir
325 mM1reservoirZnCl2
43 %(v/v)1,4-dioxane1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 1, 1995 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→8 Å / Num. obs: 88965 / % possible obs: 90 % / Observed criterion σ(I): 1 / Redundancy: 4.08 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.3
Reflection shellResolution: 1.7→1.9 Å / Redundancy: 3.59 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.2 / % possible all: 76.4
Reflection
*PLUS
Num. measured all: 371002
Reflection shell
*PLUS
% possible obs: 76.4 %

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Processing

Software
NameVersionClassification
DMmodel building
MLPHAREphasing
X-PLOR3refinement
WEISdata reduction
CCP4(SCALA)data scaling
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→8 Å / Data cutoff high absF: 1000 / Data cutoff low absF: 1 / Isotropic thermal model: GAUSS / σ(F): 2 / Details: ALL ATOMS IN AN ASYMMETRIC UNIT WERE REFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 -10 %RANDOM
Rwork0.179 ---
obs0.179 84827 90 %-
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6416 0 35 689 7140
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d1.99
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.16
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
LS refinement shellResolution: 1.7→1.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.228 -10.1 %
Rwork0.323 7415 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.99
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.16
LS refinement shell
*PLUS
Rfactor obs: 0.323

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