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- PDB-2eve: X-Ray Crystal Structure of Protein PSPTO5229 from Pseudomonas syr... -

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Basic information

Entry
Database: PDB / ID: 2eve
TitleX-Ray Crystal Structure of Protein PSPTO5229 from Pseudomonas syringae. Northeast Structural Genomics Consortium Target PsR62
Componentshypothetical protein PSPTO5229
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


: / : / EVE domain / EVE domain / ph1033 like fold / ph1033 like domains / PUA-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / EVE domain-containing protein
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato str. DC3000 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsForouhar, F. / Zhou, W. / Belachew, A. / Jayaraman, S. / Ciao, M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2009
Title: Structural genomics reveals EVE as a new ASCH/PUA-related domain.
Authors: Bertonati, C. / Punta, M. / Fischer, M. / Yachdav, G. / Forouhar, F. / Zhou, W. / Kuzin, A.P. / Seetharaman, J. / Abashidze, M. / Ramelot, T.A. / Kennedy, M.A. / Cort, J.R. / Belachew, A. / ...Authors: Bertonati, C. / Punta, M. / Fischer, M. / Yachdav, G. / Forouhar, F. / Zhou, W. / Kuzin, A.P. / Seetharaman, J. / Abashidze, M. / Ramelot, T.A. / Kennedy, M.A. / Cort, J.R. / Belachew, A. / Hunt, J.F. / Tong, L. / Montelione, G.T. / Rost, B.
History
DepositionOct 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PSPTO5229
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4954
Polymers18,1021
Non-polymers3933
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.233, 42.273, 50.655
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein hypothetical protein PSPTO5229


Mass: 18101.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato str. DC3000 (bacteria)
Species: Pseudomonas syringae group genomosp. 3 / Strain: DC3000. / Gene: 1186914 / Plasmid: pET21+Magic / Production host: Escherichia coli (E. coli) / Strain (production host): XL-Gold / References: UniProt: Q87UR7
#2: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.28 Å3/Da / Density % sol: 46.12 % / Description: The reported reflections include friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.5mM protein, 100mM MOPS, 30% PEG8000, 100mM NaH2PO4, 5mM DTT, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2005 / Details: mirrors.
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.55→30.71 Å / Num. all: 46260 / Num. obs: 46260 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.071 / Net I/σ(I): 23.75
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 8.48 / Num. unique all: 2400 / Rsym value: 0.367 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
XTALVIEWrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.6→30.71 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 586541.75 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Friedel pairs have been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.217 3858 9.6 %RANDOM
Rwork0.191 ---
all0.192 46260 --
obs0.191 40016 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.8401 Å2 / ksol: 0.367001 e/Å3
Displacement parametersBiso mean: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å20 Å2
2---0.2 Å20 Å2
3---1.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.6→30.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 25 218 1430
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.212 615 10 %
Rwork0.189 5560 -
obs-5560 87.4 %

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