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- PDB-3nov: Crystal Structure of D17E Isocyanide Hydratase from Pseudomonas f... -

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Basic information

Entry
Database: PDB / ID: 3nov
TitleCrystal Structure of D17E Isocyanide Hydratase from Pseudomonas fluorescens
ComponentsThiJ/PfpI family protein
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
ACETATE ION / 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 7, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ThiJ/PfpI family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2542
Polymers24,1951
Non-polymers591
Water5,945330
1
A: ThiJ/PfpI family protein
hetero molecules

A: ThiJ/PfpI family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5074
Polymers48,3892
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y,-z-1/21
Buried area5410 Å2
ΔGint-33 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.699, 102.569, 121.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-1041-

HOH

21A-1049-

HOH

31A-1283-

HOH

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Components

#1: Protein ThiJ/PfpI family protein


Mass: 24194.672 Da / Num. of mol.: 1 / Mutation: D17E
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 12% PEG 4000, 240 mM ammonium acetate, 100 mM sodium acetate pH=4.6, 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 Å
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. all: 111571 / Num. obs: 111571 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 32.9
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.9 / Num. unique all: 10915 / % possible all: 98

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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: PDB ENTRY 3NON

3non


Resolution: 1.05→37 Å / Num. parameters: 19999 / Num. restraintsaints: 26940 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.1743 5575 5 %RANDOM
Rwork0.1425 ---
all0.1428 111571 --
obs0.1428 111571 99.2 %-
Solvent computationSolvent model: BABINET
Refine analyzeNum. disordered residues: 21 / Occupancy sum hydrogen: 1685.1 / Occupancy sum non hydrogen: 2030.09
Refinement stepCycle: LAST / Resolution: 1.05→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1699 0 4 330 2033
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0298
X-RAY DIFFRACTIONs_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.022
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.112

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