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- PDB-3non: Crystal Structure of Isocyanide Hydratase from Pseudomonas fluorescens -

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Basic information

Entry
Database: PDB / ID: 3non
TitleCrystal Structure of Isocyanide Hydratase from Pseudomonas fluorescens
ComponentsIsocyanide hydratase
KeywordsLYASE / DJ-1 superfamily / isocyanide hydratase / isonitrile hydratase
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: 1.05 Å
AuthorsLakshminarasimhan, M. / Madzelan, P. / Nan, R. / Milkovic, N.M. / Wilson, M.A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Evolution of New Enzymatic Function by Structural Modulation of Cysteine Reactivity in Pseudomonas fluorescens Isocyanide Hydratase.
Authors: Lakshminarasimhan, M. / Madzelan, P. / Nan, R. / Milkovic, N.M. / Wilson, M.A.
History
DepositionJun 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isocyanide hydratase
B: Isocyanide hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7047
Polymers48,3932
Non-polymers3105
Water8,935496
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-15 kcal/mol
Surface area16660 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 Isocyanide hydratase


Mass: 24196.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: PFL_4109 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4K977, EC: 4.2.1.103
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 298 K / pH: 8.6
Details: 24-26% PEG 3350, 200-250 mM magnesium chloride, 100 mM Tris-HCl pH=8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC QUANTUM 315 / 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→37 Å / Num. obs: 179412 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / 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 / % possible all: 94.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P5F

1p5f


Resolution: 1.05→37 Å / Num. parameters: 40350 / Num. restraintsaints: 58380 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.169 8979 5 %RANDOM
all0.139 179412 --
obs0.139 179412 97.1 %-
Solvent computationSolvent model: BABINET
Refine analyzeNum. disordered residues: 67 / Occupancy sum hydrogen: 3116 / Occupancy sum non hydrogen: 3884.5
Refinement stepCycle: LAST / Resolution: 1.05→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3370 0 20 496 3886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.064
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.024
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.002
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.031
X-RAY DIFFRACTIONs_approx_iso_adps0.069

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