[English] 日本語
Yorodumi
- PDB-3op9: Crystal structure of transcriptional regulator from Listeria innocua -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3op9
TitleCrystal structure of transcriptional regulator from Listeria innocua
ComponentsPli0006 protein
KeywordsTRANSCRIPTION REGULATOR / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Helix-turn-helix / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Helix-turn-helix / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.898 Å
AuthorsMichalska, K. / Li, H. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of transcriptional regulator from Listeria innocua
Authors: Michalska, K. / Li, H. / Gu, M. / Joachimiak, A.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pli0006 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4312
Polymers13,3961
Non-polymers351
Water1,15364
1
A: Pli0006 protein
hetero molecules

A: Pli0006 protein
hetero molecules

A: Pli0006 protein
hetero molecules

A: Pli0006 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7268
Polymers53,5844
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation15_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area13320 Å2
ΔGint-106 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.12, 71.12, 122.13
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-144-

HOH

DetailsAUTHOR DETERMINED BIOLOGICAL ASSEMBLY: UNKNOWN

-
Components

#1: Protein Pli0006 protein


Mass: 13395.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Strain: Clip11262 / Gene: pli0006 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q926P6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M K/Na tartrate, 0.1 M Tris/HCl, 0.2 M Li2SO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97967 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 29, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97967 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 12741 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 38.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 4 / Num. unique all: 639 / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.898→26.098 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 956 7.51 %random
Rwork0.1867 ---
obs0.1894 12735 99.58 %-
all-12735 --
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.313 Å2 / ksol: 0.454 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.046 Å20 Å20 Å2
2--0.046 Å2-0 Å2
3----0.0921 Å2
Refinement stepCycle: LAST / Resolution: 1.898→26.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms885 0 1 64 950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011941
X-RAY DIFFRACTIONf_angle_d1.1681277
X-RAY DIFFRACTIONf_dihedral_angle_d15.345359
X-RAY DIFFRACTIONf_chiral_restr0.074146
X-RAY DIFFRACTIONf_plane_restr0.005162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8984-1.99850.26621340.22511653X-RAY DIFFRACTION100
1.9985-2.12360.21921480.19391638X-RAY DIFFRACTION100
2.1236-2.28750.24421350.17971673X-RAY DIFFRACTION100
2.2875-2.51760.1971220.17681672X-RAY DIFFRACTION100
2.5176-2.88150.22191250.19551693X-RAY DIFFRACTION100
2.8815-3.62880.24291380.19081701X-RAY DIFFRACTION100
3.6288-26.10080.20911540.17911749X-RAY DIFFRACTION97
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)
14.05231.40271.10975.10290.75080.98820.1546-0.54150.14030.6145-0.3010.1431-0.1076-0.20680.11450.2704-0.0025-0.03830.22270.0360.200627.685416.686244.2144
23.5381-1.12490.28063.8591-1.0880.4107-0.3311-0.01560.42480.65140.43010.2811-0.27270.0363-0.08910.32810.11250.14370.25220.11140.345521.170823.667441.2615
32.4242-0.11282.24322.983-0.76186.8243-0.18240.1031-0.1717-0.37330.1319-0.0095-0.4143-0.6097-0.05250.2171-0.0131-0.01520.25090.04850.207629.167218.558332.6852
40.88020.09130.11532.1793-0.45020.28270.0545-0.0083-0.4112-0.2592-0.0006-0.38530.96330.20170.1120.404-0.0113-0.03040.19970.02740.227426.94335.49834.8059
51.3247-0.66260.70721.4434-0.73850.70930.08270.1689-0.20140.17680.128-0.0036-0.1092-0.1007-0.13130.21710.0099-0.02660.2639-0.0010.142435.5787-0.516412.0208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:26)
2X-RAY DIFFRACTION2(chain A and resid 27:45)
3X-RAY DIFFRACTION3(chain A and resid 46:59)
4X-RAY DIFFRACTION4(chain A and resid 60:71)
5X-RAY DIFFRACTION5(chain A and resid 74:111)

+
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://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