[English] 日本語
Yorodumi
- PDB-6k2j: Crystal Structure of the DNA Complex of C. crescentus GapR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6k2j
TitleCrystal Structure of the DNA Complex of C. crescentus GapR
Components
  • 10A DNA_front
  • 10A DNA_reverse
  • UPF0335 protein CCNA_03428
KeywordsDNA BINDING PROTEIN/DNA / C. crescentus / GapR/DNA / NAPs / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homologyGapR-like / GapR-like, DNA-binding domain / GapR-like, DNA-binding domain / DNA binding / DNA / DNA (> 10) / UPF0335 protein CCNA_03428
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
Caulobacter crescentus NA1000 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsXia, B. / Huang, Q.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: GapR binds DNA through dynamic opening of its tetrameric interface.
Authors: Huang, Q. / Duan, B. / Dong, X. / Fan, S. / Xia, B.
History
DepositionMay 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UPF0335 protein CCNA_03428
B: UPF0335 protein CCNA_03428
C: UPF0335 protein CCNA_03428
D: UPF0335 protein CCNA_03428
E: 10A DNA_front
F: 10A DNA_reverse


Theoretical massNumber of molelcules
Total (without water)54,5776
Polymers54,5776
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint-100 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.310, 65.310, 274.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein
UPF0335 protein CCNA_03428 / GapR (growth-associated A/T-binding protein involved in regulation)


Mass: 11195.754 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (strain NA1000 / CB15N) (bacteria)
Strain: NA1000 / CB15N / Gene: CCNA_03428 / Variant: NA1000 / Production host: Escherichia coli (E. coli) / References: UniProt: B8H4R9
#2: DNA chain 10A DNA_front


Mass: 4902.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caulobacter crescentus NA1000 (bacteria)
#3: DNA chain 10A DNA_reverse


Mass: 4892.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caulobacter crescentus NA1000 (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 3.09 Å3/Da / Density % sol: 65.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.005M Manganese(II) chloride tetrahydrate 0.05M Sodium citrate PH 5.6 1.25M 1,6-Hexanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→48.1 Å / Num. obs: 25730 / % possible obs: 87.7 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 40
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.01 / Num. unique obs: 24904

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-20007-16data reduction
HKL-20007-16data scaling
PHENIX(1.11.1_2575: ???)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→48.098 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 2.1 / Phase error: 28.76
RfactorNum. reflection% reflection
Rfree0.268 1266 4.92 %
Rwork0.2207 --
obs0.2242 25730 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2668 612 0 204 3484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043382
X-RAY DIFFRACTIONf_angle_d0.6774652
X-RAY DIFFRACTIONf_dihedral_angle_d22.4141996
X-RAY DIFFRACTIONf_chiral_restr0.041524
X-RAY DIFFRACTIONf_plane_restr0.004496
LS refinement shellResolution: 2.4→2.44 Å
RfactorNum. reflection% reflection
Rfree0.2929 --
Rwork0.2349 --
obs-1269 99 %
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)
12.93081.3226-2.1011.3349-1.6412.34060.11280.0420.8473-0.29530.32310.0964-0.69780.3908-0.39960.7722-0.31610.09560.4077-0.04620.542920.300634.0225117.2172
2-0.05940.02941.02420.40653.37247.30350.015-0.097-0.01810.0633-0.0027-0.1489-0.1013-0.08230.00660.4239-0.0721-0.02360.34580.00730.23359.634610.1568108.5793
34.06451.6442-2.642.6989-1.20584.869-0.21910.40260.3729-0.73840.44330.0999-0.78910.0335-0.32970.7362-0.1621-0.01530.3326-0.0410.321713.239626.4623115.1547
42.05392.64510.63983.11962.48475.3237-0.32380.1471-0.3928-0.3064-0.15080.44770.2026-0.45330.49920.2915-0.0086-0.01360.3492-0.11920.373933.099344.1284130.0641
55.97381.94013.8661.26821.30824.67840.2370.159-0.15430.27510.1791-0.25820.7791.3366-0.46120.39910.21320.04490.8023-0.0930.35939.66460.6988111.0165
61.124-0.2617-3.34580.14781.02227.8523-0.2958-0.09-0.11610.0109-0.15880.06110.12990.58960.36850.26410.0490.05140.39510.0250.224313.24653.5077121.0983
72.9717-0.44550.61421.9870.38452.74710.1644-1.0965-0.34560.43630.2015-0.14720.42520.2831-0.26790.38030.03330.05690.6664-0.00620.232629.3708-1.9001113.3197
83.37551.1139-1.79790.73011.20498.22480.0184-0.55020.15990.10140.00880.312-0.06590.09770.0170.22840.04160.05380.3218-0.01410.331854.75936.736398.3032
95.1572-0.35970.63993.93950.81513.88440.30120.3435-1.4124-0.21880.41540.03960.61690.5683-0.74230.52340.0088-0.07440.4843-0.17331.099828.760215.2401113.7876
103.4036-0.702-2.77561.4916-0.55912.98790.47150.6984-0.2727-0.20120.78730.08840.2964-1.0097-1.24540.5453-0.06920.01620.9033-0.12320.915427.855917.6207112.4322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 92 )
3X-RAY DIFFRACTION3chain 'B' and (resid 14 through 54 )
4X-RAY DIFFRACTION4chain 'B' and (resid 55 through 96 )
5X-RAY DIFFRACTION5chain 'C' and (resid 13 through 51 )
6X-RAY DIFFRACTION6chain 'C' and (resid 52 through 94 )
7X-RAY DIFFRACTION7chain 'D' and (resid 14 through 54 )
8X-RAY DIFFRACTION8chain 'D' and (resid 55 through 96 )
9X-RAY DIFFRACTION9chain 'E' and (resid 1 through 15 )
10X-RAY DIFFRACTION10chain 'F' and (resid 2 through 16 )

+
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