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- PDB-7sjz: Crystal structure of aS162A mutant of Co-type nitrile hydratase f... -

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Basic information

Entry
Database: PDB / ID: 7sjz
TitleCrystal structure of aS162A mutant of Co-type nitrile hydratase from Pseudonocardia thermophila
Components
  • Cobalt-containing nitrile hydratase subunit alpha
  • Cobalt-containing nitrile hydratase subunit beta
KeywordsLYASE / Hydration Nitrile hydratase Mutant Co-type
Function / homology
Function and homology information


nitrile catabolic process / nitrile hydratase / 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 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 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 / Electron transport accessory-like domain superfamily
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsOgutu, R.A.M.I. / Holz, C.R. / Bennett, B. / St Maurice, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1808711, RCH& BB; CHE-1532168 BB & RCH United States
CitationJournal: Catalysts / Year: 2021
Title: Examination of the Catalytic Role of the Axial Cystine Ligand in the Co-Type Nitrile Hydratase from Pseudonocardia thermophila JCM 3095
Authors: Ogutu, I.R.A.M. / St Maurice, M. / Bennett, B. / Holz, R.C.
History
DepositionOct 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cobalt-containing nitrile hydratase subunit alpha
B: Cobalt-containing nitrile hydratase subunit beta


Theoretical massNumber of molelcules
Total (without water)50,6392
Polymers50,6392
Non-polymers00
Water8,629479
1
A: Cobalt-containing nitrile hydratase subunit alpha
B: Cobalt-containing nitrile hydratase subunit beta

A: Cobalt-containing nitrile hydratase subunit alpha
B: Cobalt-containing nitrile hydratase subunit beta


Theoretical massNumber of molelcules
Total (without water)101,2784
Polymers101,2784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area20170 Å2
ΔGint-117 kcal/mol
Surface area32960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.910, 65.910, 186.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-413-

HOH

21B-555-

HOH

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Components

#1: Protein Cobalt-containing nitrile hydratase subunit alpha / L-NHase / L-nitrilase


Mass: 24055.553 Da / Num. of mol.: 1 / Mutation: S162A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7SID2, nitrile hydratase
#2: Protein Cobalt-containing nitrile hydratase subunit beta / L-NHase / L-nitrilase


Mass: 26583.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7SID3, nitrile hydratase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.2 M sodium citrate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→48.66 Å / Num. obs: 40335 / % possible obs: 98.2 % / Redundancy: 8.55 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 30.2
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.05 / Num. unique obs: 40335

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IRE

1ire


Resolution: 1.85→42.05 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.292 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21121 2035 5 %RANDOM
Rwork0.16481 ---
obs0.16715 38280 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.851 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.85→42.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3387 0 0 479 3866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133557
X-RAY DIFFRACTIONr_bond_other_d0.0060.0173242
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.6534859
X-RAY DIFFRACTIONr_angle_other_deg1.4911.5717500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7225453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83222190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92915561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7671524
X-RAY DIFFRACTIONr_chiral_restr0.0920.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02812
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5131.6151748
X-RAY DIFFRACTIONr_mcbond_other1.5071.6141747
X-RAY DIFFRACTIONr_mcangle_it2.1472.4122188
X-RAY DIFFRACTIONr_mcangle_other2.1462.4132189
X-RAY DIFFRACTIONr_scbond_it2.2231.8071809
X-RAY DIFFRACTIONr_scbond_other2.2231.8081809
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2622.6322658
X-RAY DIFFRACTIONr_long_range_B_refined4.9420.1924239
X-RAY DIFFRACTIONr_long_range_B_other4.67219.3794090
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 145 -
Rwork0.172 2806 -
obs--98.4 %

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