[English] 日本語
Yorodumi
- PDB-4qii: Crystal Structure of type II MenB from Mycobacteria tuberculosis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qii
TitleCrystal Structure of type II MenB from Mycobacteria tuberculosis
Components1,4-Dihydroxy-2-naphthoyl-CoA synthase
KeywordsLYASE / 1 / 4-dihydroxy-2-naphthoyl-coenzyme A / synthase
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase activity / menaquinone biosynthetic process / protein hexamerization / plasma membrane
Similarity search - Function
1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex ...1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Salicylyl CoA / TRIETHYLENE GLYCOL / 1,4-dihydroxy-2-naphthoyl-CoA synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsSong, H.G. / Tse, Y.S. / Sung, H.P. / Guo, Z.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Ligand-dependent active-site closure revealed in the crystal structure of Mycobacterium tuberculosis MenB complexed with product analogues
Authors: Song, H. / Sung, H.P. / Tse, Y.S. / Jiang, M. / Guo, Z.H.
History
DepositionMay 31, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
B: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
C: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
D: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
E: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
F: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
G: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
H: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
I: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
J: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
K: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
L: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)454,09228
Polymers442,84012
Non-polymers11,25216
Water69,4663856
1
A: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
B: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
C: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
D: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
E: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
F: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,04614
Polymers221,4206
Non-polymers5,6268
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43150 Å2
ΔGint-171 kcal/mol
Surface area50070 Å2
MethodPISA
2
G: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
H: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
I: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
J: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
K: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
L: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,04614
Polymers221,4206
Non-polymers5,6268
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43180 Å2
ΔGint-173 kcal/mol
Surface area50040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.470, 147.720, 140.820
Angle α, β, γ (deg.)90.00, 103.45, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
1,4-Dihydroxy-2-naphthoyl-CoA synthase / DHNA-CoA synthase


Mass: 36903.301 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WNP5, 1,4-dihydroxy-2-naphthoyl-CoA synthase
#2: Chemical
ChemComp-2NE / Salicylyl CoA


Mass: 887.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C28H40N7O18P3S
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3856 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M NaCl, 0.1M HEPES pH 8.5, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.64→34.96 Å / Num. obs: 439236 / Biso Wilson estimate: 16.5 Å2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q52

1q52


Resolution: 1.64→34.955 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 18.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1812 22018 5.02 %
Rwork0.1508 --
obs0.1523 438964 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→34.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28083 0 724 3856 32663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00629523
X-RAY DIFFRACTIONf_angle_d1.07840129
X-RAY DIFFRACTIONf_dihedral_angle_d14.710703
X-RAY DIFFRACTIONf_chiral_restr0.0454163
X-RAY DIFFRACTIONf_plane_restr0.0055283
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.64-1.65860.27227220.25331376098
1.6586-1.67810.28817720.24431370298
1.6781-1.69860.26477580.23421378999
1.6986-1.72010.27797490.22811373499
1.7201-1.74270.25667400.2131381399
1.7427-1.76660.24517060.20151384899
1.7666-1.79190.24087640.19531382799
1.7919-1.81860.22697190.17961384599
1.8186-1.8470.237650.181381399
1.847-1.87730.21917160.17761387399
1.8773-1.90970.21867570.17771392999
1.9097-1.94440.21136870.17561389799
1.9444-1.98180.19016950.15571393699
1.9818-2.02220.1947450.15341389599
2.0222-2.06620.19787410.15281392299
2.0662-2.11430.19727070.14811391099
2.1143-2.16710.1827240.14291400299
2.1671-2.22570.18387310.14411394499
2.2257-2.29120.17396810.144714005100
2.2912-2.36510.18067550.14813884100
2.3651-2.44960.17367640.143413956100
2.4496-2.54770.18597300.149314004100
2.5477-2.66360.17756950.144214048100
2.6636-2.8040.17427550.14413990100
2.804-2.97960.18477210.149314010100
2.9796-3.20950.16077720.14531394599
3.2095-3.53220.15227020.13461392199
3.5322-4.04260.14177470.121358397
4.0426-5.09080.13337610.115114107100
5.0908-34.96340.17977370.15581405499
Refinement TLS params.Method: refined / Origin x: 158.7066 Å / Origin y: 6.1818 Å / Origin z: 210.0187 Å
111213212223313233
T0.0766 Å20.0034 Å20.0187 Å2-0.0872 Å2-0.0006 Å2--0.1093 Å2
L0.0797 °2-0.0037 °20.0989 °2-0.0752 °2-0.0112 °2--0.2348 °2
S-0.0003 Å °-0.0192 Å °-0.0102 Å °0.0207 Å °0.0098 Å °0.013 Å °-0.0179 Å °-0.0274 Å °-0.0089 Å °
Refinement TLS groupSelection details: all

+
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