[English] 日本語
Yorodumi
- PDB-3ha7: Crystal structure of HMA (MMAA4) from mycobacterium tuberculosis ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ha7
TitleCrystal structure of HMA (MMAA4) from mycobacterium tuberculosis complexed with S-adenosyl-N-decyl-aminoethyl (SADAE)
ComponentsMETHOXY MYCOLIC ACID SYNTHASE 4
KeywordsTRANSFERASE / S-ADENOSYLMETHIONINE-DEPENDENT METHYLTRANSFERASE FOLD / Methyltransferase
Function / homology
Function and homology information


mycolic acid biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / peptidoglycan-based cell wall / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / plasma membrane
Similarity search - Function
: / Mycolic acid cyclopropane synthase / : / Mycolic acid cyclopropane synthetase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-S-[2-(decylamino)ethyl]-5'-thioadenosine / Hydroxymycolate synthase MmaA4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 Å
AuthorsVaubourgeix, J. / Boissier, F. / Julien, S. / Mourey, L.
CitationJournal: To be Published
Title: SADAE, a potent bisubstrate inhibitor of mycobacterium tuberculosis mycolic acid methyltransferases
Authors: Vaubourgeix, J. / Bardou, F. / Boissier, F. / Julien, S. / Constant, P. / Ploux, O. / Daffe, M. / Quemard, A. / Mourey, L.
History
DepositionMay 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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: METHOXY MYCOLIC ACID SYNTHASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9882
Polymers36,5211
Non-polymers4671
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.429, 57.429, 205.079
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

-
Components

#1: Protein METHOXY MYCOLIC ACID SYNTHASE 4 / MMAA4 (METHYL MYCOLIC ACID SYNTHASE 4) (MMA4) (HYDROXY MYCOLIC ACID SYNTHASE)


Mass: 36521.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: mmaA4, MMAA4 (RV0642C), Rv0642c / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: Q79FX8, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-B32 / 5'-S-[2-(decylamino)ethyl]-5'-thioadenosine / S-adenosyl-N-decyl-aminoethyl (SADAE)


Mass: 466.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H38N6O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 4-28% PEG 3350, pH 5-9, VAPOR DIFFUSION, HANGING DROP, temperature 285K
PH range: 5-9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2007
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.35→18.96 Å / Num. all: 16765 / Num. obs: 16765 / % possible obs: 98.2 % / Redundancy: 4.4 % / Biso Wilson estimate: 60.2 Å2 / Rsym value: 0.046 / Net I/σ(I): 10.1
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2422 / Rsym value: 0.327 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2FK8

2fk8


Resolution: 2.35→18.96 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / SU B: 15.335 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24297 849 5.1 %RANDOM
Rwork0.21097 ---
obs0.21251 15905 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 76.932 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20.59 Å20 Å2
2--1.18 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.35→18.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 32 45 2158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222167
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.972939
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9975267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40823.43896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08915326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6541513
X-RAY DIFFRACTIONr_chiral_restr0.1060.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021653
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.2948
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21542
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3790.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6451.51390
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07922143
X-RAY DIFFRACTIONr_scbond_it1.7643907
X-RAY DIFFRACTIONr_scangle_it2.5994.5796
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 68 -
Rwork0.236 1139 -
obs--98.77 %
Refinement TLS params.Method: refined / Origin x: -32.2881 Å / Origin y: 5.9566 Å / Origin z: 16.9297 Å
111213212223313233
T-0.1571 Å20.0648 Å2-0.0352 Å2--0.1799 Å2-0.0016 Å2---0.2201 Å2
L3.1581 °2-1.5419 °20.3698 °2-4.1303 °2-0.7764 °2--5.0745 °2
S-0.2006 Å °0.1831 Å °0.4496 Å °0.0792 Å °0.1888 Å °-0.2439 Å °-0.4334 Å °-0.1045 Å °0.0119 Å °

+
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