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- PDB-2oce: Crystal structure of Tex family protein PA5201 from Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 2oce
TitleCrystal structure of Tex family protein PA5201 from Pseudomonas aeruginosa
ComponentsHypothetical protein PA5201Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved hypothetical protein PA5201 / putative transcriptional accessory protein / PSI / Protein Structure Initiative / New York Structural Genomics Research Consortium / NYSGRC / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


nucleobase-containing compound metabolic process / structural constituent of ribosome / translation / mRNA binding / cytosol
Similarity search - Function
Tex RuvX-like domain-like / Tex-like protein, N-terminal / Tex protein, YqgF-like domain / Tex, S1 domain / Tex-like protein N-terminal domain / Tex protein YqgF-like domain / RuvA domain 2-like / Tex N-terminal region-like / Tex N-terminal region-like / Helix-hairpin-helix motif ...Tex RuvX-like domain-like / Tex-like protein, N-terminal / Tex protein, YqgF-like domain / Tex, S1 domain / Tex-like protein N-terminal domain / Tex protein YqgF-like domain / RuvA domain 2-like / Tex N-terminal region-like / Tex N-terminal region-like / Helix-hairpin-helix motif / YqgF/RNase H-like domain / HHH domain 9 / HHH domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / YqgF/RNase H-like domain superfamily / RuvA domain 2-like / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding proteins / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H-like superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S1 motif domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsJin, X. / Min, T. / Burley, S.K. / Shapiro, L. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein PA5201 from Pseudomonas aeruginosa
Authors: Jin, X. / Min, T. / Burley, S.K. / Shapiro, L.
History
DepositionDec 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein PA5201


Theoretical massNumber of molelcules
Total (without water)85,1511
Polymers85,1511
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.974, 113.027, 144.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer in the asymmetric unit

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Components

#1: Protein Hypothetical protein PA5201 / Hypothesis


Mass: 85151.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PA01 / Gene: PA5201 / Plasmid: pNYSGXRC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HTY8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.87 Å3/Da / Density % sol: 57.12 %
Crystal growTemperature: 277 K / pH: 6.5
Details: 13% PEG 8000, 0.1M Sodium cacodylate pH 6.5, 0.12M Magnesium acetate, 5% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 18, 2003
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 18579 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 12.9 % / Rmerge(I) obs: 0.173 / Rsym value: 0.183 / Net I/σ(I): 20
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 12.3 / Rsym value: 0.773 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.1→50 Å / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.279 743 -
Rwork0.208 --
obs0.208 18408 99.7 %
all-18623 -
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5610 0 0 266 5876
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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