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- PDB-3nor: Crystal Structure of T102S Isocyanide Hydratase from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 3nor
TitleCrystal Structure of T102S 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
CITRIC ACID / Isonitrile hydratase InhA
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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)24,3592
Polymers24,1671
Non-polymers1921
Water4,324240
1
A: ThiJ/PfpI family protein
hetero molecules

A: ThiJ/PfpI family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7174
Polymers48,3332
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y,-z-1/21
Buried area5860 Å2
ΔGint-27 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.602, 102.722, 121.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein ThiJ/PfpI family protein


Mass: 24166.621 Da / Num. of mol.: 1 / Mutation: T102S
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 50.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 19-22% PEG 4000, 140-160 mM sodium citrate pH=5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 12, 2009 / Details: Osmic Blue confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→78 Å / Num. all: 18463 / Num. obs: 18463 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1853 / % possible all: 97.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NOO

3noo


Resolution: 1.9→78 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.618 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.128 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20196 996 5.1 %RANDOM
Rwork0.15521 ---
all0.15759 18463 --
obs0.15759 18463 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.146 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--1.1 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.9→78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 13 240 1954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221790
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.9732453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5915239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31323.57170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93215264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7731513
X-RAY DIFFRACTIONr_chiral_restr0.0960.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211384
X-RAY DIFFRACTIONr_mcbond_it2.3071.51178
X-RAY DIFFRACTIONr_mcangle_it3.22721887
X-RAY DIFFRACTIONr_scbond_it5.6813612
X-RAY DIFFRACTIONr_scangle_it8.4924.5566
LS refinement shellResolution: 1.896→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 59 -
Rwork0.31 1270 -
obs--93.99 %
Refinement TLS params.Method: refined / Origin x: 1.875 Å / Origin y: -6.514 Å / Origin z: -18.719 Å
111213212223313233
T0.0324 Å20.012 Å20.007 Å2-0.0229 Å20.0051 Å2--0.0512 Å2
L1.4165 °20.0635 °20.015 °2-0.5505 °2-0.1965 °2--2.5315 °2
S0.0017 Å °-0.1504 Å °-0.0683 Å °0.0249 Å °-0.0318 Å °0.0417 Å °0.0907 Å °0.0404 Å °0.0301 Å °

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