[English] 日本語
Yorodumi
- PDB-3f51: Crystal Structure of the clp gene regulator ClgR from Corynebacte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f51
TitleCrystal Structure of the clp gene regulator ClgR from Corynebacterium glutamicum
ComponentsClp gene regulator (ClgR)
KeywordsTRANSCRIPTION ACTIVATOR / gene regulator / helix-turn-helix / transcriptional activator / human pathogen
Function / homology
Function and homology information


DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription
Similarity search - Function
Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Predicted transcriptional regulators
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsRusso, S. / Schweitzer, J.E. / Polen, T. / Bott, M. / Pohl, E.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structure of the caseinolytic protease gene regulator, a transcriptional activator in actinomycetes
Authors: Russo, S. / Schweitzer, J.E. / Polen, T. / Bott, M. / Pohl, E.
History
DepositionNov 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3May 30, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_assembly_gen / pdbx_struct_oper_list
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Clp gene regulator (ClgR)
B: Clp gene regulator (ClgR)
C: Clp gene regulator (ClgR)
D: Clp gene regulator (ClgR)
E: Clp gene regulator (ClgR)
F: Clp gene regulator (ClgR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,29810
Polymers75,8846
Non-polymers4144
Water3,387188
1
A: Clp gene regulator (ClgR)
E: Clp gene regulator (ClgR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4724
Polymers25,2952
Non-polymers1772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-26 kcal/mol
Surface area10320 Å2
MethodPISA
2
B: Clp gene regulator (ClgR)
C: Clp gene regulator (ClgR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4133
Polymers25,2952
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-27 kcal/mol
Surface area9970 Å2
MethodPISA
3
D: Clp gene regulator (ClgR)
F: Clp gene regulator (ClgR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4133
Polymers25,2952
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-25 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.440, 84.820, 71.430
Angle α, β, γ (deg.)90.00, 95.87, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Clp gene regulator (ClgR)


Mass: 12647.396 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg2152, Cgl1962, Clg1962 / Plasmid: pEKEx1 / Production host: Escherichia coli (E. coli) / Strain (production host): BB1553 / References: UniProt: Q8NP59
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.652.67
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, sitting drop4.60.1 M sodium chloride, 23% 2-methyl-2,4-pentanediol, 15% glycerol, 0.085 M sodium acetate , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
2982vapor diffusion, sitting drop4.60.0085 M cobalt chloride, 0.85 M 1,6-hexanediol, 15% glycerol, 0.085 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11
SYNCHROTRONSLS X06SA20.9790,0.9793,0.9717
DetectorType: PHILLIPS / Detector: PIXEL / Date: Nov 9, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1sagitally focused Si (111),bending mirror for vertical focusing, spot size 80x20umSINGLE WAVELENGTHMx-ray1
2sagitally focused Si (111),bending mirror for vertical focusing, spot size 50x20umMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791
30.97931
40.97171
ReflectionResolution: 2.05→46 Å / Num. all: 48793 / Num. obs: 48625 / % possible obs: 99.7 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Rsym value: 0.052 / Net I/σ(I): 16
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 6411 / Rsym value: 0.699 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
RemDAqdata collection
SHARPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.05→45.74 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.732 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 1.7 / σ(I): 3 / ESU R: 0.17 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23801 2432 5 %RANDOM
Rwork0.21234 ---
obs0.21359 46193 100 %-
all-46193 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.438 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-1.89 Å2
2---0.44 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4073 0 4 212 4289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214145
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9955617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5995557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55722.956159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85615682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7811542
X-RAY DIFFRACTIONr_chiral_restr0.0950.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023060
X-RAY DIFFRACTIONr_nbd_refined0.2210.22074
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22985
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2161
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.222
X-RAY DIFFRACTIONr_mcbond_it1.0441.52848
X-RAY DIFFRACTIONr_mcangle_it1.65824333
X-RAY DIFFRACTIONr_scbond_it3.1331442
X-RAY DIFFRACTIONr_scangle_it5.0284.51281
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 179 -
Rwork0.291 3399 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8967-1.40770.42642.7723-1.17590.6590.121-0.2307-0.09050.0546-0.0733-0.35670.02270.2381-0.0477-0.0489-0.0563-0.0198-0.14240.0312-0.0955-20.8535-44.0699-40.3366
26.095-3.15993.90081.7461-1.91922.59490.19890.1288-0.5402-0.1047-0.0347-0.19880.48270.3831-0.16420.0127-0.0145-0.01060.1760.05210.19463.3976-67.9288-26.2153
35.92223.65143.51652.25142.16822.08810.3681-1.0277-0.38340.3982-0.1542-0.12130.11630.1156-0.2139-0.0748-0.133-0.10720.33120.19390.037-9.059-64.5787-11.3955
42.58622.29760.7463.25280.99013.1321-0.0973-0.29310.2926-0.02670.1624-0.1033-0.1517-0.277-0.0651-0.08440.0625-0.0135-0.1382-0.16080.02121.5498-43.9644-2.4444
50.40930.01830.11310.8005-1.72664.0173-0.04710.14090.0443-0.011-0.01690.1124-0.1143-0.24070.064-0.0922-0.00690.0034-0.17450.009-0.1197-34.2149-58.0358-35.4438
60.1404-0.16710.50730.2078-0.46264.06450.021-0.103-0.1370.19940.0042-0.15220.13530.0174-0.0253-0.0128-0.0024-0.0136-0.075-0.065-0.0701-32.171-63.0466-71.6366
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 113
2X-RAY DIFFRACTION2B19 - 111
3X-RAY DIFFRACTION3C23 - 111
4X-RAY DIFFRACTION4D21 - 111
5X-RAY DIFFRACTION5E20 - 111
6X-RAY DIFFRACTION6F22 - 111

+
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