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- PDB-7lb9: Pseudomonas fluorescens G150T isocyanide hydratase (G150T-3) at 2... -

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Basic information

Entry
Database: PDB / ID: 7lb9
TitlePseudomonas fluorescens G150T isocyanide hydratase (G150T-3) at 274K, Refmac5-refined
ComponentsIsonitrile hydratase InhA
KeywordsLYASE / DJ-1/PfpI superfamily
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: 1.101 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 7, 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

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Assembly

Deposited unit
A: Isonitrile hydratase InhA


Theoretical massNumber of molelcules
Total (without water)24,2251
Polymers24,2251
Non-polymers00
Water3,585199
1
A: Isonitrile hydratase InhA

A: Isonitrile hydratase InhA


Theoretical massNumber of molelcules
Total (without water)48,4492
Polymers48,4492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5050 Å2
ΔGint-31 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.295, 59.716, 69.505
Angle α, β, γ (deg.)90.000, 110.876, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-373-

HOH

21A-486-

HOH

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Components

#1: Protein Isonitrile hydratase InhA


Mass: 24224.699 Da / Num. of mol.: 1
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


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
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: 1.101→35.222 Å / Num. obs: 82868 / % possible obs: 95.7 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rrim(I) all: 0.057 / Net I/σ(I): 11.8
Reflection shellResolution: 1.101→1.12 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3983 / CC1/2: 0.334 / Rrim(I) all: 1.839 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoXDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ni4

6ni4


Resolution: 1.101→35.222 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.983 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.026
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1406 2457 2.965 %random
Rwork0.1267 80407 --
all0.127 ---
obs-82864 95.293 %-
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: 16.172 Å2
Baniso -1Baniso -2Baniso -3
1-0.061 Å2-0 Å2-0.113 Å2
2--0.131 Å2-0 Å2
3----0.082 Å2
Refinement stepCycle: LAST / Resolution: 1.101→35.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 0 199 1872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131940
X-RAY DIFFRACTIONr_bond_other_d0.0350.0171892
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.642680
X-RAY DIFFRACTIONr_angle_other_deg2.2541.5724345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8195270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.08420.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20415304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0041520
X-RAY DIFFRACTIONr_chiral_restr0.0820.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022345
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02467
X-RAY DIFFRACTIONr_nbd_refined0.2280.2388
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.21564
X-RAY DIFFRACTIONr_nbtor_refined0.1620.2932
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0670.2880
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1590.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.213
X-RAY DIFFRACTIONr_nbd_other0.1890.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.219
X-RAY DIFFRACTIONr_mcbond_it1.1831.3231020
X-RAY DIFFRACTIONr_mcbond_other1.1831.3191019
X-RAY DIFFRACTIONr_mcangle_it1.5641.9971310
X-RAY DIFFRACTIONr_mcangle_other1.5641.9991311
X-RAY DIFFRACTIONr_scbond_it1.7651.758920
X-RAY DIFFRACTIONr_scbond_other1.7671.759921
X-RAY DIFFRACTIONr_scangle_it2.2852.51370
X-RAY DIFFRACTIONr_scangle_other2.2852.5021371
X-RAY DIFFRACTIONr_lrange_it2.86317.5452108
X-RAY DIFFRACTIONr_lrange_other2.59517.0682081
X-RAY DIFFRACTIONr_rigid_bond_restr11.40733832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.101-1.1290.2831510.2815756X-RAY DIFFRACTION91.8948
1.129-1.160.251580.2455718X-RAY DIFFRACTION94.4087
1.16-1.1940.2191910.2155570X-RAY DIFFRACTION94.6132
1.194-1.230.1861470.25200X-RAY DIFFRACTION91.0128
1.23-1.2710.1631640.1755354X-RAY DIFFRACTION95.8818
1.271-1.3150.1841780.1575100X-RAY DIFFRACTION95.8939
1.315-1.3650.1581490.1384991X-RAY DIFFRACTION96.003
1.365-1.4210.1561450.124829X-RAY DIFFRACTION96.3207
1.421-1.4840.1191560.1054528X-RAY DIFFRACTION95.2613
1.484-1.5560.1271330.0934228X-RAY DIFFRACTION92.5313
1.556-1.640.1221400.0894228X-RAY DIFFRACTION97.7838
1.64-1.740.1191440.0914023X-RAY DIFFRACTION97.6336
1.74-1.860.1161090.0923822X-RAY DIFFRACTION97.9566
1.86-2.0080.104950.0953526X-RAY DIFFRACTION97.2342
2.008-2.20.114890.1013054X-RAY DIFFRACTION92.1971
2.2-2.4590.14830.112999X-RAY DIFFRACTION98.7821
2.459-2.8380.131770.1222637X-RAY DIFFRACTION98.5834
2.838-3.4730.137720.1352200X-RAY DIFFRACTION97.6784
3.473-4.90.135480.121643X-RAY DIFFRACTION92.9121
4.9-35.2220.151280.1581001X-RAY DIFFRACTION99.6128

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