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- PDB-3a8l: Crystal structure of photo-activation state of Nitrile Hydratase ... -

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Basic information

Entry
Database: PDB / ID: 3a8l
TitleCrystal structure of photo-activation state of Nitrile Hydratase mutant S113A
Components
  • Nitrile hydratase subunit alpha
  • Nitrile hydratase subunit beta
KeywordsLYASE / Nitrile Hydratase / Fe / Iron / Metal-binding / Oxidation
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: 1.63 Å
AuthorsYamanaka, Y. / Hashimoto, K. / Ohtaki, A. / Noguchi, K. / Yohda, M. / Odaka, M.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2010
Title: Kinetic and structural studies on roles of the serine ligand and a strictly conserved tyrosine residue in nitrile hydratase
Authors: Yamanaka, Y. / Hashimoto, K. / Ohtaki, A. / Noguchi, K. / Yohda, M. / Odaka, M.
History
DepositionOct 6, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)46,6193
Polymers46,5632
Non-polymers561
Water11,440635
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-54 kcal/mol
Surface area16630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.324, 60.104, 81.885
Angle α, β, γ (deg.)90.00, 124.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23049.066 Da / Num. of mol.: 1 / Mutation: S113A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Strain: N-771 / Plasmid: pRCN103 / Production host: Escherichia coli (E. coli) / References: UniProt: P13448, nitrile hydratase
#2: Protein Nitrile hydratase subunit beta / Nitrile hydratase beta-subunit / Nitrilase / NHase


Mass: 23514.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Strain: N-771 / Plasmid: pHSGB / Production host: Escherichia coli (E. coli) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O
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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4850.32
2
Crystal grow
Crystal-IDMethodDetails
1vapor diffusion, hanging dropVAPOR DIFFUSION, HANGING DROP
2vapor diffusion, hanging dropVAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 56325 / % possible obs: 99.1 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 18

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ahj

2ahj


Resolution: 1.63→33.08 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.47 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19148 2848 5.1 %RANDOM
Rwork0.16524 ---
obs0.16659 53451 99.12 %-
all-56325 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.118 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.63→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 0 1 635 3838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223358
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.964586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.7825.047422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71623.141156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.94315515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3851528
X-RAY DIFFRACTIONr_chiral_restr0.080.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022643
X-RAY DIFFRACTIONr_nbd_refined0.1990.21731
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22343
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2428
X-RAY DIFFRACTIONr_metal_ion_refined0.0050.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.231
X-RAY DIFFRACTIONr_mcbond_it0.7441.52131
X-RAY DIFFRACTIONr_mcangle_it1.15423369
X-RAY DIFFRACTIONr_scbond_it1.88531411
X-RAY DIFFRACTIONr_scangle_it2.9144.51217
LS refinement shellResolution: 1.631→1.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 189 -
Rwork0.202 3933 -
obs--98.47 %

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