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- PDB-8i6n: Crystal structure of Co-type nitrile hydratase mutant from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 8i6n
TitleCrystal structure of Co-type nitrile hydratase mutant from Pseudomonas thermophila - L6T
Components
  • Cobalt-containing nitrile hydratase subunit alpha
  • Cobalt-containing nitrile hydratase subunit beta
KeywordsLYASE / hydratase / catalyze the hydration of nitriles to form amides
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: 2.2 Å
AuthorsMa, D. / Cheng, Z.Y. / Lai, Q.P. / Hou, X.D. / Yin, D.J. / Rao, Y.J. / Zhou, Z.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of Co-type nitrile hydratase mutant L6T from Pseudomonas thermophila at 2.2 Angstroms resolution.
Authors: Cheng, Z.Y. / Ma, D. / Yin, M. / Lai, Q.P. / Peplowski, L. / Han, L.C. / Hou, X.D. / Yin, D.J. / Rao, Y.J. / Zhou, Z.M.
History
DepositionJan 29, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: 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: Cobalt-containing nitrile hydratase subunit alpha
B: Cobalt-containing nitrile hydratase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9213
Polymers49,8622
Non-polymers591
Water6,143341
1
A: Cobalt-containing nitrile hydratase subunit alpha
B: Cobalt-containing nitrile hydratase subunit beta
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)99,8426
Polymers99,7254
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area21410 Å2
ΔGint-124 kcal/mol
Surface area32800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.64, 65.64, 184.07
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
11A-411-

HOH

21B-420-

HOH

31B-440-

HOH

41B-441-

HOH

51B-494-

HOH

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Components

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


Mass: 23278.615 Da / Num. of mol.: 1 / Mutation: L6T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Gene: SAMN05443637_10360 / Production host: Escherichia coli BL21(DE3) (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) / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: sodium citrate, HEPES-NaOH, pH 7.5

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Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.542 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.999→24.17 Å / Num. obs: 23492 / % possible obs: 99.67 % / Redundancy: 2.23 % / Rsym value: 0.25 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Num. unique obsRsym valueDiffraction-ID
1.999-2.07597560.251
2.07-2.153539220.2491
2.153-2.251479700.2451
2.251-2.37419090.2411
2.37-2.518359760.2371
2.518-2.712299350.2331
2.712-2.985239440.2291
2.985-3.416179850.2251
3.416-4.3119830.2221

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Processing

Software
NameVersionClassification
REFMAC1.18_3845refinement
SAINTV8.38Adata scaling
SAINTdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→24.16 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.889 / SU B: 6.583 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24438 1126 4.8 %RANDOM
Rwork0.18326 ---
obs0.18617 22393 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.614 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å2-0 Å2
3----0.49 Å2
Refinement stepCycle: 1 / Resolution: 2.2→24.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 1 341 3779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133535
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173203
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.6574800
X-RAY DIFFRACTIONr_angle_other_deg1.2731.5747445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0615425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56821.724203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53715580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4961528
X-RAY DIFFRACTIONr_chiral_restr0.0730.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023971
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02773
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_it1.1621.631706
X-RAY DIFFRACTIONr_mcbond_other1.1611.6291705
X-RAY DIFFRACTIONr_mcangle_it1.922.442129
X-RAY DIFFRACTIONr_mcangle_other1.922.4412130
X-RAY DIFFRACTIONr_scbond_it1.6921.821829
X-RAY DIFFRACTIONr_scbond_other1.6921.8211830
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7692.6512672
X-RAY DIFFRACTIONr_long_range_B_refined4.44619.4484252
X-RAY DIFFRACTIONr_long_range_B_other4.44519.4534253
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.254 Å
RfactorNum. reflection% reflection
Rfree0.256 71 -
Rwork0.22 1457 -
obs--87.36 %

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