[English] 日本語
Yorodumi
- PDB-3by6: Crystal structure of a transcriptional regulator from Oenococcus oeni -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3by6
TitleCrystal structure of a transcriptional regulator from Oenococcus oeni
ComponentsPredicted transcriptional regulator
KeywordsTRANSCRIPTION REGULATOR / Transcriptional regulator / structural genomics / PSI-2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / DNA-binding / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Helix Hairpins - #100 / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Helix Hairpins - #100 / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator, GntR family
Similarity search - Component
Biological speciesOenococcus oeni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhang, R. / Volkart, L. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a transcriptional regulator from Oenococcus oeni.
Authors: Zhang, R. / Volkart, L. / Gu, M. / Joachimiak, A.
History
DepositionJan 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: 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: Predicted transcriptional regulator
B: Predicted transcriptional regulator
C: Predicted transcriptional regulator
D: Predicted transcriptional regulator
E: Predicted transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2858
Polymers69,1645
Non-polymers1203
Water2,594144
1
A: Predicted transcriptional regulator
D: Predicted transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7063
Polymers27,6662
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
MethodPISA
2
B: Predicted transcriptional regulator
hetero molecules

E: Predicted transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)27,7063
Polymers27,6662
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area3900 Å2
MethodPISA
3
C: Predicted transcriptional regulator
hetero molecules

C: Predicted transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7464
Polymers27,6662
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.434, 103.893, 131.393
Angle α, β, γ (deg.)90.00, 102.85, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Predicted transcriptional regulator


Mass: 13832.881 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oenococcus oeni (bacteria) / Strain: PSU-1 / Gene: GI:116491763, OEOE_1803 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q04D30
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 4.01 Å3/Da / Density % sol: 69.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M NaCl, 0.1M Tris-HCl, 30% PEG 3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2007 / Details: Mirrors
RadiationMonochromator: Si(111) channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 2.2→64.02 Å / Num. all: 52664 / Num. obs: 51521 / % possible obs: 97.83 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.48
Reflection shellResolution: 2.2→2.257 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 4.26 / Num. unique all: 4108 / % possible all: 87.17

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→41.78 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / SU B: 13.781 / SU ML: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.207 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27786 2778 5.1 %RANDOM
Rwork0.23875 ---
obs0.24076 51521 97.83 %-
all-51521 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.602 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å20 Å2-2.82 Å2
2--0.61 Å20 Å2
3----4.79 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 3 144 4777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224658
X-RAY DIFFRACTIONr_bond_other_d0.0020.023209
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9846280
X-RAY DIFFRACTIONr_angle_other_deg0.98737950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0085597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52426.042192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40315935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.061530
X-RAY DIFFRACTIONr_chiral_restr0.0870.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025055
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02767
X-RAY DIFFRACTIONr_nbd_refined0.2280.21121
X-RAY DIFFRACTIONr_nbd_other0.1810.23133
X-RAY DIFFRACTIONr_nbtor_refined0.170.22352
X-RAY DIFFRACTIONr_nbtor_other0.0890.22378
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2161
X-RAY DIFFRACTIONr_metal_ion_refined0.5470.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.25
X-RAY DIFFRACTIONr_mcbond_it0.8891.53162
X-RAY DIFFRACTIONr_mcbond_other0.161.51214
X-RAY DIFFRACTIONr_mcangle_it1.44224853
X-RAY DIFFRACTIONr_scbond_it2.11331739
X-RAY DIFFRACTIONr_scangle_it3.3674.51427
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 169 -
Rwork0.289 3412 -
obs-3581 87.17 %
Refinement TLS params.Method: refined / Origin x: 20.836 Å / Origin y: 58.894 Å / Origin z: 26.856 Å
111213212223313233
T0.0626 Å2-0.0305 Å2-0.0741 Å2-0.0554 Å20.006 Å2---0.1045 Å2
L0.1834 °2-0.1054 °20.3037 °2-0.1857 °20.0138 °2--0.7867 °2
S-0.0732 Å °0.0687 Å °0.0285 Å °0.0272 Å °0.0131 Å °0.0567 Å °-0.0207 Å °0.1967 Å °0.0601 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 402 - 43
2X-RAY DIFFRACTION1AA41 - 8044 - 83
3X-RAY DIFFRACTION1AA81 - 11784 - 120
4X-RAY DIFFRACTION1BB0 - 403 - 43
5X-RAY DIFFRACTION1BB41 - 8044 - 83
6X-RAY DIFFRACTION1BB81 - 11784 - 120
7X-RAY DIFFRACTION1CC0 - 403 - 43
8X-RAY DIFFRACTION1CC41 - 8044 - 83
9X-RAY DIFFRACTION1CC81 - 11784 - 120
10X-RAY DIFFRACTION1DD0 - 403 - 43
11X-RAY DIFFRACTION1DD41 - 8044 - 83
12X-RAY DIFFRACTION1DD81 - 11784 - 120
13X-RAY DIFFRACTION1EE-1 - 402 - 43
14X-RAY DIFFRACTION1EE41 - 8044 - 83
15X-RAY DIFFRACTION1EE81 - 11984 - 122

+
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