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- PDB-8vq1: Pseudomonas fluorescens G150T isocyanide hydratase at 298 K XFEL ... -

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Basic information

Entry
Database: PDB / ID: 8vq1
TitlePseudomonas fluorescens G150T isocyanide hydratase at 298 K XFEL data, thioimidate intermediate
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 / N-(4-nitrophenyl)methanimine / Isonitrile hydratase InhA
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 1.3 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
CitationJournal: Sci Adv / Year: 2024
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 3rd, 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 3rd, F.R. / Mittan-Moreau, D.W. / 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.
History
DepositionJan 17, 2024Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 21, 2024ID: 8TSN
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)24,4103
Polymers24,2251
Non-polymers1862
Water2,774154
1
A: Isonitrile hydratase InhA
hetero molecules

A: Isonitrile hydratase InhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8216
Polymers48,4492
Non-polymers3714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5520 Å2
ΔGint-61 kcal/mol
Surface area16790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.136, 59.758, 56.110
Angle α, β, γ (deg.)90.000, 115.883, 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-544-

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-QCV / N-(4-nitrophenyl)methanimine


Mass: 150.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 45.23 % / Description: plate-like crystals
Crystal growTemperature: 298 K / Method: batch mode / pH: 8.8
Details: 15.5% PEG 3350, 125 MM MGCL2, AND 62 MM TRIS-HCL PH 8.8

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.033 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Apr 10, 2021 / Frequency: 30
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.3→21.98 Å / Num. obs: 52683 / % possible obs: 99.97 % / Redundancy: 40.51 % / Biso Wilson estimate: 15.15 Å2 / CC1/2: 0.97 / R split: 0.163 / Net I/σ(I): 4.7
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 16.85 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2580 / CC1/2: 0.527 / R split: 0.636 / % possible all: 100
Serial crystallography measurementFocal spot size: 9 µm2 / Pulse duration: 40 fsec. / Pulse photon energy: 12 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: coMESH / Method: injection
Serial crystallography sample delivery injectionFlow rate: 6 µL/min / Injector diameter: 100 µm / Power by: HPLC
Serial crystallography data reductionCrystal hits: 17590 / Lattices indexed: 20372

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
cctbx.xfeldata reduction
cctbx.xfel.mergedata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.3→21.98 Å / SU ML: 0.1502 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7696
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1713 2000 3.8 %
Rwork0.137 50672 -
obs0.1383 52672 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.25 Å2
Refinement stepCycle: LAST / Resolution: 1.3→21.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 12 154 1839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522036
X-RAY DIFFRACTIONf_angle_d0.78672817
X-RAY DIFFRACTIONf_chiral_restr0.0756322
X-RAY DIFFRACTIONf_plane_restr0.0071387
X-RAY DIFFRACTIONf_dihedral_angle_d11.7587755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.30891410.26123573X-RAY DIFFRACTION99.97
1.33-1.370.26081420.21263602X-RAY DIFFRACTION100
1.37-1.410.24511420.1863602X-RAY DIFFRACTION100
1.41-1.450.19821430.15253636X-RAY DIFFRACTION100
1.45-1.510.18261430.14493604X-RAY DIFFRACTION100
1.51-1.570.18361420.14643604X-RAY DIFFRACTION100
1.57-1.640.19421420.12563583X-RAY DIFFRACTION100
1.64-1.720.17451430.12823639X-RAY DIFFRACTION100
1.72-1.830.18471420.12843602X-RAY DIFFRACTION99.97
1.83-1.970.16721430.12883610X-RAY DIFFRACTION99.87
1.97-2.170.1571430.11253636X-RAY DIFFRACTION100
2.17-2.490.13411450.11653653X-RAY DIFFRACTION100
2.49-3.130.17351430.13643639X-RAY DIFFRACTION99.97
3.13-21.980.16111460.14453689X-RAY DIFFRACTION99.9

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