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- PDB-3bu2: Crystal structure of a tRNA-binding protein from Staphylococcus s... -

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Basic information

Entry
Database: PDB / ID: 3bu2
TitleCrystal structure of a tRNA-binding protein from Staphylococcus saprophyticus subsp. saprophyticus. Northeast Structural Genomics Consortium target SyR77
ComponentsPutative tRNA-binding protein
KeywordsRNA BINDING PROTEIN / RNA-binding / tRNA-binding / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Nucleic acid-binding protein fold / YtpR-like / Domain of unknown function DUF4479 / YtpR-like superfamily / Domain of unknown function (DUF4479) / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Nucleic acid-binding proteins ...Nucleic acid-binding protein fold / YtpR-like / Domain of unknown function DUF4479 / YtpR-like superfamily / Domain of unknown function (DUF4479) / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Putative tRNA-binding protein
Similarity search - Component
Biological speciesStaphylococcus saprophyticus subsp. saprophyticus ATCC 15305 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsSeetharaman, J. / Su, M. / Forouhar, F. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xia, R. / Liu, J. / Baran, M.C. ...Seetharaman, J. / Su, M. / Forouhar, F. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xia, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of a tRNA-binding protein from Staphylococcus saprophyticus subsp. saprophyticus.
Authors: Seetharaman, J. / Su, M. / Forouhar, F. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xia, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionDec 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Remark 999SEQUENCE AUTHORS STATE THAT IT IS A TRNA BINDING PROTEIN ACCORDING TO SWISSPROT ANNOTATION BASED ON ...SEQUENCE AUTHORS STATE THAT IT IS A TRNA BINDING PROTEIN ACCORDING TO SWISSPROT ANNOTATION BASED ON SEQUENCE HOMOLOGY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative tRNA-binding protein
B: Putative tRNA-binding protein
C: Putative tRNA-binding protein
D: Putative tRNA-binding protein


Theoretical massNumber of molelcules
Total (without water)86,7064
Polymers86,7064
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.902, 79.795, 139.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative tRNA-binding protein


Mass: 21676.619 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 (bacteria)
Species: Staphylococcus saprophyticus / Strain: DSM 20229 / Gene: SSP1021 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q49YH3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MgCl2, HEPES, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→45 Å / Num. all: 44771 / Num. obs: 44771 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 50.7 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.092 / Net I/σ(I): 12.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.2 / Num. unique all: 4465 / Rsym value: 0.203 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→40.1 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 93765 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2100 5.1 %RANDOM
Rwork0.25 ---
obs0.25 41405 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10.2486 Å2 / ksol: 0.318693 e/Å3
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å20 Å20 Å2
2---1.24 Å20 Å2
3----1.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.7→40.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5908 0 0 191 6099
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d0.85
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 296 5 %
Rwork0.321 5630 -
obs--79.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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