[English] 日本語
Yorodumi
- PDB-1efc: INTACT ELONGATION FACTOR FROM E.COLI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1efc
TitleINTACT ELONGATION FACTOR FROM E.COLI
ComponentsPROTEIN (ELONGATION FACTOR)
KeywordsRNA BINDING PROTEIN / TRANSPORT AND PROTECTION PROTEIN
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / plasma membrane / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. ...Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu 1 / Elongation factor Tu 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsSong, H. / Parsons, M.R. / Rowsell, S. / Leonard, G. / Phillips, S.E.V.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05 A resolution.
Authors: Song, H. / Parsons, M.R. / Rowsell, S. / Leonard, G. / Phillips, S.E.
#1: Journal: Structure / Year: 1996
Title: An Alpha to Beta Conformational Switch in EF-TU
Authors: Abel, K. / Yoder, M.D. / Hilgenfeld, R. / Jurnak, F.
#2: Journal: Structure / Year: 1996
Title: Helix Unwinding in the Effector Region of Elongation Factor EF-TU-Gdp
Authors: Polekhina, G. / Thirup, S. / Kjeldgaard, M. / Nissen, P. / Lippmann, C. / Nyborg, J.
#3: Journal: Science / Year: 1995
Title: Crystal Structure of the Ternary Complex of Phe-tRNA, EF-TU and GTP Analogue
Authors: Nissen, P. / Kjeldgaard, M. / Thirup, S. / Polekhina, G. / Reshetnikova, L. / Clark, B.F.C. / Nyborg, J.
#4: Journal: Structure / Year: 1993
Title: The Crystal Structure of Elongation Factor EF-TU from T. Aquaticus in the GTP Conformation
Authors: Kjeldgaard, M. / Nissen, P. / Thirup, S. / Nyborg, J.
#5: Journal: J.Mol.Biol. / Year: 1992
Title: Refined Structure of Elongation Factor EF-TU from E. Coli
Authors: Kjeldgaard, M. / Nyborg, J.
History
DepositionNov 24, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Mar 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (ELONGATION FACTOR)
B: PROTEIN (ELONGATION FACTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4146
Polymers86,4792
Non-polymers9354
Water8,035446
1
A: PROTEIN (ELONGATION FACTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7073
Polymers43,2391
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (ELONGATION FACTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7073
Polymers43,2391
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)243.120, 61.080, 66.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

-
Components

#1: Protein PROTEIN (ELONGATION FACTOR) / EFTU


Mass: 43239.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6N1, UniProt: P0CE47*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEF-TU IS CODED FOR BY TWO DIFFERENT GENES. THE SEQUENCE STRUCTURE ANALYSIS CARRIED OUT ON THIS ...EF-TU IS CODED FOR BY TWO DIFFERENT GENES. THE SEQUENCE STRUCTURE ANALYSIS CARRIED OUT ON THIS MIXTURE SHOWS THAT THE C-TERMINAL RESIDUE OCCURS AS GLY/SER IN THE RATIO OF 3/ 1. THIS RESIDUE IS IDENTIFIED AS GLY ON THE *SEQRES* RECORDS BELOW.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
2100 mMTris-HCl1drop
310 mM1dropMgCl2
41.2 Mammonium sulfate1drop
5100 mMTris-HCl1reservoir
610 mM1reservoirMgCl2
71.5 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97899,0.97916,0.91850
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1996 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978991
20.979161
30.91851
ReflectionResolution: 2.05→25 Å / Num. obs: 61876 / % possible obs: 90.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.274 / % possible all: 91.7
Reflection
*PLUS
Num. measured all: 217915
Reflection shell
*PLUS
% possible obs: 91.7 %

-
Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→10 Å / Cross valid method: THROUGHOUT / ESU R: 0.18
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2640 5 %RANDOM
Rwork0.203 ---
obs0.203 52808 90.5 %-
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5940 0 58 446 6444
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d0.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more