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- PDB-9mxy: Pseudomonas fluorescens isocyanide hydratase D17N mutant, pH=6.5 -

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Basic information

Entry
Database: PDB / ID: 9mxy
TitlePseudomonas fluorescens isocyanide hydratase D17N mutant, pH=6.5
ComponentsCyclohexyl-isocyanide hydratase
KeywordsLYASE / isonitrile / pH / cysteine
Function / homology:
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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 21, 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)48,4304
Polymers48,3592
Non-polymers712
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-56 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.079, 40.828, 83.560
Angle α, β, γ (deg.)90.000, 104.314, 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 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 1.95 Å3/Da / Density % sol: 36.95 %
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: 0.82653 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: 1.15→37.37 Å / Num. obs: 122870 / % possible obs: 92.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 11.72 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.111 / Net I/σ(I): 9.6
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5516 / CC1/2: 0.401 / Rrim(I) all: 2.369 / % possible all: 84

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→37.37 Å / SU ML: 0.1212 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.3679
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1576 5998 4.91 %
Rwork0.125 116243 -
obs0.1266 122241 91.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.99 Å2
Refinement stepCycle: LAST / Resolution: 1.15→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3376 0 2 644 4022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573878
X-RAY DIFFRACTIONf_angle_d0.90115365
X-RAY DIFFRACTIONf_chiral_restr0.0766617
X-RAY DIFFRACTIONf_plane_restr0.011735
X-RAY DIFFRACTIONf_dihedral_angle_d13.04451436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.28031540.25213204X-RAY DIFFRACTION76.13
1.16-1.180.26062070.22353738X-RAY DIFFRACTION89.99
1.18-1.190.23481950.2113719X-RAY DIFFRACTION88.39
1.19-1.20.25692050.21133695X-RAY DIFFRACTION87.96
1.2-1.220.25331500.20533422X-RAY DIFFRACTION81.46
1.22-1.240.26941880.20793639X-RAY DIFFRACTION86.08
1.24-1.250.22682070.18823906X-RAY DIFFRACTION93.95
1.25-1.270.25712190.1853971X-RAY DIFFRACTION93.9
1.27-1.290.21972080.16973880X-RAY DIFFRACTION94
1.29-1.310.20342110.14693963X-RAY DIFFRACTION94.16
1.31-1.340.16691880.14063951X-RAY DIFFRACTION94.26
1.34-1.360.18681990.13373995X-RAY DIFFRACTION94.04
1.36-1.390.17592110.1323966X-RAY DIFFRACTION94.14
1.39-1.420.16331990.12133944X-RAY DIFFRACTION94.31
1.42-1.450.16981950.11733964X-RAY DIFFRACTION94.27
1.45-1.480.16681790.1183986X-RAY DIFFRACTION93.66
1.48-1.520.15512100.11743912X-RAY DIFFRACTION93.13
1.52-1.560.16591860.11143923X-RAY DIFFRACTION92.61
1.56-1.60.15172020.11343792X-RAY DIFFRACTION90.67
1.6-1.660.15031710.113547X-RAY DIFFRACTION83.97
1.66-1.720.15351970.10273831X-RAY DIFFRACTION90.35
1.72-1.780.12792360.09974055X-RAY DIFFRACTION96.08
1.78-1.870.13832030.10584056X-RAY DIFFRACTION96.6
1.87-1.960.14742150.11054060X-RAY DIFFRACTION96.24
1.96-2.090.14192030.10334075X-RAY DIFFRACTION96.18
2.09-2.250.12542130.10244068X-RAY DIFFRACTION95.47
2.25-2.470.12382470.10673972X-RAY DIFFRACTION94.45
2.47-2.830.13322050.12023885X-RAY DIFFRACTION91.27
2.83-3.570.14351830.12393748X-RAY DIFFRACTION87.01
3.57-37.370.17152120.13114376X-RAY DIFFRACTION99.03

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