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- PDB-6ni4: Pseudomonas fluorescens isocyanide hydratase at 277 K G150T mutant -

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Basic information

Entry
Database: PDB / ID: 6ni4
TitlePseudomonas fluorescens isocyanide hydratase at 277 K G150T mutant
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: 1.1 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isonitrile hydratase InhA


Theoretical massNumber of molelcules
Total (without water)24,2251
Polymers24,2251
Non-polymers00
Water2,684149
1
A: Isonitrile hydratase InhA

A: Isonitrile hydratase InhA


Theoretical massNumber of molelcules
Total (without water)48,4492
Polymers48,4492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4980 Å2
ΔGint-32 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.110, 59.744, 56.125
Angle α, β, γ (deg.)90.00, 115.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

21A-443-

HOH

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Components

#1: Protein Isonitrile hydratase InhA


Mass: 24224.699 Da / Num. of mol.: 1 / Mutation: G150T
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.: 149 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
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: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9753 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 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: 0.9753 Å / Relative weight: 1
ReflectionResolution: 1.1→35.5 Å / Num. obs: 84284 / % possible obs: 97.2 % / Redundancy: 2.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.022 / Rrim(I) all: 0.042 / Net I/σ(I): 9.7
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8284 / CC1/2: 0.715 / Rpim(I) all: 0.365 / Rrim(I) all: 0.59 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NON

3non


Resolution: 1.1→35.144 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 11.03
RfactorNum. reflection% reflectionSelection details
Rfree0.1283 4186 4.97 %RANDOM
Rwork0.1098 ---
obs0.1108 84275 97.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.1→35.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 0 149 1822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111922
X-RAY DIFFRACTIONf_angle_d1.3762653
X-RAY DIFFRACTIONf_dihedral_angle_d12.156716
X-RAY DIFFRACTIONf_chiral_restr0.087308
X-RAY DIFFRACTIONf_plane_restr0.008362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1001-1.11260.22941150.23322542X-RAY DIFFRACTION93
1.1126-1.12570.23431400.2082645X-RAY DIFFRACTION96
1.1257-1.13950.19051330.18152681X-RAY DIFFRACTION97
1.1395-1.15390.17291450.1692622X-RAY DIFFRACTION97
1.1539-1.16910.16851460.15092718X-RAY DIFFRACTION98
1.1691-1.18510.15441380.14112603X-RAY DIFFRACTION97
1.1851-1.2020.16181360.13382716X-RAY DIFFRACTION98
1.202-1.220.1651130.12382718X-RAY DIFFRACTION97
1.22-1.2390.14541390.11822641X-RAY DIFFRACTION98
1.239-1.25930.15061440.1112657X-RAY DIFFRACTION97
1.2593-1.28110.12411390.10252643X-RAY DIFFRACTION97
1.2811-1.30440.13921430.09982684X-RAY DIFFRACTION97
1.3044-1.32940.09991250.09172674X-RAY DIFFRACTION97
1.3294-1.35660.11321470.0872643X-RAY DIFFRACTION97
1.3566-1.38610.1121390.08452650X-RAY DIFFRACTION97
1.3861-1.41830.11231500.08092693X-RAY DIFFRACTION97
1.4183-1.45380.10711180.07532648X-RAY DIFFRACTION97
1.4538-1.49310.09571230.07322644X-RAY DIFFRACTION97
1.4931-1.5370.10631550.07282663X-RAY DIFFRACTION97
1.537-1.58670.0961240.07672650X-RAY DIFFRACTION97
1.5867-1.64340.10521520.07652648X-RAY DIFFRACTION96
1.6434-1.70920.09691580.08342656X-RAY DIFFRACTION97
1.7092-1.78690.10611550.08572664X-RAY DIFFRACTION98
1.7869-1.88110.10921630.08642727X-RAY DIFFRACTION99
1.8811-1.9990.11811210.09012771X-RAY DIFFRACTION99
1.999-2.15330.1091540.09262711X-RAY DIFFRACTION99
2.1533-2.370.11911460.09962725X-RAY DIFFRACTION99
2.37-2.71280.12461330.11772750X-RAY DIFFRACTION99
2.7128-3.41740.13441400.14062691X-RAY DIFFRACTION97
3.4174-35.16140.15251520.12342611X-RAY DIFFRACTION93

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