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- PDB-1ire: Crystal Structure of Co-type nitrile hydratase from Pseudonocardi... -

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Basic information

Entry
Database: PDB / ID: 1ire
TitleCrystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila
Components(Nitrile Hydratase) x 2
KeywordsLYASE / Cysteine-sulfinic acid / cysteine-sulfenic acid / post-translational modification / non-corrin cobalt / nitrile / hydration
Function / homology
Function and homology information


nitrile catabolic process / nitrile hydratase activity / nitrile hydratase / indole-3-acetonitrile nitrile hydratase activity / cobalt ion binding / 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
: / Cobalt-containing nitrile hydratase subunit alpha / Cobalt-containing nitrile hydratase subunit beta
Similarity search - Component
Biological speciesPseudonocardia thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMiyanaga, A. / Fushinobu, S. / Ito, K. / Wakagi, T.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2001
Title: Crystal structure of cobalt-containing nitrile hydratase.
Authors: Miyanaga, A. / Fushinobu, S. / Ito, K. / Wakagi, T.
#1: Journal: J.FERMENT.BIOENG. / Year: 1997
Title: Cloning and Sequencing of a Nitrile Hydratase Gene from Pseudonocardia thermophila JCM3095
Authors: Yamaki, T. / Oikawa, T. / Ito, K. / Nakamura, T.
History
DepositionOct 1, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
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_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_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_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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrile Hydratase
B: Nitrile Hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4493
Polymers49,3902
Non-polymers591
Water5,837324
1
A: Nitrile Hydratase
B: Nitrile Hydratase
hetero molecules

A: Nitrile Hydratase
B: Nitrile Hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8976
Polymers98,7794
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area21500 Å2
ΔGint-135 kcal/mol
Surface area32650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)65.501, 65.501, 184.614
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a (alpha/beta)2 generated from the heterodimer in the asymmetric unit by the operation: x, y, -z.

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Components

#1: Protein Nitrile Hydratase /


Mass: 23219.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q7SID2, nitrile hydratase
#2: Protein Nitrile Hydratase /


Mass: 26170.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q7SID3, nitrile hydratase
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium citrate, HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal grow
*PLUS
Temperature: 5 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
21.4 Mtrisodium citrate1reservoir
30.1 MHEPES-NaOH1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→28.03 Å / Num. all: 431214 / Num. obs: 431183 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.09 / Net I/σ(I): 5.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6251 / Rsym value: 0.331 / % possible all: 100
Reflection
*PLUS
Num. obs: 43623 / % possible obs: 99.8 % / Num. measured all: 431214 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 100 % / Rmerge(I) obs: 0.331

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AHJ

2ahj


Resolution: 1.8→28.03 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1965839.22 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1905 2155 4.9 %RANDOM
Rwork0.1781 ---
all0.1786 43592 --
obs0.1786 43561 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.6635 Å2 / ksol: 0.38989 e/Å3
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.08 Å20 Å2
2--0.12 Å20 Å2
3----0.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 1 324 3793
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.542
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.233 331 4.7 %
Rwork0.21 6786 -
obs-6786 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1WATER.PARAMWATER.TOP
X-RAY DIFFRACTION2ION.PARAMcION.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.191 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11
LS refinement shell
*PLUS
Rfactor Rwork: 0.21

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