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- PDB-6nia: Pseudomonas fluorescens isocyanide hydratase at 100 K helical dis... -

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Basic information

Entry
Database: PDB / ID: 6nia
TitlePseudomonas fluorescens isocyanide hydratase at 100 K helical disorder model
ComponentsIsonitrile hydratase InhA
KeywordsLYASE / DJ-1 superfamily / ThiJ/PfpI
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: 1.05 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7969
Polymers48,3612
Non-polymers4347
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-12 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.576, 56.466, 68.233
Angle α, β, γ (deg.)90.00, 112.49, 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.: 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, EC: 4.2.1.103
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 24-26% PEG 3350, 200-250 MM MAGNESIUM CHLORIDE, 100 MM TRIS-HCL PH=8.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2009 / Details: BENT CONICAL SI-MIRROR (RH COATED)
RadiationMonochromator: BENT GE(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.05→38 Å / Num. obs: 179412 / % possible obs: 97.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.8
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 17341 / % possible all: 94.2

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Processing

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

3non


Resolution: 1.05→37.822 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 11.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1342 8979 5.01 %Random
Rwork0.117 ---
obs0.1178 179399 97.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→37.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 28 484 3898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094693
X-RAY DIFFRACTIONf_angle_d1.1116487
X-RAY DIFFRACTIONf_dihedral_angle_d19.4711744
X-RAY DIFFRACTIONf_chiral_restr0.085735
X-RAY DIFFRACTIONf_plane_restr0.008895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.06190.24872710.21055486X-RAY DIFFRACTION94
1.0619-1.07440.2293060.1985435X-RAY DIFFRACTION94
1.0744-1.08750.19182700.18355557X-RAY DIFFRACTION94
1.0875-1.10130.18772770.17535490X-RAY DIFFRACTION95
1.1013-1.11570.1763150.16155503X-RAY DIFFRACTION95
1.1157-1.1310.16372890.14895560X-RAY DIFFRACTION95
1.131-1.14720.15982750.13795584X-RAY DIFFRACTION96
1.1472-1.16430.15832910.13595576X-RAY DIFFRACTION96
1.1643-1.18250.14072830.1225610X-RAY DIFFRACTION96
1.1825-1.20190.13713050.125566X-RAY DIFFRACTION96
1.2019-1.22260.13292910.11865600X-RAY DIFFRACTION96
1.2226-1.24490.13113110.10815597X-RAY DIFFRACTION97
1.2449-1.26880.13642910.1045683X-RAY DIFFRACTION97
1.2688-1.29470.13482660.10165667X-RAY DIFFRACTION97
1.2947-1.32290.11973300.10065638X-RAY DIFFRACTION97
1.3229-1.35360.13562720.10085702X-RAY DIFFRACTION97
1.3536-1.38750.13833150.09455680X-RAY DIFFRACTION97
1.3875-1.4250.12362980.09435742X-RAY DIFFRACTION98
1.425-1.46690.10763000.08685678X-RAY DIFFRACTION98
1.4669-1.51430.10953330.08775704X-RAY DIFFRACTION98
1.5143-1.56840.11253050.08885750X-RAY DIFFRACTION98
1.5684-1.63120.11283010.0885780X-RAY DIFFRACTION99
1.6312-1.70540.11053170.08695783X-RAY DIFFRACTION99
1.7054-1.79540.11083140.09485785X-RAY DIFFRACTION99
1.7954-1.90780.11423160.09695786X-RAY DIFFRACTION99
1.9078-2.05510.11372710.09985873X-RAY DIFFRACTION99
2.0551-2.26190.12123370.10145848X-RAY DIFFRACTION100
2.2619-2.58920.12693180.115861X-RAY DIFFRACTION100
2.5892-3.26180.14273180.12955896X-RAY DIFFRACTION100
3.2618-37.84640.15012930.14436000X-RAY DIFFRACTION99

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