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- PDB-8tsu: Pseudomonas fluorescens G150T-1 isocyanide hydratase at 274 K -

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Basic information

Entry
Database: PDB / ID: 8tsu
TitlePseudomonas fluorescens G150T-1 isocyanide hydratase at 274 K
ComponentsIsonitrile hydratase InhA
KeywordsLYASE / isocyanide / isonitrile / X-ray free electron laser / serial crystallography
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: 1.15 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 11, 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 area5340 Å2
ΔGint-56 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.190, 59.717, 56.295
Angle α, β, γ (deg.)90.000, 115.895, 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-459-

HOH

21A-569-

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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 25% PEG 3350, 200 MM MAGNESIUM CHLORIDE, 100MM TRIS-HCL, PH 8.6, 2 MM 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: 1.15→39.47 Å / Num. obs: 74206 / % possible obs: 97.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 13.84 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.052 / Net I/σ(I): 12
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3528 / CC1/2: 0.366 / Rrim(I) all: 1.72 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoXDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→35.2 Å / SU ML: 0.1304 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.8869
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1405 3801 5.14 %
Rwork0.1196 70119 -
obs0.1207 73920 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.46 Å2
Refinement stepCycle: LAST / Resolution: 1.15→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 1 178 1852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072066
X-RAY DIFFRACTIONf_angle_d0.882864
X-RAY DIFFRACTIONf_chiral_restr0.0807331
X-RAY DIFFRACTIONf_plane_restr0.0093394
X-RAY DIFFRACTIONf_dihedral_angle_d12.1718770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.28621140.31132347X-RAY DIFFRACTION87.83
1.16-1.180.29671200.27142537X-RAY DIFFRACTION94.52
1.18-1.20.25611270.26232498X-RAY DIFFRACTION93.35
1.2-1.210.2641480.26312418X-RAY DIFFRACTION92.2
1.21-1.230.2431460.23472582X-RAY DIFFRACTION96.46
1.23-1.250.21421540.22392571X-RAY DIFFRACTION96.49
1.25-1.270.23861330.19842639X-RAY DIFFRACTION97.09
1.27-1.290.23991340.19562544X-RAY DIFFRACTION96.85
1.29-1.320.23271290.18622620X-RAY DIFFRACTION96.93
1.32-1.340.19791620.16412609X-RAY DIFFRACTION97.19
1.34-1.370.1911520.15332606X-RAY DIFFRACTION97.98
1.37-1.40.16931410.14022601X-RAY DIFFRACTION98.1
1.4-1.430.16711450.13432622X-RAY DIFFRACTION98.05
1.43-1.470.15411510.12972620X-RAY DIFFRACTION97.78
1.47-1.510.15241230.12152526X-RAY DIFFRACTION93.41
1.51-1.550.14351450.10652603X-RAY DIFFRACTION97.83
1.55-1.60.11351430.0812626X-RAY DIFFRACTION98.54
1.6-1.660.14091510.08172658X-RAY DIFFRACTION98.73
1.66-1.720.11421390.07912661X-RAY DIFFRACTION98.9
1.72-1.80.10731550.07912651X-RAY DIFFRACTION99.01
1.8-1.90.10981490.0842617X-RAY DIFFRACTION98.82
1.9-2.020.10961340.08412682X-RAY DIFFRACTION98.74
2.02-2.170.10751220.08862559X-RAY DIFFRACTION94.27
2.17-2.390.11241550.09372661X-RAY DIFFRACTION99.51
2.39-2.740.14011400.10982706X-RAY DIFFRACTION99.55
2.74-3.450.16271410.12892672X-RAY DIFFRACTION98.77
3.45-35.20.1121480.12182683X-RAY DIFFRACTION96.99

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