[English] 日本語
Yorodumi
- PDB-5uai: Crystal structure of Methionyl-tRNA formyltransferase from Pseudo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uai
TitleCrystal structure of Methionyl-tRNA formyltransferase from Pseudomonas aeruginosa
ComponentsMethionyl-tRNA formyltransferase
KeywordsTRANSFERASE / SSGCID / fmt / Methionyl-tRNA formyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


methionyl-tRNA formyltransferase / conversion of methionyl-tRNA to N-formyl-methionyl-tRNA / methionyl-tRNA formyltransferase activity / regulation of transmembrane transporter 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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Methionyl-tRNA formyltransferase from Pseudomonas aeruginosa
Authors: Conrady, D.G. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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: Methionyl-tRNA formyltransferase
B: Methionyl-tRNA formyltransferase
C: Methionyl-tRNA formyltransferase
D: Methionyl-tRNA formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,4475
Polymers136,3854
Non-polymers621
Water3,873215
1
A: Methionyl-tRNA formyltransferase


Theoretical massNumber of molelcules
Total (without water)34,0961
Polymers34,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionyl-tRNA formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1582
Polymers34,0961
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Methionyl-tRNA formyltransferase


Theoretical massNumber of molelcules
Total (without water)34,0961
Polymers34,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Methionyl-tRNA formyltransferase


Theoretical massNumber of molelcules
Total (without water)34,0961
Polymers34,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.920, 109.060, 109.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 28 or (resid 29...
21(chain B and (resid 4 through 57 or (resid 58...
31(chain C and (resid 4 through 177 or (resid 178...
41(chain D and (resid 4 through 57 or (resid 58...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4 through 28 or (resid 29...A4 - 28
121(chain A and (resid 4 through 28 or (resid 29...A29
131(chain A and (resid 4 through 28 or (resid 29...A4 - 313
141(chain A and (resid 4 through 28 or (resid 29...A4 - 313
151(chain A and (resid 4 through 28 or (resid 29...A4 - 313
161(chain A and (resid 4 through 28 or (resid 29...A4 - 313
211(chain B and (resid 4 through 57 or (resid 58...B4 - 57
221(chain B and (resid 4 through 57 or (resid 58...B58
231(chain B and (resid 4 through 57 or (resid 58...B3 - 393
241(chain B and (resid 4 through 57 or (resid 58...B3 - 393
251(chain B and (resid 4 through 57 or (resid 58...B3 - 393
261(chain B and (resid 4 through 57 or (resid 58...B3 - 393
311(chain C and (resid 4 through 177 or (resid 178...C4 - 177
321(chain C and (resid 4 through 177 or (resid 178...C178 - 179
331(chain C and (resid 4 through 177 or (resid 178...C3 - 313
341(chain C and (resid 4 through 177 or (resid 178...C3 - 313
351(chain C and (resid 4 through 177 or (resid 178...C3 - 313
361(chain C and (resid 4 through 177 or (resid 178...C3 - 313
411(chain D and (resid 4 through 57 or (resid 58...D4 - 57
421(chain D and (resid 4 through 57 or (resid 58...D58
431(chain D and (resid 4 through 57 or (resid 58...D3 - 313
441(chain D and (resid 4 through 57 or (resid 58...D3 - 313
451(chain D and (resid 4 through 57 or (resid 58...D3 - 313
461(chain D and (resid 4 through 57 or (resid 58...D3 - 313

-
Components

#1: Protein
Methionyl-tRNA formyltransferase /


Mass: 34096.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: fmt, PA0018 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O85732, methionyl-tRNA formyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 20.7 mg/mL PsaeA.17389.a.B1.PW37587 crystallized in sitting drop vapor diffusion with Rigaku MCSG1 B5: 0.2 M MgCl2; 0.1 M Tris pH 8.5; 25% PEG3350, cryo: 20% EG. tray 259534b5, puck rzw4-7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.75→49.084 Å / Num. obs: 36266 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.402 % / Biso Wilson estimate: 36.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Net I/σ(I): 18.88
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.75-2.827.5460.5314.360.9341100
2.82-2.97.5380.4115.570.9571100
2.9-2.987.5280.3576.370.9671100
2.98-3.077.5510.3147.180.9731100
3.07-3.187.5090.2468.980.9831100
3.18-3.297.520.19111.180.9911100
3.29-3.417.4980.1513.70.9931100
3.41-3.557.4780.12516.240.9951100
3.55-3.717.4750.10319.440.9961100
3.71-3.897.4460.08422.830.9971100
3.89-4.17.4270.06727.350.9981100
4.1-4.357.4350.05830.650.9991100
4.35-4.657.3660.05233.280.999199.9
4.65-5.027.3310.05232.340.9991100
5.02-5.57.3130.05930.120.9981100
5.5-6.157.2670.05929.310.998199.9
6.15-7.17.1750.05232.530.999199.8
7.1-8.77.0080.03641.080.9991100
8.7-12.36.650.02748.451199.8
12.3-49.0845.4320.02836.430.999196

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FMT

1fmt


Resolution: 2.75→49.084 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.16
RfactorNum. reflection% reflection
Rfree0.2344 2192 6.3 %
Rwork0.1666 --
obs0.1709 34774 95.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.63 Å2 / Biso mean: 36.0318 Å2 / Biso min: 0.39 Å2
Refinement stepCycle: final / Resolution: 2.75→49.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8955 0 4 215 9174
Biso mean--36.49 24.56 -
Num. residues----1243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089139
X-RAY DIFFRACTIONf_angle_d1.05712479
X-RAY DIFFRACTIONf_chiral_restr0.0551476
X-RAY DIFFRACTIONf_plane_restr0.0081651
X-RAY DIFFRACTIONf_dihedral_angle_d12.6415522
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5441X-RAY DIFFRACTION8.327TORSIONAL
12B5441X-RAY DIFFRACTION8.327TORSIONAL
13C5441X-RAY DIFFRACTION8.327TORSIONAL
14D5441X-RAY DIFFRACTION8.327TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.80970.35961180.27061901201991
2.8097-2.87510.32931210.23361894201590
2.8751-2.9470.3031270.21431917204492
2.947-3.02670.30871570.22321933209093
3.0267-3.11570.32141370.22131937207493
3.1157-3.21630.32821150.22212022213795
3.2163-3.33120.27191230.20492037216096
3.3312-3.46450.27161550.1912014216997
3.4645-3.62220.27041470.18062048219597
3.6222-3.81310.22871380.15892065220398
3.8131-4.05190.20951450.13512093223898
4.0519-4.36450.18391260.12482134226099
4.3645-4.80340.15321540.11362099225399
4.8034-5.49770.19361340.13522142227699
5.4977-6.92340.19691510.15152133228499
6.9234-49.09140.19891440.14822213235797
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)
13.1175-0.0119-0.15992.6736-0.17631.69-0.0742-0.17690.32670.056-0.0071-0.1229-0.40380.02180.11520.2937-0.0163-0.05530.1336-0.01420.1937-22.022319.8068-45.1393
21.05140.4373-0.28693.001-0.85652.7286-0.08510.0171-0.02060.0766-0.1006-0.3942-0.0180.29070.11810.09690.0212-0.00540.19090.01810.1748-14.95183.1928-43.5443
34.42390.6931-0.11675.41321.79394.2249-0.1466-0.0662-0.00330.1686-0.12920.6866-0.1667-0.32560.21260.2493-0.01420.02590.2625-0.04980.2516-40.7358-14.0559-40.1034
42.4363-0.4047-0.2551.83062.03812.25320.08250.04850.20940.8993-0.311.31580.0901-1.07860.65270.04120.01770.59910.5121-0.34841.0375-52.7009-15.8994-36.4451
52.0575-0.01720.31952.3273-0.1974.1080.23120.0659-0.0924-0.0461-0.08410.38150.5663-0.2832-0.08520.2031-0.0565-0.04960.2002-0.00520.2725-41.31217.7063-61.2997
61.0826-0.19580.11024.49670.46341.89350.08180.0807-0.1377-0.43480.0075-0.11710.08770.0308-0.08390.1490.0104-0.0040.2088-0.00320.1754-37.56420.3071-68.9816
72.58840.6541-0.4312.24520.95564.79150.4242-0.43690.12990.6047-0.34590.2580.2945-0.0432-0.11590.3091-0.07310.05950.3215-0.02450.2036-45.075840.5514-41.3826
80.0152-0.0493-0.4011.65540.38373.54260.4422-0.01470.311-0.0827-0.0188-0.1638-1.69260.1601-0.22510.6316-0.1160.10520.2684-0.03890.3789-37.1898-8.12578.8328
90.58720.29310.04893.3251.46163.2844-0.05550.05910.1736-0.11910.18790.1068-0.1092-0.0324-0.11210.1671-0.00710.01670.24340.03240.1999-42.5107-31.9524.2716
103.9864-2.22583.38175.8578-2.65035.53220.09540.3064-0.5426-0.00720.05240.2172-0.10320.1828-0.08120.3219-0.06790.06010.15890.04920.2319-18.0973-20.0649-15.3705
113.0708-0.591-3.14512.03560.56953.17170.13810.1837-0.1697-0.1798-0.21210.1204-0.0165-0.01130.05360.3689-0.06630.02230.30070.02550.3232-27.4494-22.5698-8.3861
126.8267-0.65080.73912.326-1.46313.9813-0.4551-1.439-0.78691.21580.14570.33910.2633-0.1551-0.03830.72410.06060.03120.44910.16830.2883-17.8104-24.5084-0.2071
133.70432.29431.80754.9127-1.50432.9805-0.3063-0.56190.00310.45790.4924-0.7947-0.09730.2565-0.06270.28690.1010.00320.3251-0.02220.2637-13.9366-18.0702-5.576
142.9133-0.37220.40893.7672-0.19681.2627-0.0866-0.0725-0.1261-0.0140.0383-0.12340.15540.10290.05790.18480.0113-0.00880.2020.00860.1224-14.2734-4.7553-13.1084
154.991-0.90191.41313.72221.75272.7145-0.21540.10660.11590.12240.15410.9681-0.1043-0.2880.0670.22760.01640.02710.37140.10220.3552-39.684811.5352-15.8921
160.3156-0.4859-0.96442.82830.50143.29150.18020.18770.143-0.7220.24971.96130.0199-1.5192-0.15190.39230.0237-0.25020.63170.14881.1107-51.201411.4796-20.3633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 81 )A4 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 211 )A82 - 211
3X-RAY DIFFRACTION3chain 'A' and (resid 212 through 294 )A212 - 294
4X-RAY DIFFRACTION4chain 'A' and (resid 295 through 313 )A295 - 313
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 59 )B3 - 59
6X-RAY DIFFRACTION6chain 'B' and (resid 60 through 211 )B60 - 211
7X-RAY DIFFRACTION7chain 'B' and (resid 212 through 313 )B212 - 313
8X-RAY DIFFRACTION8chain 'C' and (resid 3 through 81 )C3 - 81
9X-RAY DIFFRACTION9chain 'C' and (resid 82 through 313 )C82 - 313
10X-RAY DIFFRACTION10chain 'D' and (resid 3 through 25 )D3 - 25
11X-RAY DIFFRACTION11chain 'D' and (resid 26 through 58 )D26 - 58
12X-RAY DIFFRACTION12chain 'D' and (resid 59 through 81 )D59 - 81
13X-RAY DIFFRACTION13chain 'D' and (resid 82 through 96 )D82 - 96
14X-RAY DIFFRACTION14chain 'D' and (resid 97 through 211 )D97 - 211
15X-RAY DIFFRACTION15chain 'D' and (resid 212 through 291 )D212 - 291
16X-RAY DIFFRACTION16chain 'D' and (resid 292 through 313 )D292 - 313

+
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