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- PDB-7l9z: Pseudomonas fluorescens G150A isocyanide hydratase (G150A-1) at 2... -

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Basic information

Entry
Database: PDB / ID: 7l9z
TitlePseudomonas fluorescens G150A isocyanide hydratase (G150A-1) 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: 1.3 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)48,3892
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 area4910 Å2
ΔGint-34 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.249, 58.133, 69.087
Angle α, β, γ (deg.)90.000, 112.782, 90.000
Int Tables number4
Space group name H-MP1211

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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


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: 2.19 Å3/Da / Density % sol: 43.85 %
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: 1.3→39.11 Å / Num. obs: 100703 / % possible obs: 98 % / Redundancy: 2.9 % / CC1/2: 0.998 / Rrim(I) all: 0.057 / Net I/σ(I): 10.4
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 2.8 % / Num. unique obs: 4869 / CC1/2: 0.405 / Rrim(I) all: 1.259 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoXDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NI5

6ni5


Resolution: 1.3→39.109 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.982 / SU B: 1.867 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.046 / ESU R Free: 0.042
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1463 3076 3.058 %random
Rwork0.1191 97521 --
all0.12 ---
obs-100597 97.88 %-
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: 19.397 Å2
Baniso -1Baniso -2Baniso -3
1-0.025 Å20 Å20.231 Å2
2---0.265 Å20 Å2
3---0.034 Å2
Refinement stepCycle: LAST / Resolution: 1.3→39.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 0 334 3708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134517
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174319
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.6426270
X-RAY DIFFRACTIONr_angle_other_deg1.4261.5739944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3035632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.5720.705241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80115693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8181544
X-RAY DIFFRACTIONr_chiral_restr0.0770.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025556
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021092
X-RAY DIFFRACTIONr_nbd_refined0.2220.2893
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.23433
X-RAY DIFFRACTIONr_nbtor_refined0.1580.21970
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21776
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0370.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1220.213
X-RAY DIFFRACTIONr_nbd_other0.1810.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.210
X-RAY DIFFRACTIONr_mcbond_it1.421.7082351
X-RAY DIFFRACTIONr_mcbond_other1.4161.7062350
X-RAY DIFFRACTIONr_mcangle_it1.8412.5673042
X-RAY DIFFRACTIONr_mcangle_other1.8422.5693043
X-RAY DIFFRACTIONr_scbond_it2.0652.1262166
X-RAY DIFFRACTIONr_scbond_other2.0652.1282167
X-RAY DIFFRACTIONr_scangle_it2.5793.0513228
X-RAY DIFFRACTIONr_scangle_other2.5793.0533229
X-RAY DIFFRACTIONr_lrange_it3.12221.2684789
X-RAY DIFFRACTIONr_lrange_other2.9520.8674733
X-RAY DIFFRACTIONr_rigid_bond_restr1.438836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.3340.312060.2987138X-RAY DIFFRACTION96.7716
1.334-1.370.3052060.2617000X-RAY DIFFRACTION98.161
1.37-1.410.2552230.2266889X-RAY DIFFRACTION98.6134
1.41-1.4530.2342160.26628X-RAY DIFFRACTION98.7163
1.453-1.5010.1852010.1596476X-RAY DIFFRACTION98.3793
1.501-1.5540.1661890.1326041X-RAY DIFFRACTION95.6402
1.554-1.6120.1491880.1135955X-RAY DIFFRACTION97.477
1.612-1.6780.1391750.0965833X-RAY DIFFRACTION98.946
1.678-1.7530.1311850.0865594X-RAY DIFFRACTION99.1252
1.753-1.8380.1321860.095331X-RAY DIFFRACTION99.1553
1.838-1.9370.1421520.0875115X-RAY DIFFRACTION98.6699
1.937-2.0550.1151740.0834747X-RAY DIFFRACTION98.1452
2.055-2.1970.1311520.0954390X-RAY DIFFRACTION96.2492
2.197-2.3720.1151330.0924107X-RAY DIFFRACTION96.4294
2.372-2.5980.1171340.0993881X-RAY DIFFRACTION98.8186
2.598-2.9040.151020.1183523X-RAY DIFFRACTION98.5322
2.904-3.3530.138850.1273101X-RAY DIFFRACTION98.0308
3.353-4.1030.129610.1092622X-RAY DIFFRACTION96.5803
4.103-5.7910.137710.1171971X-RAY DIFFRACTION94.9326
5.791-39.1090.157360.1411167X-RAY DIFFRACTION98.6066

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