[English] 日本語
Yorodumi
- PDB-3tqq: Structure of the methionyl-tRNA formyltransferase (fmt) from Coxi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tqq
TitleStructure of the methionyl-tRNA formyltransferase (fmt) from Coxiella burnetii
ComponentsMethionyl-tRNA formyltransferase
KeywordsTRANSFERASE / Protein synthesis
Function / homology
Function and homology information


methionyl-tRNA formyltransferase / conversion of methionyl-tRNA to N-formyl-methionyl-tRNA / methionyl-tRNA formyltransferase activity / cytosol
Similarity search - Function
Methionyl-tRNA formyltransferase / Methionyl-tRNA formyltransferase, N-terminal domain / Formyl transferase, C-terminal domain / Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 / Formyl transferase, C-terminal domain superfamily / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site ...Methionyl-tRNA formyltransferase / Methionyl-tRNA formyltransferase, N-terminal domain / Formyl transferase, C-terminal domain / Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 / Formyl transferase, C-terminal domain superfamily / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Methionyl-tRNA formyltransferase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRudolph, M. / Cheung, J. / Franklin, M.C. / 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 27, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methionyl-tRNA formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6992
Polymers34,6601
Non-polymers391
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.820, 56.295, 62.868
Angle α, β, γ (deg.)90.000, 113.660, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Methionyl-tRNA formyltransferase /


Mass: 34659.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: fmt, CBU_1997 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q83AA8, methionyl-tRNA formyltransferase
#2: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 mM Ammonium Sulfate, 20% PEG 3350, pH 7.5, vapor diffusion, sitting drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
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→50 Å / Num. all: 11896 / Num. obs: 21868 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.106 / Χ2: 1.673 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.08572.90.2855011.436184.9
2.52-2.5730.2345111.231187.7
2.57-2.623.10.245311.42189.5
2.62-2.6730.2765281.83191.3
2.67-2.733.10.2435601.747193.3
2.73-2.793.20.255501.722194.8
2.79-2.863.20.2395651.522194.6
2.86-2.943.30.2175652.104197.4
2.94-3.033.50.216001.909197.6
3.03-3.123.50.1895551.76197.7
3.12-3.243.60.1786052.171198.7
3.24-3.373.70.1455772.292198.6
3.37-3.523.70.1435791.868199
3.52-3.73.70.1316001.559198.8
3.7-3.943.70.1255911.985199.3
3.94-4.243.70.0895951.714199.7
4.24-4.673.70.0975941.112199.2
4.67-5.343.60.0735941.064199.3
5.34-6.733.60.0696021.475199.7
6.73-503.50.0696181.359197.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→17.842 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8127 / SU ML: 0.28 / σ(F): 0 / Phase error: 25.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1116 5.1 %Random
Rwork0.1956 ---
all0.1982 ---
obs0.1982 21868 96.29 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.014 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 158.37 Å2 / Biso mean: 36.689 Å2 / Biso min: 13.81 Å2
Baniso -1Baniso -2Baniso -3
1-2.2844 Å2-0 Å2-2.7836 Å2
2---1.4839 Å2-0 Å2
3----0.8005 Å2
Refinement stepCycle: LAST / Resolution: 2→17.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 1 273 2606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052370
X-RAY DIFFRACTIONf_angle_d0.9573207
X-RAY DIFFRACTIONf_chiral_restr0.067374
X-RAY DIFFRACTIONf_plane_restr0.003415
X-RAY DIFFRACTIONf_dihedral_angle_d13.818891
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.08570.24951390.18012463260292
2.0857-2.19550.27911320.1912629276199
2.1955-2.33280.31711310.25452539267093
2.3328-2.51240.30511390.22862620275998
2.5124-2.76440.29051470.23042584273197
2.7644-3.16250.29781410.21472589273096
3.1625-3.97720.20861420.18882650279298
3.9772-17.84230.20421450.16342678282397
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)
11.6880.96330.97981.26521.20571.6176-0.17060.04590.5409-0.2559-0.05940.2294-0.338-0.10380.24310.2742-0.0375-0.05570.24780.01510.31973.051114.9816-11.1992
21.07060.7237-0.47060.503-0.30860.2091-0.37770.33630.2242-0.2670.23110.08280.01490.02740.10070.2776-0.1559-0.08640.27730.09340.2282-5.11855.1308-21.3268
31.78550.27590.15360.98190.59580.3775-0.29220.4454-0.0388-0.38830.2679-0.0459-0.0240.05790.02720.2861-0.13290.01040.2835-0.0150.18451.5452-1.358-21.3254
41.31291.52860.20011.882-0.03050.6073-0.26850.36110.2168-0.21920.20610.2346-0.1081-0.01030.09970.2333-0.0409-0.02910.24620.07220.1882-17.9216-8.6872-17.3129
50.35450.30310.11591.5028-0.02680.8771-0.0893-0.0392-0.10290.02730.0340.18060.133-0.20910.05010.1371-0.00380.01680.16160.00160.1958-24.1957-19.9722-1.4408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:84)A1 - 84
2X-RAY DIFFRACTION2(CHAIN A AND RESID 85:130)A85 - 130
3X-RAY DIFFRACTION3(CHAIN A AND RESID 131:193)A131 - 193
4X-RAY DIFFRACTION4(CHAIN A AND RESID 194:233)A194 - 233
5X-RAY DIFFRACTION5(CHAIN A AND RESID 234:314)A234 - 314

+
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