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- PDB-8tsy: Pseudomonas fluorescens G150T-2 isocyanide hydratase at 274 K -

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Basic information

Entry
Database: PDB / ID: 8tsy
TitlePseudomonas fluorescens G150T-2 isocyanide hydratase at 274 K
ComponentsIsonitrile hydratase InhA
KeywordsLYASE / isocyanide / isonitrile / room temperature
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: 1.2 Å
AuthorsWilson, M.A. / Smith, N. / Dasgupta, M. / Dolamore, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM139978 United States
Citation
Journal: Biorxiv / Year: 2023
Title: Changes in an Enzyme Ensemble During Catalysis Observed by High Resolution XFEL Crystallography.
Authors: Smith, N. / Dasgupta, M. / Wych, D.C. / Dolamore, C. / Sierra, R.G. / Lisova, S. / Marchany-Rivera, D. / Cohen, A.E. / Boutet, S. / Hunter, M.S. / Kupitz, C. / Poitevin, F. / Moss, F.R. / ...Authors: Smith, N. / Dasgupta, M. / Wych, D.C. / Dolamore, C. / Sierra, R.G. / Lisova, S. / Marchany-Rivera, D. / Cohen, A.E. / Boutet, S. / Hunter, M.S. / Kupitz, C. / Poitevin, F. / Moss, F.R. / Brewster, A.S. / Sauter, N.K. / Young, I.D. / Wolff, A.M. / Tiwari, V.K. / Kumar, N. / Berkowitz, D.B. / Hadt, R.G. / Thompson, M.C. / Follmer, A.H. / Wall, M.E. / Wilson, M.A.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionAug 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2602
Polymers24,2251
Non-polymers351
Water3,207178
1
A: Isonitrile hydratase InhA
hetero molecules

A: Isonitrile hydratase InhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5204
Polymers48,4492
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5350 Å2
ΔGint-57 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.202, 59.725, 56.373
Angle α, β, γ (deg.)90.000, 115.880, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

21A-570-

HOH

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Components

#1: Protein Isonitrile hydratase InhA / Isocyanide hydratase


Mass: 24224.699 Da / Num. of mol.: 1 / Mutation: G150T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: inhA, PFL_4109 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4K977
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 23% polyethylene glycol (PEG) 3350, 100mM Tris-HCl, pH 8.6, 200mM magnesium chloride, and 2mM dithiothreitol

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Data collection

DiffractionMean temperature: 274 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2018
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.775 Å / Relative weight: 1
ReflectionResolution: 1.2→35.21 Å / Num. obs: 66132 / % possible obs: 98.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.04 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.078 / Net I/σ(I): 7.3
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3293 / CC1/2: 0.334 / Rrim(I) all: 2.243 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoXDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→35.21 Å / SU ML: 0.1245 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.3828
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1371 3331 5.04 %
Rwork0.1175 62751 -
obs0.1185 66082 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.75 Å2
Refinement stepCycle: LAST / Resolution: 1.2→35.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 1 178 1852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972066
X-RAY DIFFRACTIONf_angle_d1.02952864
X-RAY DIFFRACTIONf_chiral_restr0.0854331
X-RAY DIFFRACTIONf_plane_restr0.0102394
X-RAY DIFFRACTIONf_dihedral_angle_d12.2754770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.31041320.29142474X-RAY DIFFRACTION95.01
1.22-1.230.29931260.25252558X-RAY DIFFRACTION95.04
1.23-1.250.24331390.23472428X-RAY DIFFRACTION92.4
1.25-1.270.24371240.21622634X-RAY DIFFRACTION97.94
1.27-1.30.20561360.19992640X-RAY DIFFRACTION99.18
1.3-1.320.20581420.17322581X-RAY DIFFRACTION98.98
1.32-1.350.19741290.16212704X-RAY DIFFRACTION99.51
1.35-1.370.17811290.15522631X-RAY DIFFRACTION99.5
1.37-1.40.18771280.14172638X-RAY DIFFRACTION99.07
1.4-1.440.16141570.13682626X-RAY DIFFRACTION99.32
1.44-1.470.14161250.12672642X-RAY DIFFRACTION99.07
1.47-1.510.15911300.11552624X-RAY DIFFRACTION97.59
1.51-1.560.12611360.09832509X-RAY DIFFRACTION94.87
1.56-1.610.13431480.08732555X-RAY DIFFRACTION96.54
1.61-1.660.12341480.08292676X-RAY DIFFRACTION99.82
1.66-1.730.1121510.08232631X-RAY DIFFRACTION99.82
1.73-1.810.12311640.08112644X-RAY DIFFRACTION99.57
1.81-1.90.11461620.08762601X-RAY DIFFRACTION99.35
1.9-2.020.12261290.08632670X-RAY DIFFRACTION99.43
2.02-2.180.09831380.08952611X-RAY DIFFRACTION98.04
2.18-2.40.10921370.09592619X-RAY DIFFRACTION97.42
2.4-2.750.11351340.11112691X-RAY DIFFRACTION99.86
2.75-3.460.1611340.13062674X-RAY DIFFRACTION99.22
3.46-35.210.12941530.12462690X-RAY DIFFRACTION98.37

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