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- PDB-9mxp: Pseudomonas fluorescens isocyanide hydratase D17N mutant, pH=8.8 -

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Basic information

Entry
Database: PDB / ID: 9mxp
TitlePseudomonas fluorescens isocyanide hydratase D17N mutant, pH=8.8
ComponentsCyclohexyl-isocyanide hydratase
KeywordsLYASE / isonitrile / pH / cysteine
Function / homology:
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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: Cyclohexyl-isocyanide hydratase
B: Cyclohexyl-isocyanide hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4906
Polymers48,3592
Non-polymers1314
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-66 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.931, 70.241, 102.289
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cyclohexyl-isocyanide hydratase


Mass: 24179.662 Da / Num. of mol.: 2 / Mutation: D17N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: SAMN03159460_06101 / Plasmid: pet15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A9Q7VXC7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 23% PEG 3350, 200 mM MgCl2, 100 mM Tris-HCl pH=8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.82653 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82653 Å / Relative weight: 1
ReflectionResolution: 1.2→37.74 Å / Num. obs: 126519 / % possible obs: 99.7 % / Redundancy: 13.5 % / Biso Wilson estimate: 13.6 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.108 / Net I/σ(I): 12.4
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5941 / CC1/2: 0.404 / Rrim(I) all: 3.262 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→37.74 Å / SU ML: 0.1207 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.8473
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1656 6326 5.02 %
Rwork0.1388 119622 -
obs0.1402 125948 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.09 Å2
Refinement stepCycle: LAST / Resolution: 1.2→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 4 552 3952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00763729
X-RAY DIFFRACTIONf_angle_d0.9415137
X-RAY DIFFRACTIONf_chiral_restr0.078601
X-RAY DIFFRACTIONf_plane_restr0.0122695
X-RAY DIFFRACTIONf_dihedral_angle_d13.30581359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.33792000.32273368X-RAY DIFFRACTION84.71
1.21-1.230.31821990.27743937X-RAY DIFFRACTION99.61
1.23-1.240.29932130.25573976X-RAY DIFFRACTION99.67
1.24-1.260.27992250.23683916X-RAY DIFFRACTION99.83
1.26-1.270.26582220.22933974X-RAY DIFFRACTION99.95
1.27-1.290.25951850.21583985X-RAY DIFFRACTION99.95
1.29-1.310.25072180.20413972X-RAY DIFFRACTION99.93
1.31-1.330.24271970.19413984X-RAY DIFFRACTION99.93
1.33-1.350.21772040.18453974X-RAY DIFFRACTION99.88
1.35-1.370.20781960.17873980X-RAY DIFFRACTION99.86
1.37-1.40.21132070.16213980X-RAY DIFFRACTION99.93
1.4-1.420.18422250.14733966X-RAY DIFFRACTION99.9
1.42-1.450.19772110.1393974X-RAY DIFFRACTION99.88
1.45-1.480.21362050.12593999X-RAY DIFFRACTION99.83
1.48-1.510.16692340.11823946X-RAY DIFFRACTION99.83
1.51-1.550.15362150.11253979X-RAY DIFFRACTION99.88
1.55-1.580.16392170.11023975X-RAY DIFFRACTION100
1.58-1.630.15942050.10484008X-RAY DIFFRACTION100
1.63-1.670.15931850.10964018X-RAY DIFFRACTION99.86
1.67-1.730.15412080.10344007X-RAY DIFFRACTION100
1.73-1.790.15541950.10774046X-RAY DIFFRACTION100
1.79-1.860.13222200.10524013X-RAY DIFFRACTION100
1.86-1.950.15652120.10494018X-RAY DIFFRACTION100
1.95-2.050.12242000.10984018X-RAY DIFFRACTION100
2.05-2.180.13412060.11524034X-RAY DIFFRACTION100
2.18-2.350.16062300.11814050X-RAY DIFFRACTION99.93
2.35-2.580.14312160.12354042X-RAY DIFFRACTION99.93
2.58-2.960.14942200.13554078X-RAY DIFFRACTION99.63
2.96-3.720.15262140.14524128X-RAY DIFFRACTION99.79
3.72-37.740.16712420.15784277X-RAY DIFFRACTION99.85

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