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- PDB-5j3b: Structure of translation elongation factor P from Acinetobacter b... -

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Basic information

Entry
Database: PDB / ID: 5j3b
TitleStructure of translation elongation factor P from Acinetobacter baumannii
ComponentsElongation factor P
KeywordsTRANSLATION / SSGCID / Acinetobacter baumannii / translation elongation factor P / protein biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


peptide biosynthetic process / translation elongation factor activity / cytoplasm
Similarity search - Function
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 ...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
: / Elongation factor P
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of translation elongation factor P from Acinetobacter baumannii
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Source and taxonomy
Revision 1.2Sep 27, 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 / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor P
B: Elongation factor P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0025
Polymers43,8922
Non-polymers1103
Water57632
1
A: Elongation factor P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9812
Polymers21,9461
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Elongation factor P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0203
Polymers21,9461
Non-polymers752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.760, 52.230, 90.170
Angle α, β, γ (deg.)90.000, 130.620, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3:6 or (resid 7 and (name...
21(chain B and (resid 3:28 or (resid 29 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNTHRTHR(chain A and (resid 3:6 or (resid 7 and (name...AA3 - 611 - 14
12ASNASNASNASN(chain A and (resid 3:6 or (resid 7 and (name...AA715
13ALAALAALAALA(chain A and (resid 3:6 or (resid 7 and (name...AA2 - 18910 - 197
14ALAALAALAALA(chain A and (resid 3:6 or (resid 7 and (name...AA2 - 18910 - 197
15ALAALAALAALA(chain A and (resid 3:6 or (resid 7 and (name...AA2 - 18910 - 197
16ALAALAALAALA(chain A and (resid 3:6 or (resid 7 and (name...AA2 - 18910 - 197
21ASNASNGLUGLU(chain B and (resid 3:28 or (resid 29 and (name...BB3 - 2811 - 36
22TYRTYRTYRTYR(chain B and (resid 3:28 or (resid 29 and (name...BB2937
23ASNASNALAALA(chain B and (resid 3:28 or (resid 29 and (name...BB3 - 18911 - 197
24ASNASNALAALA(chain B and (resid 3:28 or (resid 29 and (name...BB3 - 18911 - 197
25ASNASNALAALA(chain B and (resid 3:28 or (resid 29 and (name...BB3 - 18911 - 197
26ASNASNALAALA(chain B and (resid 3:28 or (resid 29 and (name...BB3 - 18911 - 197

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Components

#1: Protein Elongation factor P / Translation elongation factor P


Mass: 21945.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: efp / Plasmid: AcbaC.17944.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V5VBC5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.67 Å3/Da / Density % sol: 54 % / Mosaicity: 0.2 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG1 screen D4: 20% PEG 3350, 200mM KSCN; AcbaC.17944.a.B1.PW37730 at 18mg/ml; cryo: 15% EG ; tray 265235d4, puck ecq0-81

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 30, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→45.027 Å / Num. obs: 20641 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 56.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 20.33
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.360.5572.88199.5
2.36-2.420.4183.64198.6
2.42-2.490.3214.79198.9
2.49-2.570.2356.17199.7
2.57-2.660.1778.27198.8
2.66-2.750.13210.84199.1
2.75-2.850.11113.1199.6
2.85-2.970.07817.34199.4
2.97-3.10.06521.08198.9
3.1-3.250.0526.62199.4
3.25-3.430.04529.86199.2
3.43-3.640.04132.81199.2
3.64-3.890.03435.94199.1
3.89-4.20.03139.21199
4.2-4.60.02941.2199.4
4.6-5.140.02942.2199.3
5.14-5.940.02941.12198.4
5.94-7.270.0341.79198.8
7.27-10.290.02842.16195.6
10.29-500.03138.45170

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.25 Å45.02 Å
Translation2.25 Å45.02 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIXdev_2356refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3a5z

3a5z


Resolution: 2.3→45.027 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.06
RfactorNum. reflection% reflection
Rfree0.2367 2003 9.71 %
Rwork0.1933 --
obs0.1975 20634 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 150.56 Å2 / Biso mean: 69.2766 Å2 / Biso min: 29.45 Å2
Refinement stepCycle: final / Resolution: 2.3→45.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 3 32 2682
Biso mean--107.13 55.92 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082696
X-RAY DIFFRACTIONf_angle_d0.9693675
X-RAY DIFFRACTIONf_chiral_restr0.056427
X-RAY DIFFRACTIONf_plane_restr0.006486
X-RAY DIFFRACTIONf_dihedral_angle_d14.5591613
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1517X-RAY DIFFRACTION7.391TORSIONAL
12B1517X-RAY DIFFRACTION7.391TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.35760.39711420.299413361478100
2.3576-2.42130.30471710.26491278144999
2.4213-2.49260.3541440.24861314145899
2.4926-2.5730.25631440.235513131457100
2.573-2.6650.31321250.23541343146899
2.665-2.77170.29181240.225713491473100
2.7717-2.89780.30321440.24113321476100
2.8978-3.05050.32551310.243713581489100
3.0505-3.24160.27521440.224913131457100
3.2416-3.49180.26871440.222913511495100
3.4918-3.8430.25661550.206213161471100
3.843-4.39870.21861420.151913521494100
4.3987-5.54030.17151410.142413621503100
5.5403-45.03560.18321520.17551314146695
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)
18.1306-3.24450.28316.7951-0.09162.830.66080.2730.3683-0.5926-0.8202-0.24480.02940.45630.21580.69440.07020.06760.65210.25550.71689.139620.235510.7045
20.6476-0.50180.23014.9321-1.34911.5920.26921.17730.7921-0.38590.0518-0.3766-0.2940.0375-0.0150.47040.04290.08430.68610.23810.544923.7557-0.381613.0837
36.03772.5276-1.69094.1301-1.12364.9919-0.05340.23990.0219-0.3583-0.0450.01130.7449-0.00850.10350.38760.0566-0.03740.4316-0.03460.317414.4802-12.647322.4179
44.90886.0305-0.95568.1273-0.23411.2327-0.1845-0.11631.1104-1.01750.15950.9281-0.02-0.34540.15390.767-0.05090.02770.63790.27451.251921.2337-45.882556.5087
52.65091.4364-0.42984.7185-0.34341.7684-0.167-0.6617-0.71710.01580.0481-0.40870.15680.20370.18640.38310.0120.00930.49920.09090.462631.84-22.773452.0725
67.8403-1.83611.49373.1009-0.79275.3206-0.2411-0.2275-0.0760.1297-0.0471-0.046-0.6764-0.45310.24270.4466-0.0192-0.02540.3918-0.03270.327418.0814-12.233846.3013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 57 )A2 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 106 )A58 - 106
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 189 )A107 - 189
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 57 )B3 - 57
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 106 )B58 - 106
6X-RAY DIFFRACTION6chain 'B' and (resid 107 through 189 )B107 - 189

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