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- PDB-7ldm: G150T Pseudomonas fluorescens isocyanide hydratase (G150T-1) at 2... -

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Basic information

Entry
Database: PDB / ID: 7ldm
TitleG150T Pseudomonas fluorescens isocyanide hydratase (G150T-1) at 274K, Phenix-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: 1.15 Å
AuthorsSu, Z. / Dasgupta, M. / 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 13, 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:
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Assembly

Deposited unit
A: Isonitrile hydratase InhA


Theoretical massNumber of molelcules
Total (without water)24,2251
Polymers24,2251
Non-polymers00
Water3,513195
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 area5010 Å2
ΔGint-31 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.295, 59.717, 69.504
Angle α, β, γ (deg.)90.000, 110.876, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-365-

HOH

21A-483-

HOH

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Components

#1: Protein Isonitrile hydratase InhA


Mass: 24224.699 Da / Num. of mol.: 1 / Mutation: G150T
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.: 195 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
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: 1.15→39.5 Å / Num. obs: 74206 / % possible obs: 97.4 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rrim(I) all: 0.052 / Net I/σ(I): 12
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3528 / CC1/2: 0.366 / Rrim(I) all: 1.72 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
autoXDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NI4

6ni4


Resolution: 1.15→35.2 Å / SU ML: 0.1359 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.0569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1387 2237 3.02 %random
Rwork0.1221 71947 --
obs0.1226 74184 97.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.27 Å2
Refinement stepCycle: LAST / Resolution: 1.15→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 0 195 1868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051966
X-RAY DIFFRACTIONf_angle_d0.80472717
X-RAY DIFFRACTIONf_chiral_restr0.0737313
X-RAY DIFFRACTIONf_plane_restr0.0055373
X-RAY DIFFRACTIONf_dihedral_angle_d24.3985738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.170.31081330.29414358X-RAY DIFFRACTION94.17
1.17-1.20.2981350.26884332X-RAY DIFFRACTION94.24
1.2-1.230.25031280.25254399X-RAY DIFFRACTION95.83
1.23-1.270.25171330.21434483X-RAY DIFFRACTION96.77
1.27-1.30.2331520.19554479X-RAY DIFFRACTION97.25
1.3-1.340.20151520.17244456X-RAY DIFFRACTION97.01
1.34-1.390.19741380.15084498X-RAY DIFFRACTION97.97
1.39-1.450.15371270.13964551X-RAY DIFFRACTION98.07
1.45-1.510.14321630.13194359X-RAY DIFFRACTION94.9
1.51-1.590.12181460.08924530X-RAY DIFFRACTION98.42
1.59-1.690.11541590.08414558X-RAY DIFFRACTION98.72
1.69-1.820.11251310.08184605X-RAY DIFFRACTION98.93
1.82-2.010.10191280.08694601X-RAY DIFFRACTION98.79
2.01-2.30.11151430.0914463X-RAY DIFFRACTION96.38
2.3-2.90.14131330.11554644X-RAY DIFFRACTION99.48
2.9-35.20.12211360.12484631X-RAY DIFFRACTION97.6

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