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- PDB-9mxn: Pseudomonas fluorescens isocyanide hydratase, pH=6.5 -

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Basic information

Entry
Database: PDB / ID: 9mxn
TitlePseudomonas fluorescens isocyanide hydratase, pH=6.5
ComponentsIsonitrile hydratase InhA
KeywordsLYASE / isonitrile / pH / cysteine
Function / homology: / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase-like / regulation of DNA-templated transcription / Isonitrile hydratase InhA
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.89 Å
AuthorsSmith, N. / Prososki, K. / Wilson, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM153337 United States
CitationJournal: J.Chem.Inf.Model. / Year: 2025
Title: Combining Reactive Quantum-Mechanical Molecular-Dynamics Simulations with Mutagenesis, Crystallography, and Enzyme Kinetics to Reveal Plausible Steps of Isocyanide Hydratase Catalysis.
Authors: Corrigan Grove, R.A. / Moxley, M.A. / Negre, C.F.A. / Cawkwell, M.J. / Niklasson, A.M.N. / Mniszewski, S.M. / Smith, N. / Prososki, K. / Wilson, M.A. / Wall, M.E.
History
DepositionJan 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isonitrile hydratase InhA
B: Isonitrile hydratase InhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,99110
Polymers48,3612
Non-polymers6308
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-6 kcal/mol
Surface area16760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.755, 56.634, 68.363
Angle α, β, γ (deg.)90.000, 112.473, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Isonitrile hydratase InhA / isocyanide hydratase


Mass: 24180.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: inhA / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4K977
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 23% PEG 3350, 200 mM MgCl2, 100 mM MES pH=6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.72929 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72929 Å / Relative weight: 1
ReflectionResolution: 0.89→38.48 Å / Num. obs: 299145 / % possible obs: 97.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 9.84 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.058 / Net I/σ(I): 14
Reflection shellResolution: 0.89→0.9 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 12835 / CC1/2: 0.305 / Rrim(I) all: 2.459 / % possible all: 85.3

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.89→37.93 Å / SU ML: 0.0889 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 13.6282
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1345 3046 1.02 %
Rwork0.1211 295388 -
obs0.1212 298434 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.02 Å2
Refinement stepCycle: LAST / Resolution: 0.89→37.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 40 567 3974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764305
X-RAY DIFFRACTIONf_angle_d0.99445947
X-RAY DIFFRACTIONf_chiral_restr0.081673
X-RAY DIFFRACTIONf_plane_restr0.0116822
X-RAY DIFFRACTIONf_dihedral_angle_d12.84361610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.89-0.90.3991920.346111051X-RAY DIFFRACTION80.58
0.9-0.920.33021250.301212921X-RAY DIFFRACTION94.18
0.92-0.930.26891200.259813190X-RAY DIFFRACTION95.78
0.93-0.950.21991540.225613299X-RAY DIFFRACTION97.21
0.95-0.970.2141280.201813471X-RAY DIFFRACTION98.29
0.97-0.990.17881620.180113620X-RAY DIFFRACTION98.66
0.99-1.010.16211460.160113535X-RAY DIFFRACTION98.94
1.01-1.030.14891670.147213555X-RAY DIFFRACTION98.69
1.03-1.060.13431340.135913535X-RAY DIFFRACTION98.52
1.06-1.090.16411170.131413364X-RAY DIFFRACTION97.04
1.09-1.120.12721650.114213610X-RAY DIFFRACTION99.26
1.12-1.160.1051320.09913657X-RAY DIFFRACTION99.1
1.16-1.20.10331360.095613598X-RAY DIFFRACTION98.98
1.2-1.250.1061370.095313618X-RAY DIFFRACTION99.05
1.25-1.30.10771490.097313645X-RAY DIFFRACTION99.19
1.3-1.370.11991730.099713643X-RAY DIFFRACTION99.07
1.37-1.460.12111360.094713454X-RAY DIFFRACTION97.36
1.46-1.570.10831410.094613554X-RAY DIFFRACTION98.68
1.57-1.730.11291310.098313721X-RAY DIFFRACTION99.37
1.73-1.980.11681500.104513720X-RAY DIFFRACTION99.18
1.98-2.490.11671260.114713813X-RAY DIFFRACTION99.29
2.49-37.930.15721250.134613814X-RAY DIFFRACTION98.11

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