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- PDB-3ewn: Crystal structure of a THiJ/PfpI family protein from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 3ewn
TitleCrystal structure of a THiJ/PfpI family protein from Pseudomonas syringae
ComponentsThiJ/PfpI family protein
Keywordsstructural genomics / unknown function / Monomer / THiJ/PfpI family protein / Pseudomonas syringae / PSI-II / NYSGRC / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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
ThiJ/PfpI family protein
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsSugadev, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a THiJ/PfpI family protein from Pseudomonas syringae
Authors: Sugadev, R. / Burley, S.K. / Swaminathan, S.
History
DepositionOct 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 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: ThiJ/PfpI family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5742
Polymers27,4821
Non-polymers921
Water5,368298
1
A: ThiJ/PfpI family protein
hetero molecules

A: ThiJ/PfpI family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1494
Polymers54,9642
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6290 Å2
ΔGint-61 kcal/mol
Surface area18180 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.749, 63.749, 103.193
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ThiJ/PfpI family protein


Mass: 27482.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: Tomato strain DC3001 / Gene: PSPTO2847, PSPTO_2847 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q881P0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES 7.5, 1.4M Sodium Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 8, 2008 / Details: Mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 29919 / Num. obs: 29919 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 15.8
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2 / Num. unique all: 2940 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
SHARPphasing
ARPmodel building
WARPmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→31.88 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 106499.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1159 4 %RANDOM
Rwork0.179 ---
all0.204 29919 --
obs0.179 29133 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.5748 Å2 / ksol: 0.414029 e/Å3
Displacement parametersBiso mean: 14.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.73 Å20 Å2
2--0.68 Å20 Å2
3----1.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.65→31.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 6 298 2075
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.422
X-RAY DIFFRACTIONc_scbond_it2.62
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.213 188 4.1 %
Rwork0.213 4420 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5gol_xplor.par

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