[English] 日本語
Yorodumi
- PDB-6not: Crystal structure of a full length elongation factor G (EF-G) fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6not
TitleCrystal structure of a full length elongation factor G (EF-G) from Rickettsia prowazekii
ComponentsElongation factor GEF-G
KeywordsTRANSLATION / National Institute of Allergy and Infectious Diseases / NIAID / structural genomics / GTPase / multi-domain protein / RNA-binding protein / Seattle Structural Genomics Center for Infectious Disease / SSGCID / HYDROLASE
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV ...Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Translation factors / EF-G domain III/V-like / Ribosomal Protein S5; domain 2 / 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 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / P-loop containing nucleotide triphosphate hydrolases / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesRickettsia prowazekii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a full length elongation factor G (EF-G) from Rickettsia prowazekii
Authors: Edwards, T.E. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJan 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Elongation factor G
B: Elongation factor G


Theoretical massNumber of molelcules
Total (without water)157,7552
Polymers157,7552
Non-polymers00
Water68538
1
A: Elongation factor G


Theoretical massNumber of molelcules
Total (without water)78,8771
Polymers78,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Elongation factor G


Theoretical massNumber of molelcules
Total (without water)78,8771
Polymers78,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.670, 79.560, 95.470
Angle α, β, γ (deg.)103.850, 95.320, 92.170
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Elongation factor G / EF-G / EF-G


Mass: 78877.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia prowazekii (strain Madrid E) (bacteria)
Strain: Madrid E / Gene: fusA, RP132 / Production host: Escherichia coli (E. coli) / References: UniProt: P41084
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: RiprA.18013.a.B1.PW38427 at 10.98 mg/mL against MCSG1 screen condition H6: 0.1 M sodium acetate pH 4.6, 3.5 M sodium formate with direct cryo, crystal tracking ID 299862h6, unique puck ID pxh5-7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.4→32.597 Å / Num. obs: 62945 / % possible obs: 98.2 % / Redundancy: 3.284 % / Biso Wilson estimate: 70.926 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.047 / Χ2: 1.015 / Net I/σ(I): 15.9 / Num. measured all: 206687 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.463.3430.5962.0515550476846510.7730.71297.5
2.46-2.533.3340.4522.615062461645180.8680.5497.9
2.53-2.63.3340.3553.3414645449643920.9070.42497.7
2.6-2.683.3350.2674.3714234435542680.9430.31898
2.68-2.773.3290.1995.5913822423641520.9660.23898
2.77-2.873.3270.1517.3313442411640400.980.1898.2
2.87-2.983.3320.1089.7712818392038470.990.12998.1
2.98-3.13.3060.08112.5812344380037340.9940.09698.3
3.1-3.243.2970.06315.8311823364735860.9960.07598.3
3.24-3.393.2770.0519.3111332351234580.9970.0698.5
3.39-3.583.2590.04223.3210568329732430.9970.0598.4
3.58-3.793.240.03725.9610052314031020.9980.04498.8
3.79-4.063.2370.03429.069277291028660.9980.0498.5
4.06-4.383.2150.0331.968803276827380.9980.03598.9
4.38-4.83.2350.02834.148062251024920.9980.03399.3
4.8-5.373.2220.02834.247289229622620.9980.03398.5
5.37-6.23.1770.02933.886266199119720.9980.03599
6.2-7.593.1630.02834.975285169616710.9980.03498.5
7.59-10.733.1610.02736.554112132413010.9980.03298.3
10.73-32.5972.9160.02834.9719017096520.9980.03492

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX(dev_3374)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4juw

4juw
PDB Unreleased entry


Resolution: 2.4→32.597 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 30.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 3132 4.98 %
Rwork0.1972 59759 -
obs0.1995 62891 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 196.27 Å2 / Biso mean: 88.4532 Å2 / Biso min: 37.94 Å2
Refinement stepCycle: final / Resolution: 2.4→32.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9309 0 0 38 9347
Biso mean---73.51 -
Num. residues----1266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3999-2.43740.35961190.30722721284098
2.4374-2.47730.3911450.29542689283497
2.4773-2.520.34121510.28682719287098
2.52-2.56580.35451660.27572679284598
2.5658-2.61520.31841460.26462713285998
2.6152-2.66850.30551380.26852675281398
2.6685-2.72650.3541450.24852726287198
2.7265-2.78990.32011440.25122705284998
2.7899-2.85970.27361190.25532745286498
2.8597-2.93690.34071470.24922714286198
2.9369-3.02330.34981370.262712284998
3.0233-3.12080.28161400.25362705284598
3.1208-3.23220.27721420.242736287898
3.2322-3.36150.27461420.22972707284999
3.3615-3.51430.2781410.22512717285899
3.5143-3.69940.29221170.20642757287498
3.6994-3.93080.20941330.19442735286899
3.9308-4.23370.20271640.16112708287299
4.2337-4.65870.19221410.14542747288899
4.6587-5.33030.18731530.14932764291799
5.3303-6.70590.22751610.19322692285399
6.7059-32.60010.21821410.1712693283497
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)
18.40023.9914-5.14346.8001-1.99483.2306-0.0357-0.09520.2229-0.60590.03350.3696-0.65450.26880.04080.65540.052-0.0360.3862-0.01540.4209-9.01234.74518.5611
23.57420.8888-0.74782.1986-0.14812.1568-0.22010.24670.1288-0.71440.1385-0.02680.08950.3020.0720.64080.0532-0.02940.34790.01470.4011-9.0835-1.35568.3214
33.0298-0.4731-1.13042.4611-0.41842.70620.2411-0.41881.15750.8735-0.2851.0259-0.3413-1.0327-0.6961-0.05950.0470.20180.835-0.02192.1527-10.168712.069739.4055
43.13440.6235-3.64441.4413-0.34096.0165-0.1128-0.62190.13110.4050.0860.17470.6609-0.0790.02270.57210.0526-0.01450.8840.01830.4268-4.3489-9.484148.3929
52.51330.34141.28223.18442.6235.22310.3027-0.02710.0010.1955-0.233-0.3912-0.407-0.1755-0.10350.61120.00980.10270.55450.07130.43927.9849-22.8265-49.5813
62.1320.54670.23743.99370.74594.1850.2882-0.5890.16960.8982-0.26420.4649-0.4113-0.8683-0.09280.62960.00540.15170.63580.01260.497620.0722-24.0631-46.6915
72.73391.1402-0.51944.4067-0.70893.4664-0.01710.24110.1436-0.7590.0467-0.6592-0.17450.3073-0.12460.69190.07020.10180.4291-0.03060.638737.3198-27.0149-71.744
81.68330.324-0.03972.4523-0.2923.9928-0.12770.3772-0.1366-0.9440.238-0.10190.3404-0.2745-0.12071.1124-0.01520.11750.49620.04070.48731.4117-5.6985-85.5214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 113 )A5 - 113
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 419 )A114 - 419
3X-RAY DIFFRACTION3chain 'A' and (resid 420 through 475 )A420 - 475
4X-RAY DIFFRACTION4chain 'A' and (resid 476 through 698 )A476 - 698
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 143 )B-1 - 143
6X-RAY DIFFRACTION6chain 'B' and (resid 144 through 351 )B144 - 351
7X-RAY DIFFRACTION7chain 'B' and (resid 352 through 469 )B352 - 469
8X-RAY DIFFRACTION8chain 'B' and (resid 470 through 698 )B470 - 698

+
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