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- PDB-3tre: Structure of a translation elongation factor P (efp) from Coxiell... -

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Basic information

Entry
Database: PDB / ID: 3tre
TitleStructure of a translation elongation factor P (efp) from Coxiella burnetii
ComponentsElongation factor P
KeywordsTRANSLATION / Protein synthesis
Function / homology
Function and homology information


peptide biosynthetic process / translation elongation factor activity / cytoplasm
Similarity search - Function
Translation elongation factor P/YeiP, conserved site / Elongation factor P signature. / Translation elongation factor P / Translation elongation factor P/YeiP, central / Translation elongation factor, KOW-like / Elongation factor P, C-terminal / Translation elongation factor P/YeiP / Elongation factor P (EF-P) OB domain / Elongation factor P, C-terminal / Elongation factor P, C-terminal ...Translation elongation factor P/YeiP, conserved site / Elongation factor P signature. / Translation elongation factor P / Translation elongation factor P/YeiP, central / Translation elongation factor, KOW-like / Elongation factor P, C-terminal / Translation elongation factor P/YeiP / Elongation factor P (EF-P) OB domain / Elongation factor P, C-terminal / Elongation factor P, C-terminal / Elongation factor P (EF-P) OB domain / Elongation factor P (EF-P) KOW-like domain / SH3 type barrels. - #30 / Nucleic acid-binding proteins / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Roll / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.899 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
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
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor P


Theoretical massNumber of molelcules
Total (without water)21,6271
Polymers21,6271
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.619, 82.619, 79.096
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Elongation factor P / EF-P


Mass: 21626.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_1816, efp / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83AR4
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: 3.6 Å3/Da / Density % sol: 65.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05M potassium thiocyanate 16% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.899→50 Å / Num. all: 13462 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.067 / Χ2: 0.947 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-2.952.40.5317020.376199.9
2.95-32.40.3536730.418199.9
3-3.062.40.2776730.405199.3
3.06-3.122.40.2186430.4071100
3.12-3.192.40.1736860.4721100
3.19-3.272.40.1346910.491199.4
3.27-3.352.40.1266270.568199.8
3.35-3.442.40.1196640.773196.7
3.44-3.542.40.1056530.916198.6
3.54-3.652.40.0846701.01199.6
3.65-3.782.40.0726431.124195.3
3.78-3.942.30.0746451.336194
3.94-4.112.40.0426491.107199.4
4.11-4.332.40.0366731.13199.1
4.33-4.62.40.0346611.316199.5
4.6-4.962.40.0336951.27199.3
4.96-5.464.40.0966591.221100
5.46-6.244.70.0986501.032199.7
6.24-7.864.60.0756821.0121100
7.86-504.10.0536621.437197.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YBY

1yby


Resolution: 2.899→41.31 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7507 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2714 327 4.76 %RANDOM
Rwork0.2354 ---
all0.2371 7236 --
obs0.2371 6869 99.44 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.3 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso max: 263.95 Å2 / Biso mean: 102.8239 Å2 / Biso min: 38.71 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å2-0 Å20 Å2
2---2.34 Å20 Å2
3---4.68 Å2
Refinement stepCycle: LAST / Resolution: 2.899→41.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 0 0 1029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071054
X-RAY DIFFRACTIONf_angle_d1.1981425
X-RAY DIFFRACTIONf_chiral_restr0.078150
X-RAY DIFFRACTIONf_plane_restr0.004187
X-RAY DIFFRACTIONf_dihedral_angle_d16.681387
LS refinement shellResolution: 2.8987→3.6517 Å / Total num. of bins used: 2
RfactorNum. reflection% reflection
Rfree0.2895 179 -
Rwork0.2548 3243 -
all-3422 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3256-0.58240.25792.14220.06180.92790.38660.13360.705-0.20060.1776-0.04110.31590.10760.00220.75920.02870.03410.47180.14010.520446.3032-10.02117.1447
21.15821.1486-1.34841.3134-1.29931.50150.23780.091-0.0298-0.11920.1158-0.0790.00510.55810.00250.61650.04440.060.3690.09620.470845.5219-16.32988.3324
30.9641-0.77430.77320.7053-0.34651.51150.6879-1.0438-0.64090.07640.23181.31420.9156-1.00350.11460.88030.0280.34610.44320.17350.898338.06763.1177-9.9284
40.65170.4638-0.31521.17860.00461.1694-0.38110.2638-0.09910.04220.03740.28810.93050.0858-0.45041.0767-0.1873-0.12130.29080.46520.295438.62183.3327-18.828
50.56330.3304-0.16380.21440.28714.14070.3439-0.2418-0.3129-0.34980.010.96590.24370.1160.34760.98510.02060.11180.36160.29321.439535.768-5.7767-16.171
61.2587-0.2969-0.30321.61140.80170.4606-0.11541.3343-1.9571.2048-0.46992.196-0.0590.6598-0.02730.9087-0.01890.18510.95360.10930.991835.51891.1182-12.1925
71.6237-0.2198-0.01170.79490.47370.2891.3297-2.73620.92880.3307-0.2177-0.62990.2375-0.55510.03090.8558-0.03680.28181.32090.21181.101835.0116-2.6653-9.3906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:30)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 31:66)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 67:74)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 75:91)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 92:106)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 107:118)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 119:131)A0

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