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- PDB-6ni9: Pseudomonas fluorescens isocyanide hydratase at 274 K qFit multic... -

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Basic information

Entry
Database: PDB / ID: 6ni9
TitlePseudomonas fluorescens isocyanide hydratase at 274 K qFit multiconformer model
Components(Isonitrile hydratase InhA) x 2
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: 1.201 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 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 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_author.identifier_ORCID / _pdbx_audit_support.funding_organization
Revision 1.3Oct 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)48,3772
Polymers48,3772
Non-polymers00
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-32 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.241, 58.032, 69.086
Angle α, β, γ (deg.)90.00, 112.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Isonitrile hydratase InhA


Mass: 24180.646 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: Protein Isonitrile hydratase InhA


Mass: 24196.646 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 43.61 %
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
Temp details: room temperature

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Data collection

DiffractionMean temperature: 274 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.82654 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2016
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: 0.82654 Å / Relative weight: 1
ReflectionResolution: 1.2→39.04 Å / Num. obs: 126373 / % possible obs: 97.4 % / Redundancy: 2.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.041 / Rrim(I) all: 0.072 / Net I/σ(I): 10.4
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.8 % / Rmerge(I) obs: 1.349 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5922 / CC1/2: 0.225 / Rpim(I) all: 1.001 / Rrim(I) all: 1.689 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NON

3non


Resolution: 1.201→31.837 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 13.69
RfactorNum. reflection% reflectionSelection details
Rfree0.1402 6203 5.02 %Random
Rwork0.1078 ---
obs0.1094 123572 95.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.201→31.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 0 382 3768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116458
X-RAY DIFFRACTIONf_angle_d1.3999097
X-RAY DIFFRACTIONf_dihedral_angle_d13.7672446
X-RAY DIFFRACTIONf_chiral_restr0.0831103
X-RAY DIFFRACTIONf_plane_restr0.0081244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.201-1.21460.26281640.22073239X-RAY DIFFRACTION79
1.2146-1.22890.25041890.19683262X-RAY DIFFRACTION81
1.2289-1.24390.212110.18883417X-RAY DIFFRACTION84
1.2439-1.25970.22582070.18073687X-RAY DIFFRACTION90
1.2597-1.27620.22441870.17733739X-RAY DIFFRACTION91
1.2762-1.29370.20342230.17073760X-RAY DIFFRACTION92
1.2937-1.31220.19381950.16333849X-RAY DIFFRACTION94
1.3122-1.33180.20561980.17233829X-RAY DIFFRACTION93
1.3318-1.35260.21242140.15723925X-RAY DIFFRACTION97
1.3526-1.37480.1792000.14543987X-RAY DIFFRACTION97
1.3748-1.39850.1812290.14053973X-RAY DIFFRACTION97
1.3985-1.42390.19182210.13494016X-RAY DIFFRACTION98
1.4239-1.45130.18752200.12644036X-RAY DIFFRACTION98
1.4513-1.48090.13772010.11124019X-RAY DIFFRACTION98
1.4809-1.51310.13791910.0994041X-RAY DIFFRACTION98
1.5131-1.54830.14542030.09624053X-RAY DIFFRACTION98
1.5483-1.5870.13252310.08993994X-RAY DIFFRACTION98
1.587-1.62990.12572090.08544033X-RAY DIFFRACTION97
1.6299-1.67790.11861820.0853896X-RAY DIFFRACTION95
1.6779-1.73210.11392150.07694088X-RAY DIFFRACTION99
1.7321-1.7940.11231930.07644108X-RAY DIFFRACTION99
1.794-1.86580.11082220.07354073X-RAY DIFFRACTION99
1.8658-1.95070.11832070.07634064X-RAY DIFFRACTION99
1.9507-2.05350.10522440.084022X-RAY DIFFRACTION98
2.0535-2.18210.1261960.08854073X-RAY DIFFRACTION98
2.1821-2.35060.11931970.08863944X-RAY DIFFRACTION95
2.3506-2.5870.11452170.09723996X-RAY DIFFRACTION97
2.587-2.96110.14022220.11274068X-RAY DIFFRACTION99
2.9611-3.72980.14522050.11554108X-RAY DIFFRACTION98
3.7298-31.84810.13372100.11134070X-RAY DIFFRACTION96

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