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- PDB-6ni7: Pseudomonas fluorescens isocyanide hydratase at 277 K -

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Basic information

Entry
Database: PDB / ID: 6ni7
TitlePseudomonas fluorescens isocyanide hydratase at 277 K
ComponentsIsonitrile hydratase InhA
KeywordsLYASE / ThiJ/PfpI / DJ-1 superfamily
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
: / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isonitrile hydratase InhA
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsWilson, M.A. / Dasgupta, M. / van den Bedem, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM123159 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.
Authors: Dasgupta, M. / Budday, D. / de Oliveira, S.H.P. / Madzelan, P. / Marchany-Rivera, D. / Seravalli, J. / Hayes, B. / Sierra, R.G. / Boutet, S. / Hunter, M.S. / Alonso-Mori, R. / Batyuk, A. / ...Authors: Dasgupta, M. / Budday, D. / de Oliveira, S.H.P. / Madzelan, P. / Marchany-Rivera, D. / Seravalli, J. / Hayes, B. / Sierra, R.G. / Boutet, S. / Hunter, M.S. / Alonso-Mori, R. / Batyuk, A. / Wierman, J. / Lyubimov, A. / Brewster, A.S. / Sauter, N.K. / Applegate, G.A. / Tiwari, V.K. / Berkowitz, D.B. / Thompson, M.C. / Cohen, A.E. / Fraser, J.S. / Wall, M.E. / van den Bedem, H. / Wilson, M.A.
History
DepositionDec 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)48,3932
Polymers48,3932
Non-polymers00
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-31 kcal/mol
Surface area16960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.154, 57.965, 69.092
Angle α, β, γ (deg.)90.00, 112.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Isonitrile hydratase InhA


Mass: 24196.646 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


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.59 %
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 dithiotheritol
Temp details: room temperature

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97534 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 2015 / Details: Rh coated flat bent mirror
RadiationMonochromator: Si(111) side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97534 Å / Relative weight: 1
ReflectionResolution: 1.15→42.87 Å / Num. obs: 145885 / % possible obs: 98.9 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.029 / Rrim(I) all: 0.059 / Net I/σ(I): 12.5
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 6657 / CC1/2: 0.488 / Rpim(I) all: 0.569 / Rrim(I) all: 0.959 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NON

3non


Resolution: 1.15→38.532 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.87
RfactorNum. reflection% reflectionSelection details
Rfree0.1353 7300 5.01 %Random
Rwork0.1128 ---
obs0.1139 145829 98.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.15→38.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 0 323 3689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084595
X-RAY DIFFRACTIONf_angle_d1.026370
X-RAY DIFFRACTIONf_dihedral_angle_d20.5451707
X-RAY DIFFRACTIONf_chiral_restr0.081722
X-RAY DIFFRACTIONf_plane_restr0.007882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.16310.26072050.26334218X-RAY DIFFRACTION90
1.1631-1.17680.26112300.24414429X-RAY DIFFRACTION95
1.1768-1.19110.26732250.22914541X-RAY DIFFRACTION97
1.1911-1.20620.23542390.21654551X-RAY DIFFRACTION98
1.2062-1.22210.24412350.20414593X-RAY DIFFRACTION99
1.2221-1.23880.21542540.19154659X-RAY DIFFRACTION99
1.2388-1.25650.18582540.17724597X-RAY DIFFRACTION99
1.2565-1.27530.19552570.17314563X-RAY DIFFRACTION99
1.2753-1.29520.2022140.16264650X-RAY DIFFRACTION99
1.2952-1.31640.16242270.14834661X-RAY DIFFRACTION99
1.3164-1.33910.17762780.13964565X-RAY DIFFRACTION99
1.3391-1.36350.15092290.1264678X-RAY DIFFRACTION99
1.3635-1.38970.15822380.11724639X-RAY DIFFRACTION99
1.3897-1.41810.15022430.11044579X-RAY DIFFRACTION99
1.4181-1.44890.13022630.10394674X-RAY DIFFRACTION99
1.4489-1.48260.11792260.09174620X-RAY DIFFRACTION99
1.4826-1.51970.12232730.0844586X-RAY DIFFRACTION100
1.5197-1.56080.12132500.08194631X-RAY DIFFRACTION99
1.5608-1.60670.12172480.07774672X-RAY DIFFRACTION99
1.6067-1.65860.1152410.07944616X-RAY DIFFRACTION99
1.6586-1.71790.11252550.07984613X-RAY DIFFRACTION99
1.7179-1.78660.10722470.084662X-RAY DIFFRACTION100
1.7866-1.8680.09382440.07614703X-RAY DIFFRACTION100
1.868-1.96640.10552500.07924670X-RAY DIFFRACTION100
1.9664-2.08960.10322310.0864699X-RAY DIFFRACTION100
2.0896-2.2510.12152670.08954638X-RAY DIFFRACTION100
2.251-2.47740.1142370.09664717X-RAY DIFFRACTION100
2.4774-2.83580.132540.11054706X-RAY DIFFRACTION100
2.8358-3.57250.14972550.12784670X-RAY DIFFRACTION99
3.5725-38.55360.13582310.12234729X-RAY DIFFRACTION98

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