[English] 日本語
Yorodumi
- PDB-3lap: The Structure of the Intermediate Complex of the Arginine Repress... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lap
TitleThe Structure of the Intermediate Complex of the Arginine Repressor from Mycobacterium tuberculosis Bound to its DNA Operator and L-canavanine.
Components
  • 5'-D(*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*A)-3'
  • 5'-D(*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*A)-3'
  • Arginine repressor
KeywordsTRANSCRIPTION REGULATOR/DNA / Mycobacterium tuberculosis / arginine repressor / DNA binding / ArgR-DNA-canavanine ternary complex / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB / Amino-acid biosynthesis / Arginine biosynthesis / Cytoplasm / DNA-binding / Repressor / Transcription / Transcription regulation / TRANSCRIPTION REGULATOR / TRANSCRIPTION REGULATOR-DNA complex
Function / homology
Function and homology information


arginine biosynthetic process / arginine binding / protein complex oligomerization / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Gyrase A; domain 2 - #40 / Gyrase A; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Gyrase A; domain 2 - #40 / Gyrase A; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
L-CANAVANINE / DNA / DNA (> 10) / Arginine repressor / Arginine repressor
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCherney, L.T. / Cherney, M.M. / Garen, C.R. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: crystal structure of the intermediate complex of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator reveals detailed mechanism of arginine repression.
Authors: Cherney, L.T. / Cherney, M.M. / Garen, C.R. / James, M.N.
History
DepositionJan 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Arginine repressor
B: Arginine repressor
C: Arginine repressor
D: Arginine repressor
E: Arginine repressor
F: Arginine repressor
G: 5'-D(*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*A)-3'
H: 5'-D(*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*A)-3'
I: 5'-D(*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*A)-3'
J: 5'-D(*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*A)-3'
K: 5'-D(*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*A)-3'
L: 5'-D(*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,40926
Polymers133,58312
Non-polymers1,82614
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30500 Å2
ΔGint-248 kcal/mol
Surface area45660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.750, 106.532, 117.752
Angle α, β, γ (deg.)90.00, 121.40, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
33
14
24
34
15
25
35

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain F and (resseq 17:170 )
211chain E and (resseq 17:170 )
311chain D and (resseq 17:170 )
112chain B and (resseq 90:170 )
212chain A and (resseq 90:170 )
312chain C and (resseq 90:170 )
113chain A and (resseq 15:82 )
213chain B and (resseq 15:82 )
313chain C and (resseq 15:82 )
114chain G and (resseq 1:16 )
214chain I and (resseq 1:16 )
314chain K and (resseq 1:16 )
115chain H and (resseq 1:16 )
215chain J and (resseq 1:16 )
315chain L and (resseq 1:16 )

NCS ensembles :
ID
1
2
3
4
5

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Arginine repressor


Mass: 17366.635 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: ahrC, argR, MT1695, MTCY06H11.22, Rv1657 / Plasmid: PGST-1657 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P0A4Y8, UniProt: P9WPY9*PLUS

-
DNA chain , 2 types, 6 molecules GIKHJL

#2: DNA chain 5'-D(*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*A)-3'


Mass: 4906.217 Da / Num. of mol.: 3 / Fragment: ARG box DNA segment, strand G / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*A)-3'


Mass: 4888.189 Da / Num. of mol.: 3 / Fragment: ARG box DNA segment, strand H / Source method: obtained synthetically

-
Non-polymers , 3 types, 686 molecules

#4: Chemical
ChemComp-GGB / L-CANAVANINE / L-2-AMINO-4-(GUANIDINOOXY)BUTYRIC ACID / Canavanine


Type: L-peptide linking / Mass: 176.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H12N4O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1M ammonium sulfate, 100 mM bis-tris buffer, 1% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 105420 / Num. obs: 96776 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 11.5
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.433 / % possible all: 95.1

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→39.004 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 20.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2049 4830 4.99 %
Rwork0.1844 --
obs0.1855 96750 91.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.759 Å2 / ksol: 0.36 e/Å3
Refinement stepCycle: LAST / Resolution: 2.15→39.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 1950 112 672 9292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088968
X-RAY DIFFRACTIONf_angle_d1.36612581
X-RAY DIFFRACTIONf_dihedral_angle_d22.6643445
X-RAY DIFFRACTIONf_chiral_restr0.0641489
X-RAY DIFFRACTIONf_plane_restr0.0071331
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11F1124X-RAY DIFFRACTIONPOSITIONAL
12E1124X-RAY DIFFRACTIONPOSITIONAL0.048
13D1100X-RAY DIFFRACTIONPOSITIONAL0.062
21B590X-RAY DIFFRACTIONPOSITIONAL
22A590X-RAY DIFFRACTIONPOSITIONAL0.075
23C590X-RAY DIFFRACTIONPOSITIONAL0.09
31A492X-RAY DIFFRACTIONPOSITIONAL
32B492X-RAY DIFFRACTIONPOSITIONAL0.06
33C492X-RAY DIFFRACTIONPOSITIONAL0.061
41G326X-RAY DIFFRACTIONPOSITIONAL
42I326X-RAY DIFFRACTIONPOSITIONAL0.019
43K326X-RAY DIFFRACTIONPOSITIONAL0.022
51H324X-RAY DIFFRACTIONPOSITIONAL
52J324X-RAY DIFFRACTIONPOSITIONAL0.021
53L324X-RAY DIFFRACTIONPOSITIONAL0.021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1503-2.17470.26911630.2492972X-RAY DIFFRACTION88
2.1747-2.20030.27581510.26553123X-RAY DIFFRACTION95
2.2003-2.22720.29351610.24583172X-RAY DIFFRACTION95
2.2272-2.25530.28661680.24353150X-RAY DIFFRACTION94
2.2553-2.2850.24351800.22673109X-RAY DIFFRACTION95
2.285-2.31630.22841580.21653180X-RAY DIFFRACTION94
2.3163-2.34940.23731710.21423123X-RAY DIFFRACTION94
2.3494-2.38450.28481580.20723122X-RAY DIFFRACTION94
2.3845-2.42170.24631700.21433178X-RAY DIFFRACTION94
2.4217-2.46140.27081530.20493128X-RAY DIFFRACTION94
2.4614-2.50390.22181500.21053090X-RAY DIFFRACTION94
2.5039-2.54940.24111670.20943134X-RAY DIFFRACTION94
2.5494-2.59840.24981640.20643169X-RAY DIFFRACTION93
2.5984-2.65140.23531840.20383038X-RAY DIFFRACTION93
2.6514-2.70910.21291600.18423085X-RAY DIFFRACTION93
2.7091-2.77210.2311640.18933120X-RAY DIFFRACTION93
2.7721-2.84140.18581800.18973061X-RAY DIFFRACTION92
2.8414-2.91820.24381520.18963076X-RAY DIFFRACTION92
2.9182-3.0040.24451590.18983084X-RAY DIFFRACTION92
3.004-3.10090.20081630.19643087X-RAY DIFFRACTION92
3.1009-3.21170.17671580.17642996X-RAY DIFFRACTION90
3.2117-3.34020.2051600.18063034X-RAY DIFFRACTION90
3.3402-3.49220.18251490.17033016X-RAY DIFFRACTION90
3.4922-3.67620.18531600.15893053X-RAY DIFFRACTION90
3.6762-3.90630.15411530.15832955X-RAY DIFFRACTION89
3.9063-4.20760.19061460.15323022X-RAY DIFFRACTION89
4.2076-4.63040.13261410.1412956X-RAY DIFFRACTION88
4.6304-5.2990.19541830.1612939X-RAY DIFFRACTION88
5.299-6.67070.19441410.17992923X-RAY DIFFRACTION86
6.6707-39.01030.17721630.1642825X-RAY DIFFRACTION82

+
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