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- PDB-6ni5: Pseudomonas fluorescens isocyanide hydratase at 274 K G150A mutant -

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Basic information

Entry
Database: PDB / ID: 6ni5
TitlePseudomonas fluorescens isocyanide hydratase at 274 K G150A mutant
ComponentsIsonitrile hydratase InhA
KeywordsLYASE / DJ-1 superfamily
Function / homologyDJ-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 / Isonitrile hydratase InhA
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-32 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.038, 57.895, 69.110
Angle α, β, γ (deg.)90.00, 112.55, 90.00
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 / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
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 DTT

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Data collection

DiffractionMean temperature: 274 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.82653 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: 0.82653 Å / Relative weight: 1
ReflectionResolution: 1.3→38.96 Å / Num. obs: 100249 / % possible obs: 98.1 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.036 / Rrim(I) all: 0.066 / Net I/σ(I): 9.1
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3 % / Rmerge(I) obs: 1.513 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4568 / CC1/2: 0.318 / Rpim(I) all: 0.846 / Rrim(I) all: 1.513 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NON

3non


Resolution: 1.3→33.595 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1519 4970 4.97 %RANDOM
Rwork0.1192 ---
obs0.1208 99966 97.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→33.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3388 0 0 323 3711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145056
X-RAY DIFFRACTIONf_angle_d1.297011
X-RAY DIFFRACTIONf_dihedral_angle_d22.4671882
X-RAY DIFFRACTIONf_chiral_restr0.097794
X-RAY DIFFRACTIONf_plane_restr0.009975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.31591510.27452877X-RAY DIFFRACTION89
1.3148-1.33030.27441500.26582978X-RAY DIFFRACTION91
1.3303-1.34650.28671590.24363029X-RAY DIFFRACTION95
1.3465-1.36350.25221760.22463176X-RAY DIFFRACTION99
1.3635-1.38150.26111870.20563190X-RAY DIFFRACTION100
1.3815-1.40040.20311780.19223174X-RAY DIFFRACTION99
1.4004-1.42040.23471700.17923179X-RAY DIFFRACTION99
1.4204-1.44160.23511740.16823204X-RAY DIFFRACTION99
1.4416-1.46410.18211670.15233172X-RAY DIFFRACTION99
1.4641-1.48810.17121510.13213206X-RAY DIFFRACTION99
1.4881-1.51380.17261550.12123187X-RAY DIFFRACTION99
1.5138-1.54130.16661550.11883208X-RAY DIFFRACTION98
1.5413-1.5710.15821910.11543128X-RAY DIFFRACTION98
1.571-1.6030.14111580.11073150X-RAY DIFFRACTION98
1.603-1.63790.15851600.11213119X-RAY DIFFRACTION96
1.6379-1.6760.15491440.11263015X-RAY DIFFRACTION94
1.676-1.71790.15041650.09913239X-RAY DIFFRACTION99
1.7179-1.76430.15521530.09033217X-RAY DIFFRACTION100
1.7643-1.81630.12131710.08553221X-RAY DIFFRACTION99
1.8163-1.87490.11571720.08283221X-RAY DIFFRACTION100
1.8749-1.94190.12681680.08763167X-RAY DIFFRACTION99
1.9419-2.01960.13351880.08773201X-RAY DIFFRACTION99
2.0196-2.11150.11891770.09523225X-RAY DIFFRACTION99
2.1115-2.22280.13451510.09563249X-RAY DIFFRACTION99
2.2228-2.36210.13331550.09863063X-RAY DIFFRACTION95
2.3621-2.54440.14321690.10653215X-RAY DIFFRACTION99
2.5444-2.80030.14671860.11763218X-RAY DIFFRACTION100
2.8003-3.20520.16781550.13173246X-RAY DIFFRACTION99
3.2052-4.03720.13741700.11863236X-RAY DIFFRACTION99
4.0372-33.60590.14411640.12573286X-RAY DIFFRACTION98

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