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- PDB-5tbf: Crystal structure of SeMet derivatives of domain2 and domain 3 of RctB -

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Basic information

Entry
Database: PDB / ID: 5tbf
TitleCrystal structure of SeMet derivatives of domain2 and domain 3 of RctB
ComponentsTranslation elongation factor
KeywordsTRANSLATION / RctB
Function / homologyReplication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / translation elongation factor activity / Translation elongation factor / Uncharacterized protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.003 Å
AuthorsLi, M. / Wlodawer, A. / Chattoraj, D. / Jha, J.
CitationJournal: To Be Published
Title: Crystal Structure of core domains of RctB
Authors: Li, M. / Wlodawer, A. / Jha, J. / Chattoraj, D. / Gustchina, A.
History
DepositionSep 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Translation elongation factor
B: Translation elongation factor


Theoretical massNumber of molelcules
Total (without water)76,9392
Polymers76,9392
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-8 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.526, 105.526, 137.755
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 Translation elongation factor


Mass: 38469.270 Da / Num. of mol.: 2 / Fragment: residues 145-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ERS013166_00020 / Plasmid: pJJ399 / Cell (production host): Bl21De3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H5VUX2, UniProt: Q9KNG2*PLUS
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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5 / Details: 1.5M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3→55 Å / Num. obs: 18054 / % possible obs: 99.1 % / Redundancy: 6.7 % / Net I/σ(I): 19.68

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Processing

Software
NameVersionClassification
PHENIX(dev-2376_1692)refinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 3.003→43.37 Å / SU ML: 0.41 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 28.06 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2783 772 4.51 %
Rwork0.2197 --
obs0.2223 17127 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.003→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4558 0 0 0 4558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044658
X-RAY DIFFRACTIONf_angle_d0.8596288
X-RAY DIFFRACTIONf_dihedral_angle_d12.7622820
X-RAY DIFFRACTIONf_chiral_restr0.046694
X-RAY DIFFRACTIONf_plane_restr0.006798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.003-3.19110.36961000.27122217X-RAY DIFFRACTION78
3.1911-3.43740.31331220.24412604X-RAY DIFFRACTION91
3.4374-3.78310.28761550.23352774X-RAY DIFFRACTION97
3.7831-4.33010.27421520.2072833X-RAY DIFFRACTION99
4.3301-5.45380.23891230.18772912X-RAY DIFFRACTION100
5.4538-43.37490.2681200.22553015X-RAY DIFFRACTION99

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