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- PDB-3bzc: Crystal Structure of the Tex protein from Pseudomonas aeruginosa,... -

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Basic information

Entry
Database: PDB / ID: 3bzc
TitleCrystal Structure of the Tex protein from Pseudomonas aeruginosa, crystal form I
ComponentsTex
KeywordsRNA BINDING PROTEIN / helix-turn-helix / helix-hairpin-helix / S1 domain / YqgF domain / TRANSCRIPTION
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.27 Å
AuthorsJohnson, S.J. / Close, D. / Hill, C.P.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa.
Authors: Johnson, S.J. / Close, D. / Robinson, H. / Vallet-Gely, I. / Dove, S.L. / Hill, C.P.
History
DepositionJan 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tex


Theoretical massNumber of molelcules
Total (without water)85,9111
Polymers85,9111
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.165, 131.849, 144.017
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tex


Mass: 85910.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+RP / References: UniProt: Q9HTY8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 19% PEG 3350, 0.1M Bis-Tris, 0.17 M ammonium sulfate, 10% glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 286.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 41117 / % possible obs: 79.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.088 / Χ2: 1.079 / Net I/σ(I): 11
Reflection shellResolution: 2.27→2.35 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1812 / Χ2: 0.948 / % possible all: 35.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SOLVEphasing
RefinementResolution: 2.27→49.281 Å / FOM work R set: 0.752 / σ(F): 0 / Stereochemistry target values: ml
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1935 4.99 %RANDOM
Rwork0.24 ---
all0.288 41052 --
obs0.288 38792 75.69 %-
Solvent computationBsol: 51.707 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso max: 143.17 Å2 / Biso mean: 66.69 Å2 / Biso min: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.639 Å20 Å2-0 Å2
2--49.311 Å20 Å2
3----12.657 Å2
Refinement stepCycle: LAST / Resolution: 2.27→49.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5619 0 0 73 5692
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.5611
X-RAY DIFFRACTIONf_bond_d0.0041
X-RAY DIFFRACTIONf_chiral_restr0.041
X-RAY DIFFRACTIONf_dihedral_angle_d10.0981
X-RAY DIFFRACTIONf_plane_restr0.0021
X-RAY DIFFRACTIONf_nbd_refined4.0521

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