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- PDB-8tt4: Pseudomonas fluorescens isocyanide hydratase pH=6.0 -

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Basic information

Entry
Database: PDB / ID: 8tt4
TitlePseudomonas fluorescens isocyanide hydratase pH=6.0
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: 1.2 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

Downloads & links

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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
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-13 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.750, 56.792, 68.414
Angle α, β, γ (deg.)90.000, 112.544, 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 / Plasmid: pET15b / 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.: 537 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 23% PEG 3350, 200 mM MgCl2, 2 mM DTT and 100mM sodium citrate pH=6.0

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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: 1.2→38.52 Å / Num. obs: 123914 / % possible obs: 99.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 12.25 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.096 / Net I/σ(I): 9.8
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 6174 / CC1/2: 0.435 / Rrim(I) all: 1.921 / % possible all: 97.5

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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→38.52 Å / SU ML: 0.1274 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.4578
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1581 6020 4.86 %
Rwork0.1288 117840 -
obs0.1303 123860 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.74 Å2
Refinement stepCycle: LAST / Resolution: 1.2→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 28 537 3937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054686
X-RAY DIFFRACTIONf_angle_d0.88976475
X-RAY DIFFRACTIONf_chiral_restr0.0722734
X-RAY DIFFRACTIONf_plane_restr0.0087893
X-RAY DIFFRACTIONf_dihedral_angle_d5.882708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.28912140.29113786X-RAY DIFFRACTION96.88
1.22-1.230.25571890.25853866X-RAY DIFFRACTION97.81
1.23-1.240.27712040.2393872X-RAY DIFFRACTION98.55
1.24-1.260.2461900.22483893X-RAY DIFFRACTION98.22
1.26-1.280.26031980.22123895X-RAY DIFFRACTION99.18
1.28-1.290.24381780.20683907X-RAY DIFFRACTION98.22
1.29-1.310.24551990.20383876X-RAY DIFFRACTION98.62
1.31-1.330.24021880.19543872X-RAY DIFFRACTION98.74
1.33-1.350.21162090.18993924X-RAY DIFFRACTION98.76
1.35-1.380.23062060.18343908X-RAY DIFFRACTION99.56
1.38-1.40.21422020.17793890X-RAY DIFFRACTION98.94
1.4-1.420.20871890.15923959X-RAY DIFFRACTION99.19
1.42-1.450.18942020.14263921X-RAY DIFFRACTION99.4
1.45-1.480.18462140.12973906X-RAY DIFFRACTION99.4
1.48-1.510.1332250.11993899X-RAY DIFFRACTION99.37
1.51-1.550.16331920.11583889X-RAY DIFFRACTION98.81
1.55-1.590.17572140.11123947X-RAY DIFFRACTION99.38
1.59-1.630.14192010.10923963X-RAY DIFFRACTION99.66
1.63-1.680.15061720.1073937X-RAY DIFFRACTION99.78
1.68-1.730.14672140.10663931X-RAY DIFFRACTION99.81
1.73-1.790.1372030.10343950X-RAY DIFFRACTION99.81
1.79-1.870.14051880.0993974X-RAY DIFFRACTION99.86
1.87-1.950.13352080.0973957X-RAY DIFFRACTION99.43
1.95-2.050.14972030.09843936X-RAY DIFFRACTION99.73
2.05-2.180.13071990.10223981X-RAY DIFFRACTION99.9
2.18-2.350.12041980.10083985X-RAY DIFFRACTION100
2.35-2.590.12772020.10643985X-RAY DIFFRACTION99.98
2.59-2.960.14392270.1193931X-RAY DIFFRACTION99.31
2.96-3.730.14951950.12544020X-RAY DIFFRACTION99.98
3.73-38.520.1571970.14544080X-RAY DIFFRACTION99.56

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