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- PDB-2qdy: Crystal Structure of Fe-type NHase from Rhodococcus erythropolis AJ270 -

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Basic information

Entry
Database: PDB / ID: 2qdy
TitleCrystal Structure of Fe-type NHase from Rhodococcus erythropolis AJ270
Components(Nitrile hydratase subunit ...) x 2
KeywordsLYASE / nitrile hydratase / post translation
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
: / 2-METHYLPROPAN-1-AMINE / Nitrile hydratase subunit alpha / Nitrile hydratase subunit beta
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSong, L. / Shi, J. / Xue, Z. / Wang, M.-X. / Qian, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: High resolution X-ray molecular structure of the nitrile hydratase from Rhodococcus erythropolis AJ270 reveals posttranslational oxidation of two cysteines into sulfinic acids and a novel ...Title: High resolution X-ray molecular structure of the nitrile hydratase from Rhodococcus erythropolis AJ270 reveals posttranslational oxidation of two cysteines into sulfinic acids and a novel biocatalytic nitrile hydration mechanism
Authors: Song, L. / Wang, M. / Shi, J. / Xue, Z. / Wang, M.-X. / Qian, S.
History
DepositionJun 22, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)47,49217
Polymers46,5952
Non-polymers89615
Water10,539585
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint-100 kcal/mol
Surface area16120 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)94,98334
Polymers93,1914
Non-polymers1,79330
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area23530 Å2
ΔGint-218 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.064, 60.068, 81.761
Angle α, β, γ (deg.)90.000, 125.150, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2248-

HOH

21B-2091-

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: 23081.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodococcus erythropolis (bacteria) / Strain: AJ270 / 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: AJ270 / References: UniProt: P13449, nitrile hydratase

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Non-polymers , 6 types, 600 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-IBN / 2-METHYLPROPAN-1-AMINE / ISOBUTYRONITRILE / Isobutylamine


Mass: 73.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11N
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 49.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 23% PEG 8000, 0.3M magnesium chloride, 0.1M TrisHCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.99 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.3→35.3 Å / Num. all: 110924 / Num. obs: 110580 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.035 / Net I/σ(I): 13.9
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.39 / Num. unique all: 10756 / Χ2: 0.988 / % possible all: 97.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AHJ

2ahj


Resolution: 1.3→35.3 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.249 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.157 5531 5 %RANDOM
Rwork0.129 ---
obs0.131 110564 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.118 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.63 Å2
2---0.24 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.3→35.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 49 585 3833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223471
X-RAY DIFFRACTIONr_angle_refined_deg1.711.9724737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7025435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64723.333168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69415560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5891531
X-RAY DIFFRACTIONr_chiral_restr0.130.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022698
X-RAY DIFFRACTIONr_nbd_refined0.2120.21833
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22384
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2460
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.232
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0260.22
X-RAY DIFFRACTIONr_mcbond_it1.6711.52152
X-RAY DIFFRACTIONr_mcangle_it2.2223411
X-RAY DIFFRACTIONr_scbond_it2.83931511
X-RAY DIFFRACTIONr_scangle_it3.734.51312
X-RAY DIFFRACTIONr_rigid_bond_restr1.64433663
X-RAY DIFFRACTIONr_sphericity_free8.9353596
X-RAY DIFFRACTIONr_sphericity_bonded6.51533376
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 379 -
Rwork0.211 7516 -
obs-7895 96.87 %

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