[English] 日本語
Yorodumi
- PDB-2eua: Structure and Mechanism of MenF, the Menaquinone-Specific Isochor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2eua
TitleStructure and Mechanism of MenF, the Menaquinone-Specific Isochorismate Synthase from Escherichia Coli
ComponentsMenaquinone-specific isochorismate synthase
KeywordsISOMERASE / ALPHA/BETA FOLD
Function / homology
Function and homology information


isochorismate synthase / isochorismate synthase activity / phylloquinone biosynthetic process / menaquinone biosynthetic process / magnesium ion binding
Similarity search - Function
Isochorismate synthase MenF / Isochorismate synthase MenF-like / Isochorismate synthase / Anthranilate synthase / Anthranilate synthase / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Isochorismate synthase MenF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsKolappan, S. / Kisker, C. / Zwahlen, J. / Zhou, R. / Tonge, P.J.
CitationJournal: Biochemistry / Year: 2007
Title: Lysine 190 is the catalytic base in MenF, the menaquinone-specific isochorismate synthase from Escherichia coli: implications for an enzyme family.
Authors: Kolappan, S. / Zwahlen, J. / Zhou, R. / Truglio, J.J. / Tonge, P.J. / Kisker, C.
History
DepositionOct 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 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
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Menaquinone-specific isochorismate synthase
B: Menaquinone-specific isochorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9474
Polymers97,6472
Non-polymers3002
Water2,702150
1
A: Menaquinone-specific isochorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9742
Polymers48,8231
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Menaquinone-specific isochorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9742
Polymers48,8231
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.408, 146.408, 125.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 4 / Auth seq-ID: 2 - 429 / Label seq-ID: 2 - 429

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Menaquinone-specific isochorismate synthase / Isochorismate mutase


Mass: 48823.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: menF / Production host: Escherichia coli (E. coli) / References: UniProt: P38051, isochorismate synthase
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.44 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8 M potassium sodium tartrate, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X26C11.2536
SYNCHROTRONNSLS X26C20.9745, 0.97971
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 24, 2004
ADSC QUANTUM 42CCDOct 31, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.25361
20.97451
30.979711
Reflection
IDNumberRmerge(I) obsΧ2D res high (Å)D res low (Å)% possible obs
1526190.1011.30435099.9
2525420.0921.12135099.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
7.395098.910.0330.909
5.877.3999.910.0651.201
5.135.8710010.0761.326
4.665.1310010.071.478
4.334.6610010.0741.487
4.074.3310010.0771.36
3.874.0710010.0931.325
3.73.8710010.1121.485
3.563.710010.1251.263
3.433.5610010.1511.283
3.333.4310010.1811.285
3.233.3310010.2231.262
3.153.2310010.2941.308
3.073.1510010.3581.314
33.0710010.4111.277
7.395099.720.0330.876
5.877.3910020.061.053
5.135.8710020.0731.243
4.665.1310020.0711.455
4.334.6610020.0721.465
4.074.3310020.0751.257
3.874.0710020.0851.106
3.73.8710020.1021.25
3.563.799.820.1110.991
3.433.5699.920.1341.046
3.333.4399.920.1621.035
3.233.3310020.1980.991
3.153.2310020.2571.038
3.073.1510020.3181.071
33.0799.920.3520.952
ReflectionResolution: 2.5→50 Å / Num. obs: 47401 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.099 / Χ2: 1.487
Reflection shellResolution: 2.5→2.54 Å / % possible obs: 85.4 % / Rmerge(I) obs: 0.543 / Num. measured obs: 1999 / Χ2: 0.866 / % possible all: 85.4

-
Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
12 wavelength10.979517.75-6.74
12 wavelength20.9811.03-11.24
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se37.120.150.9520.0540.426
2Se53.2260.6170.4290.0550.455
3Se600.1140.7380.0810.586
4Se37.4640.50.770.0790.332
5Se600.9450.1330.0350.582
6Se600.110.7050.0060.571
7Se47.0150.1340.0940.1120.482
8Se600.5830.4750.0720.53
9Se600.9080.1840.0230.613
10Se600.9050.20.1090.627
11Se600.510.8130.0070.328
Phasing dmFOM : 0.65 / FOM acentric: 0.66 / FOM centric: 0.59 / Reflection: 27280 / Reflection acentric: 24041 / Reflection centric: 3239
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.6-19.9950.90.930.821210859351
5.4-8.60.810.830.7138153148667
4.3-5.40.810.830.6946774063614
3.8-4.30.750.760.6246264136490
3.2-3.80.570.580.4580937364729
3-3.20.340.360.2148594471388

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 19.027 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.37 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2393 5.1 %RANDOM
Rwork0.229 ---
all0.232 47073 --
obs0.232 44680 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.033 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6693 0 20 150 6863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226859
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9519335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9595854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30223.519324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.43151115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5791562
X-RAY DIFFRACTIONr_chiral_restr0.1080.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025276
X-RAY DIFFRACTIONr_nbd_refined0.2250.23049
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24626
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2327
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.26
X-RAY DIFFRACTIONr_mcbond_it0.5411.54364
X-RAY DIFFRACTIONr_mcangle_it0.9326834
X-RAY DIFFRACTIONr_scbond_it1.40132814
X-RAY DIFFRACTIONr_scangle_it2.2064.52501
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3240 / Refine-ID: X-RAY DIFFRACTION

RmsTypeWeight
0.37MEDIUM POSITIONAL0.5
0.62MEDIUM THERMAL2
LS refinement shellResolution: 2.499→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 153 -
Rwork0.408 2903 -
all-3056 -
obs--88.48 %

+
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://pdbjlvh1.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