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- PDB-7ld7: G150A Pseudomonas fluorescens isocyanide hydratase (G150A-2) at 2... -

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Basic information

Entry
Database: PDB / ID: 7ld7
TitleG150A Pseudomonas fluorescens isocyanide hydratase (G150A-2) at 274K, Phenix-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: 1.25 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 12, 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
B: Isonitrile hydratase InhA


Theoretical massNumber of molelcules
Total (without water)48,3892
Polymers48,3892
Non-polymers00
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-33 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.155, 57.870, 68.988
Angle α, β, γ (deg.)90.000, 112.744, 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


Mass: 24194.674 Da / Num. of mol.: 2 / Mutation: G150A
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.: 334 / 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: 2.17 Å3/Da / Density % sol: 43.43 %
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: 1.25→39 Å / Num. obs: 109380 / % possible obs: 95.6 % / Redundancy: 3 % / CC1/2: 0.998 / Rrim(I) all: 0.071 / Net I/σ(I): 7
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5115 / CC1/2: 0.317 / Rrim(I) all: 1.851 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
autoXDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NI5

6ni5


Resolution: 1.25→38.49 Å / SU ML: 0.1174 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.0651
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1433 3308 3.06 %random
Rwork0.1182 104799 --
obs0.119 108107 94.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.43 Å2
Refinement stepCycle: LAST / Resolution: 1.25→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 0 334 3708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434540
X-RAY DIFFRACTIONf_angle_d0.81516303
X-RAY DIFFRACTIONf_chiral_restr0.0703706
X-RAY DIFFRACTIONf_plane_restr0.0055881
X-RAY DIFFRACTIONf_dihedral_angle_d22.55941715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.28471320.2553619X-RAY DIFFRACTION78.54
1.27-1.290.25481300.2374135X-RAY DIFFRACTION90.21
1.29-1.310.27461380.23284233X-RAY DIFFRACTION91.85
1.31-1.330.22281190.22044301X-RAY DIFFRACTION93.17
1.33-1.350.23661280.20624348X-RAY DIFFRACTION94.23
1.35-1.380.24091330.19914396X-RAY DIFFRACTION95.15
1.38-1.40.24911250.18424449X-RAY DIFFRACTION96.07
1.4-1.430.20091540.1744413X-RAY DIFFRACTION95.82
1.43-1.460.19241320.15564423X-RAY DIFFRACTION95.89
1.46-1.50.18171400.13544429X-RAY DIFFRACTION95.71
1.5-1.530.15651330.1274349X-RAY DIFFRACTION94.06
1.53-1.570.14671290.10973987X-RAY DIFFRACTION86.58
1.57-1.620.14691380.10654462X-RAY DIFFRACTION96.82
1.62-1.670.14691330.10194511X-RAY DIFFRACTION97.4
1.67-1.730.14431440.09544519X-RAY DIFFRACTION97.57
1.73-1.80.12381580.08984499X-RAY DIFFRACTION97.77
1.8-1.880.12621460.0874502X-RAY DIFFRACTION97.04
1.88-1.980.13521400.08654511X-RAY DIFFRACTION97.14
1.98-2.110.10991650.08944402X-RAY DIFFRACTION95.82
2.11-2.270.12321160.09074152X-RAY DIFFRACTION88.94
2.27-2.50.10811630.0964553X-RAY DIFFRACTION98.43
2.5-2.860.12441470.11264591X-RAY DIFFRACTION98.36
2.86-3.60.13331220.12244550X-RAY DIFFRACTION96.85
3.61-38.490.13931430.11894465X-RAY DIFFRACTION93.73

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