[English] 日本語
Yorodumi
- PDB-4iqf: Crystal Structure of Methyionyl-tRNA Formyltransferase from Bacil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iqf
TitleCrystal Structure of Methyionyl-tRNA Formyltransferase from Bacillus anthracis
ComponentsMethionyl-tRNA formyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta structure
Function / homology
Function and homology information


methionyl-tRNA formyltransferase / methionyl-tRNA formyltransferase activity
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
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Methionyl-tRNA formyltransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.378 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Methyionyl-tRNA Formyltransferase from Bacillus anthracis
Authors: Kim, Y. / Makowska-Grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 11, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJan 23, 2013ID: 3RFO
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methionyl-tRNA formyltransferase
B: Methionyl-tRNA formyltransferase
C: Methionyl-tRNA formyltransferase
D: Methionyl-tRNA formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,26213
Polymers141,3314
Non-polymers9319
Water9,080504
1
A: Methionyl-tRNA formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6994
Polymers35,3331
Non-polymers3663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionyl-tRNA formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5213
Polymers35,3331
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Methionyl-tRNA formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4252
Polymers35,3331
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Methionyl-tRNA formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6174
Polymers35,3331
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.856, 191.501, 89.946
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Methionyl-tRNA formyltransferase /


Mass: 35332.676 Da / Num. of mol.: 4 / Fragment: Methionyl-tRNA Formyltransferase / Mutation: full-length
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS3717, BA_4004, fmt, GBAA_4004 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q81WH2, methionyl-tRNA formyltransferase
#2: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Triethylene glycol dimethyl ether


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 3.83 Å3/Da / Density % sol: 67.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.5, 25 % w/v Polyehtlyene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 25, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.378→50 Å / Num. obs: 4160 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 44.35 Å2 / Rsym value: 0.109 / Net I/σ(I): 10.2
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3 / Num. unique all: 4160 / Rsym value: 0.72 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.378→36.589 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.55 / Stereochemistry target values: TWIN_LSQ_F
Details: The structure was solved by SAD in P212121 space group and refined in P21 with twin-option.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 4171 5.03 %random
Rwork0.181 ---
all0.183 ---
obs0.183 -97.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56 Å2
Refinement stepCycle: LAST / Resolution: 2.378→36.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9785 0 54 504 10343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410101
X-RAY DIFFRACTIONf_angle_d0.913709
X-RAY DIFFRACTIONf_dihedral_angle_d14.0283843
X-RAY DIFFRACTIONf_chiral_restr0.0561576
X-RAY DIFFRACTIONf_plane_restr0.0041754
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.378-2.41910.3151540.28313155330975
2.4191-2.4630.30612010.27483933423494
2.463-2.51030.28962130.25574021423493
2.5103-2.56140.3032070.25723914412194
2.5614-2.6170.26492230.25064003422693
2.617-2.67770.26032200.24193954417494
2.6777-2.74450.26192010.23084022422394
2.7445-2.81850.26151810.23323993417495
2.8185-2.90120.2332020.22324043424595
2.9012-2.99460.25882110.21874010422195
2.9946-3.10120.25661940.22324020421495
3.1012-3.22490.24732180.20664004422295
3.2249-3.37090.2191950.19734026422195
3.3709-3.54770.2012110.1874018422995
3.5477-3.76850.212370.16684003424094
3.7685-4.05720.16792000.15474000420094
4.0572-4.46120.18662080.13413933411193
4.4612-5.09710.13932120.12733891410391
5.0971-6.38560.17022310.15034018424994
6.3856-19.7670.20422070.15753755396287
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)
13.73810.9701-0.02212.7697-1.00291.71990.07150.13240.1475-0.0726-0.17910.0692-0.0342-0.08450.09470.2160.0194-0.01620.268-0.01750.296338.8264112.394547.6586
22.0168-0.65250.16033.02530.91231.6261-0.0216-0.3561-0.17910.2403-0.0136-0.03190.06690.04870.01710.3807-0.06960.01110.34360.07310.203946.03296.974856.5214
34.3028-0.52520.38674.35510.37873.09070.0910.192-0.2989-0.5046-0.12520.00590.34460.10530.03510.57460.0090.02680.21020.03160.471250.21576.046735.3013
43.0403-1.28640.28622.16740.64021.90860.1363-0.03540.29790.0351-0.123-0.2534-0.13420.157-0.01540.2586-0.0832-0.05770.32380.03710.744924.119692.407588.9502
51.17920.7717-0.43825.4206-1.66071.47290.06420.0784-0.37450.39220.01640.360.129-0.0365-0.08830.41-0.0058-0.04030.2716-0.05660.784314.927966.326690.3252
62.6099-1.7994-1.18382.4195-0.47511.9768-0.07160.3991-0.0697-0.3017-0.11080.86460.2062-0.17670.20240.2722-0.0597-0.09530.3969-0.00230.70561.7064110.658939.1979
74.0541-0.9514-2.41032.8648-1.03012.4016-0.518-0.5430.22070.1093-0.03970.5796-0.32120.23270.62330.3124-0.0267-0.06350.4058-0.04990.65615.2766110.354350.4426
83.2864-1.4167-1.21711.91410.25591.68770.0349-0.1068-0.3270.08290.0005-0.21820.2319-0.0589-0.03820.3417-0.0796-0.03370.3735-0.05210.71349.9618104.172846.1796
91.92051.15780.27753.54631.462.4387-0.02220.34470.2286-0.0923-0.06340.0786-0.151-0.11520.08980.25350.0147-0.02920.31160.05470.532412.4195121.484535.0801
107.50352.84752.48865.72562.09585.9497-0.07771.1567-0.4181-0.28280.5024-0.84710.00171.1394-0.37750.3650.01980.03090.30860.08850.523921.7471119.262831.8355
111.65570.28-0.46792.69440.81382.2136-0.01-0.13350.41860.5405-0.1105-0.3468-0.12140.19490.07440.57610.0139-0.14550.30310.06310.968320.7409140.257552.119
125.0592-0.3362-2.01042.6321.09892.92520.35650.10340.39140.42440.0544-0.4448-0.2212-0.0702-0.38020.6687-0.055-0.01390.25220.03770.927418.6412151.867253.2944
132.04371.3485-1.06236.3581-5.06259.19230.3729-0.59820.62970.90490.04450.27170.4485-0.0945-0.42911.0383-0.0217-0.08840.3640.00610.916112.4793142.567460.1117
143.15510.2094-1.35144.3517-0.32193.4632-0.2055-0.7968-0.47891.6567-0.12960.2705-0.45690.32420.25621.0869-0.0328-0.10550.5477-0.06051.133121.0819149.382763.5143
152.3794-0.7747-0.07224.4061-1.35223.33570.0036-0.4013-0.2790.287-0.1915-0.57030.21750.15240.15970.2607-0.0419-0.07520.35360.05390.803561.533490.684897.3912
161.74630.18790.57621.0932-0.76365.08930.05040.2646-0.282-0.1591-0.0177-0.11790.1327-0.1101-0.01210.31240.0359-0.0920.35830.0070.805658.969791.294684.3029
171.72930.18690.00741.32450.19932.06530.1065-0.0668-0.3666-0.0762-0.16570.13090.32270.07540.06930.315-0.0365-0.09940.31710.06470.860950.454383.190595.0114
181.0467-0.13920.52082.7544-1.28862.4718-0.0427-0.18270.14050.1292-0.0620.098-0.1512-0.15710.11630.3216-0.0514-0.05990.3209-0.09050.742548.277102.3093101.3368
190.5285-0.72010.51890.9855-0.85561.4318-0.03560.05270.23010.0899-0.04760.0199-0.056-0.25370.07660.4248-0.0052-0.11950.2765-0.07540.785643.0312117.978183.4654
202.11360.615-0.1171.93291.01472.0115-0.05890.01970.6877-0.2170.0527-0.2713-0.1311-0.1076-0.04140.65330.0211-0.14030.29220.01331.061745.0056127.765479.7386
215.6946-0.1073-0.29461.630.43222.4235-0.12190.45940.5134-0.81950.0271-0.06-0.3204-0.15240.09950.79340.0128-0.11320.3941-0.06740.944344.3001128.313172.0881
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 206 )
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 311 )
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 108 )
5X-RAY DIFFRACTION5chain 'B' and (resid 109 through 312 )
6X-RAY DIFFRACTION6chain 'C' and (resid -2 through 22 )
7X-RAY DIFFRACTION7chain 'C' and (resid 23 through 41 )
8X-RAY DIFFRACTION8chain 'C' and (resid 42 through 99 )
9X-RAY DIFFRACTION9chain 'C' and (resid 100 through 186 )
10X-RAY DIFFRACTION10chain 'C' and (resid 187 through 206 )
11X-RAY DIFFRACTION11chain 'C' and (resid 207 through 261 )
12X-RAY DIFFRACTION12chain 'C' and (resid 262 through 277 )
13X-RAY DIFFRACTION13chain 'C' and (resid 278 through 298 )
14X-RAY DIFFRACTION14chain 'C' and (resid 299 through 312 )
15X-RAY DIFFRACTION15chain 'D' and (resid -2 through 23 )
16X-RAY DIFFRACTION16chain 'D' and (resid 24 through 56 )
17X-RAY DIFFRACTION17chain 'D' and (resid 57 through 108 )
18X-RAY DIFFRACTION18chain 'D' and (resid 109 through 206 )
19X-RAY DIFFRACTION19chain 'D' and (resid 207 through 252 )
20X-RAY DIFFRACTION20chain 'D' and (resid 253 through 294 )
21X-RAY DIFFRACTION21chain 'D' and (resid 295 through 312 )

+
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