[English] 日本語
Yorodumi
- PDB-6dko: Crystal structure of Mycobacterium tuberculosis malate synthase i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dko
TitleCrystal structure of Mycobacterium tuberculosis malate synthase in complex with 2,6-F-phenyldiketoacid
ComponentsMalate synthase G
KeywordsLYASE/LYASE inhibitor / Acetyltransferase / Structural Genomics / TB Structural Genomics Consortium / TBSGC / TRANSFERASE / TRANSFERASE-TRANSFERASE inhibitor complex / PSI-2 / Protein Structure Initiative / LYASE / LYASE-LYASE inhibitor complex
Function / homology
Function and homology information


host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / glyoxylate catabolic process / coenzyme A binding / adhesion of symbiont to host / coenzyme A metabolic process / glyoxylate cycle / fibronectin binding ...host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / glyoxylate catabolic process / coenzyme A binding / adhesion of symbiont to host / coenzyme A metabolic process / glyoxylate cycle / fibronectin binding / laminin binding / tricarboxylic acid cycle / peptidoglycan-based cell wall / magnesium ion binding / cell surface / protein homodimerization activity / extracellular region / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Malate synthase G / : / Malate synthase G, alpha-beta insertion domain / Malate synthase, domain III / Malate synthase, domain 3 / Malate Synthase G; Chain: A; Domain 4 / Malate synthase / Malate synthase superfamily / Malate synthase, C-terminal superfamily / Malate synthase, N-terminal and TIM-barrel domains ...Malate synthase G / : / Malate synthase G, alpha-beta insertion domain / Malate synthase, domain III / Malate synthase, domain 3 / Malate Synthase G; Chain: A; Domain 4 / Malate synthase / Malate synthase superfamily / Malate synthase, C-terminal superfamily / Malate synthase, N-terminal and TIM-barrel domains / : / : / Malate synthase, TIM barrel domain / Malate synthase, N-terminal domain / Malate synthase, C-terminal / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-(2,6-difluorophenyl)-2,4-dioxobutanoic acid / Malate synthase G / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.556 Å
AuthorsKrieger, I.V. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P01AI095208 United States
Citation
Journal: J Chem Inf Model / Year: 2018
Title: Anion-pi Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids.
Authors: Ellenbarger, J.F. / Krieger, I.V. / Huang, H.L. / Gomez-Coca, S. / Ioerger, T.R. / Sacchettini, J.C. / Wheeler, S.E. / Dunbar, K.R.
#1: Journal: Chem. Biol. / Year: 2012
Title: Structure-guided discovery of phenyl-diketo acids as potent inhibitors of M. tuberculosis malate synthase.
Authors: Krieger, I.V. / Freundlich, J.S. / Gawandi, V.B. / Roberts, J.P. / Sun, Q. / Owen, J.L. / Fraile, M.T. / Huss, S.I. / Lavandera, J.L. / Ioerger, T.R. / Sacchettini, J.C.
History
DepositionMay 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7585
Polymers80,4571
Non-polymers3014
Water9,548530
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-11 kcal/mol
Surface area26940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.016, 79.016, 225.961
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Malate synthase G


Mass: 80456.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: glcB / Production host: Escherichia coli (E. coli)
References: UniProt: A0A045ITM4, UniProt: P9WK17*PLUS, malate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GXG / 4-(2,6-difluorophenyl)-2,4-dioxobutanoic acid


Mass: 228.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H6F2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, TRIS-HCl, MgCl2 / PH range: 7.5-8.5

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 100848 / % possible obs: 97.6 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 7
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 3913 / % possible all: 76.5

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N8I

1n8i


Resolution: 1.556→37.294 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.59
RfactorNum. reflection% reflection
Rfree0.2228 4875 4.89 %
Rwork0.1928 --
obs0.1942 99671 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.556→37.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5475 0 19 530 6024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065683
X-RAY DIFFRACTIONf_angle_d0.8477743
X-RAY DIFFRACTIONf_dihedral_angle_d10.5984667
X-RAY DIFFRACTIONf_chiral_restr0.053883
X-RAY DIFFRACTIONf_plane_restr0.0061024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5562-1.57390.36711080.34711895X-RAY DIFFRACTION59
1.5739-1.59240.35821210.32812325X-RAY DIFFRACTION73
1.5924-1.61180.31421520.31882659X-RAY DIFFRACTION82
1.6118-1.63220.34481420.30692894X-RAY DIFFRACTION91
1.6322-1.65370.31771680.29723030X-RAY DIFFRACTION94
1.6537-1.67640.32491620.28683149X-RAY DIFFRACTION97
1.6764-1.70030.30131610.26813197X-RAY DIFFRACTION99
1.7003-1.72570.30531500.25913256X-RAY DIFFRACTION100
1.7257-1.75270.27941510.25623245X-RAY DIFFRACTION100
1.7527-1.78140.27991590.24963234X-RAY DIFFRACTION100
1.7814-1.81210.29821500.26923252X-RAY DIFFRACTION100
1.8121-1.84510.27441460.24423238X-RAY DIFFRACTION100
1.8451-1.88060.26241810.23853287X-RAY DIFFRACTION100
1.8806-1.91890.27291590.22653222X-RAY DIFFRACTION100
1.9189-1.96070.27871820.22073243X-RAY DIFFRACTION100
1.9607-2.00630.27151750.22013245X-RAY DIFFRACTION100
2.0063-2.05640.24281850.21343218X-RAY DIFFRACTION100
2.0564-2.1120.27981680.21753261X-RAY DIFFRACTION100
2.112-2.17420.25971620.21213277X-RAY DIFFRACTION100
2.1742-2.24430.25721600.21073285X-RAY DIFFRACTION100
2.2443-2.32450.23821520.19623301X-RAY DIFFRACTION100
2.3245-2.41760.23981740.19723242X-RAY DIFFRACTION100
2.4176-2.52760.21791830.19643278X-RAY DIFFRACTION100
2.5276-2.66080.25591680.19253306X-RAY DIFFRACTION100
2.6608-2.82750.20041700.19743295X-RAY DIFFRACTION100
2.8275-3.04570.22571790.19783317X-RAY DIFFRACTION100
3.0457-3.3520.23651900.193294X-RAY DIFFRACTION100
3.352-3.83660.19481710.17353362X-RAY DIFFRACTION100
3.8366-4.83210.17031680.14543400X-RAY DIFFRACTION99
4.8321-37.30430.17081780.16443589X-RAY DIFFRACTION99

+
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