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- PDB-8tt5: Pseudomonas fluorescens isocyanide hydratase pH=8.3 -

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Basic information

Entry
Database: PDB / ID: 8tt5
TitlePseudomonas fluorescens isocyanide hydratase pH=8.3
ComponentsIsonitrile hydratase InhA
KeywordsLYASE / isocyanide / isonitrile
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: 1.02 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: 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.
#1: 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.
#2: 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
Revision 1.1May 7, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details / 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
B: Isonitrile hydratase InhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7969
Polymers48,3612
Non-polymers4347
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-10 kcal/mol
Surface area16940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.867, 56.831, 68.242
Angle α, β, γ (deg.)90.000, 112.540, 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 Isonitrile hydratase InhA / isocyanide hydratase


Mass: 24180.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: inhA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4K977
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 23% PEG 3350, 200 mM MgCl2, 2 mM DTT 100mM Tris-HCl pH=8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.886 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2019
Details: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 1.02→38.57 Å / Num. obs: 201545 / % possible obs: 99.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 9 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.071 / Net I/σ(I): 12.5
Reflection shellResolution: 1.02→1.04 Å / Redundancy: 5 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 10211 / CC1/2: 0.35 / Rrim(I) all: 1.944 / % possible all: 98.5

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Processing

Software
NameVersionClassification
phenix.refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
autoXDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.02→38.01 Å / SU ML: 0.1083 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.6875
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1377 9758 4.88 %
Rwork0.1216 190365 -
obs0.1224 200123 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.37 Å2
Refinement stepCycle: LAST / Resolution: 1.02→38.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 28 538 3938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774344
X-RAY DIFFRACTIONf_angle_d1.02016013
X-RAY DIFFRACTIONf_chiral_restr0.0818677
X-RAY DIFFRACTIONf_plane_restr0.0114836
X-RAY DIFFRACTIONf_dihedral_angle_d12.93961630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.030.30352900.29395317X-RAY DIFFRACTION82.05
1.03-1.050.26983220.2776045X-RAY DIFFRACTION95.67
1.05-1.060.26793450.26176303X-RAY DIFFRACTION98.78
1.06-1.070.22982870.25196396X-RAY DIFFRACTION99.15
1.07-1.090.33573240.31816315X-RAY DIFFRACTION98.59
1.09-1.10.29333480.26786256X-RAY DIFFRACTION98.36
1.1-1.120.233450.21846430X-RAY DIFFRACTION99.87
1.12-1.130.1953440.17566360X-RAY DIFFRACTION99.91
1.13-1.150.17123080.15066389X-RAY DIFFRACTION99.93
1.15-1.170.15283350.13046378X-RAY DIFFRACTION99.72
1.17-1.190.13583060.12166419X-RAY DIFFRACTION99.66
1.19-1.210.13463320.11556373X-RAY DIFFRACTION99.33
1.21-1.230.13943260.11176357X-RAY DIFFRACTION98.73
1.23-1.260.14913030.11576216X-RAY DIFFRACTION97.25
1.26-1.290.13733190.11516434X-RAY DIFFRACTION99.88
1.29-1.320.14473250.11836408X-RAY DIFFRACTION99.9
1.32-1.350.14313230.1166397X-RAY DIFFRACTION99.9
1.35-1.390.10433270.09126489X-RAY DIFFRACTION100
1.39-1.430.11963310.08746386X-RAY DIFFRACTION99.91
1.43-1.470.10663380.08226351X-RAY DIFFRACTION99.88
1.47-1.530.09723390.08436308X-RAY DIFFRACTION98.33
1.53-1.590.10883390.08426366X-RAY DIFFRACTION98.46
1.59-1.660.10743010.08836397X-RAY DIFFRACTION99.82
1.66-1.750.10663530.08846437X-RAY DIFFRACTION99.9
1.75-1.860.11892910.09436463X-RAY DIFFRACTION99.99
1.86-20.11873350.09716462X-RAY DIFFRACTION99.91
2-2.20.12873270.10066376X-RAY DIFFRACTION98.72
2.2-2.520.11713210.10856488X-RAY DIFFRACTION99.97
2.52-3.170.13763600.12666440X-RAY DIFFRACTION99.72
3.17-38.010.1443140.14056609X-RAY DIFFRACTION99.67

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