[English] 日本語
Yorodumi
- PDB-6a2r: Mycobacterium tuberculosis LexA C-domain II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6a2r
TitleMycobacterium tuberculosis LexA C-domain II
ComponentsLexA repressor
KeywordsHYDROLASE / Mycobacterium tuberculosis / LexA / SOS response
Function / homology
Function and homology information


repressor LexA / SOS response / peptidoglycan-based cell wall / DNA replication / response to antibiotic / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / proteolysis / DNA binding
Similarity search - Function
LexA repressor, DNA-binding domain / Transcription regulator LexA / LexA DNA binding domain / Peptidase S24, LexA-like / Umud Fragment, subunit A / Umud Fragment, subunit A / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily ...LexA repressor, DNA-binding domain / Transcription regulator LexA / LexA DNA binding domain / Peptidase S24, LexA-like / Umud Fragment, subunit A / Umud Fragment, subunit A / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Ribbon / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / LexA repressor
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsChandran, A.V. / Srikalaivani, R. / Paul, A. / Vijayan, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Biochemical characterization of Mycobacterium tuberculosis LexA and structural studies of its C-terminal segment.
Authors: Chandran, A.V. / Srikalaivani, R. / Paul, A. / Vijayan, M.
History
DepositionJun 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2024Group: 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: LexA repressor
B: LexA repressor
C: LexA repressor
D: LexA repressor
E: LexA repressor
F: LexA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4128
Polymers71,2006
Non-polymers2122
Water4,288238
1
A: LexA repressor
B: LexA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8393
Polymers23,7332
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: LexA repressor
D: LexA repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8393
Polymers23,7332
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: LexA repressor
F: LexA repressor


Theoretical massNumber of molelcules
Total (without water)23,7332
Polymers23,7332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.830, 74.830, 116.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A137 - 236
2111B137 - 236
3111C137 - 236
4111D137 - 236
5111E137 - 236
6111F137 - 236

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.488463, -0.872581, 0.002655), (-0.871818, 0.488159, 0.040417), (-0.036564, 0.017427, -0.999179)37.07896, 20.35428, 77.63329
3given(0.427875, 0.903548, 0.02289), (-0.902508, 0.428482, -0.043384), (-0.049008, -0.002095, 0.998796)-1.14836, 45.06108, -10.30692
4given(0.545508, -0.838102, -0.002422), (-0.838073, -0.54551, 0.007224), (-0.007375, -0.001911, -0.999971)-0.0354, 42.55035, 88.7055
5given(0.792365, -0.609465, -0.026651), (0.605314, 0.790898, -0.089865), (0.075848, 0.055074, 0.995597)42.86791, 53.48342, -12.17229
6given(-0.922139, -0.385654, 0.030499), (-0.386332, 0.922129, -0.020624), (-0.02017, -0.030801, -0.999322)-27.40369, 10.54084, 92.1995

-
Components

#1: Protein
LexA repressor


Mass: 11866.654 Da / Num. of mol.: 6 / Fragment: LexA C-domain II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: lexA, Rv2720, MTCY05A6.41 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P9WHR7, repressor LexA
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.63 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 8.5
Details: 100mM Tris-Hcl, 200mM megnesium chloride, 5% glycerol, 25%PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54179 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.525
11-h,-k,l20.475
ReflectionResolution: 2.25→43.22 Å / Num. obs: 34497 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.986 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.09 / Net I/σ(I): 8.9
Reflection shellResolution: 2.25→2.37 Å / Rmerge(I) obs: 0.912 / Mean I/σ(I) obs: 8.9 / Num. unique obs: 5017 / CC1/2: 0.462 / Rpim(I) all: 0.401 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IUMU

Resolution: 2.25→37.41 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.893 / SU B: 3.298 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23822 1653 4.8 %RANDOM
Rwork0.21832 ---
obs0.21932 32811 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.912 Å2
Baniso -1Baniso -2Baniso -3
1-6.2 Å20 Å20 Å2
2--6.2 Å20 Å2
3----12.4 Å2
Refinement stepCycle: 1 / Resolution: 2.25→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 14 238 4728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0154571
X-RAY DIFFRACTIONr_bond_other_d0.0040.0174367
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.7556216
X-RAY DIFFRACTIONr_angle_other_deg0.6411.72210163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8925589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.40519.844128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73515627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4481522
X-RAY DIFFRACTIONr_chiral_restr0.0580.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215093
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02779
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5212.5482373
X-RAY DIFFRACTIONr_mcbond_other2.5212.5482374
X-RAY DIFFRACTIONr_mcangle_it3.6093.8112956
X-RAY DIFFRACTIONr_mcangle_other3.6093.8112957
X-RAY DIFFRACTIONr_scbond_it2.6212.7742198
X-RAY DIFFRACTIONr_scbond_other2.6212.7742198
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8224.0793261
X-RAY DIFFRACTIONr_long_range_B_refined5.89931.4174621
X-RAY DIFFRACTIONr_long_range_B_other5.89931.424622
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1411 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Auth asym-IDRms dev position (Å)
A5.05
B7.16
C5.46
D4.59
E6.6
F5.83
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 98 -
Rwork0.333 2420 -
obs--99.96 %

+
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