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- PDB-6ni8: Pseudomonas fluorescens isocyanide hydratase rotating anode 298K -

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Basic information

Entry
Database: PDB / ID: 6ni8
TitlePseudomonas fluorescens isocyanide hydratase rotating anode 298K
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 / MOLECULAR REPLACEMENT / Resolution: 1.45 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: Biorxiv / Year: 2019
Title: Cysteine modification can gate non-equilibrium conformational dynamics during enzyme catalysis
Authors: Dasgupta, M. / Budday, D. / Madzelan, P. / Seravalli, J. / Hayes, B. / Sierra, R.G. / Applegate, G. / Tiwari, V. / Berkowitz, D.B. / Thompson, M. / Fraser, J.S. / Wall, M.E. / van den Bedem, H. / Wilson, M.A.
History
DepositionDec 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _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
B: Isonitrile hydratase InhA


Theoretical massNumber of molelcules
Total (without water)48,3612
Polymers48,3612
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-31 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.195, 58.130, 69.120
Angle α, β, γ (deg.)90.00, 112.81, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.19 Å3/Da / Density % sol: 43.84 %
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

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 3, 2018 / Details: varimax confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.45→34.57 Å / Num. obs: 73846 / % possible obs: 99.8 % / Redundancy: 3.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.038 / Rrim(I) all: 0.07 / Net I/σ(I): 9.3
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3491 / CC1/2: 0.617 / Rpim(I) all: 0.455 / Rrim(I) all: 0.811 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NON

3non


Resolution: 1.45→34.59 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.98 / SU B: 2.381 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14999 3621 4.9 %RANDOM
Rwork0.11017 ---
obs0.11211 70202 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.949 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0.12 Å2
2---1.62 Å20 Å2
3---0.89 Å2
Refinement stepCycle: 1 / Resolution: 1.45→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 0 266 3634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134015
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173762
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.6395555
X-RAY DIFFRACTIONr_angle_other_deg1.5141.5668727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.19421.225204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52915603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3411534
X-RAY DIFFRACTIONr_chiral_restr0.0910.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024810
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02852
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7642.1122106
X-RAY DIFFRACTIONr_mcbond_other2.7172.1092105
X-RAY DIFFRACTIONr_mcangle_it3.133.1772699
X-RAY DIFFRACTIONr_mcangle_other3.1393.1792700
X-RAY DIFFRACTIONr_scbond_it4.7412.7491909
X-RAY DIFFRACTIONr_scbond_other4.742.7511910
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4853.9082857
X-RAY DIFFRACTIONr_long_range_B_refined5.06426.5074352
X-RAY DIFFRACTIONr_long_range_B_other4.94726.2634323
X-RAY DIFFRACTIONr_rigid_bond_restr9.51537771
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.451→1.489 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.501 251 -
Rwork0.481 5042 -
obs--96.99 %

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