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- PDB-7l9w: Wild-type Pseudomonas fluorescens isocyanide hydratase (WT-3) at ... -

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Basic information

Entry
Database: PDB / ID: 7l9w
TitleWild-type Pseudomonas fluorescens isocyanide hydratase (WT-3) at 274K, Refmac5-refined
ComponentsIsonitrile hydratase InhA
KeywordsLYASE / DJ-1/PfpI superfamily
Function / homologyDJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase-like / Isonitrile hydratase InhA
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.199 Å
AuthorsSu, Z. / Dasgupta, M. / Poitevin, F. / Mathews, I.I. / van den Bedem, H. / Wall, M.E. / Yoon, C.H. / Wilson, M.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM139978 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM123159 United States
CitationJournal: Struct Dyn. / Year: 2021
Title: Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters.
Authors: Su, Z. / Dasgupta, M. / Poitevin, F. / Mathews, I.I. / van den Bedem, H. / Wall, M.E. / Yoon, C.H. / Wilson, M.A.
History
DepositionJan 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)48,3612
Polymers48,3612
Non-polymers00
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-31 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.310, 58.215, 69.030
Angle α, β, γ (deg.)90.000, 112.811, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Isonitrile hydratase InhA


Mass: 24180.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (bacteria)
Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: inhA, PFL_4109 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4K977
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 23% PEG 3350, 100MM TRIS-HCL PH 8.6, 200 MM MAGNESIUM CHLORIDE AND 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: 1.199→39.152 Å / Num. obs: 126107 / % possible obs: 96.5 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rrim(I) all: 0.069 / Net I/σ(I): 7.1
Reflection shellResolution: 1.199→1.22 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5967 / CC1/2: 0.309 / Rrim(I) all: 1.737 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
autoXDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NI6

6ni6


Resolution: 1.199→39.152 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.466 / SU ML: 0.027 / Cross valid method: FREE R-VALUE / ESU R: 0.035 / ESU R Free: 0.035
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.151 3768 2.988 %random
Rwork0.1244 122317 --
all0.125 ---
obs-126085 96.351 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.448 Å2
Baniso -1Baniso -2Baniso -3
1-0.134 Å2-0 Å20.215 Å2
2---0.469 Å20 Å2
3---0.114 Å2
Refinement stepCycle: LAST / Resolution: 1.199→39.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 0 355 3723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134116
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173957
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.6395706
X-RAY DIFFRACTIONr_angle_other_deg1.4891.5729101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0255575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.69521.033213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88715625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2811537
X-RAY DIFFRACTIONr_chiral_restr0.0860.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025080
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02987
X-RAY DIFFRACTIONr_nbd_refined0.2240.2802
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.23259
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21909
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21623
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2211
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1770.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1650.29
X-RAY DIFFRACTIONr_nbd_other0.1850.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.218
X-RAY DIFFRACTIONr_mcbond_it1.4081.4992156
X-RAY DIFFRACTIONr_mcbond_other1.3991.4972155
X-RAY DIFFRACTIONr_mcangle_it1.7432.2582779
X-RAY DIFFRACTIONr_mcangle_other1.7452.262780
X-RAY DIFFRACTIONr_scbond_it2.1041.9171960
X-RAY DIFFRACTIONr_scbond_other2.1041.9191961
X-RAY DIFFRACTIONr_scangle_it2.6362.7382927
X-RAY DIFFRACTIONr_scangle_other2.6362.742928
X-RAY DIFFRACTIONr_lrange_it3.14219.1354451
X-RAY DIFFRACTIONr_lrange_other2.86318.74396
X-RAY DIFFRACTIONr_rigid_bond_restr1.61238073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.199-1.2310.2882680.2678791X-RAY DIFFRACTION93.973
1.231-1.2640.2522570.2448380X-RAY DIFFRACTION92.2165
1.264-1.3010.2452720.2318585X-RAY DIFFRACTION96.7027
1.301-1.3410.2212640.2078312X-RAY DIFFRACTION96.6637
1.341-1.3850.1982550.1798075X-RAY DIFFRACTION96.3897
1.385-1.4340.1912280.167836X-RAY DIFFRACTION96.9231
1.434-1.4880.1832420.1397537X-RAY DIFFRACTION97.1889
1.488-1.5480.1562550.1237148X-RAY DIFFRACTION95.7078
1.548-1.6170.1312010.1056722X-RAY DIFFRACTION93.5793
1.617-1.6960.1221740.0946803X-RAY DIFFRACTION98.1156
1.696-1.7880.1011710.0886478X-RAY DIFFRACTION98.3289
1.788-1.8960.1191970.0856093X-RAY DIFFRACTION98.4197
1.896-2.0270.1121850.0895742X-RAY DIFFRACTION98.3898
2.027-2.1890.1281720.0965252X-RAY DIFFRACTION97.0999
2.189-2.3980.1131610.0954724X-RAY DIFFRACTION94.4509
2.398-2.680.1351390.1094513X-RAY DIFFRACTION99.2744
2.68-3.0940.1771230.1273981X-RAY DIFFRACTION99.0109
3.094-3.7870.144810.1213366X-RAY DIFFRACTION98.0097
3.787-5.3460.134680.1132501X-RAY DIFFRACTION93.8276
5.346-39.1520.179550.1521478X-RAY DIFFRACTION98.8395

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