[English] 日本語
Yorodumi
- PDB-1qrv: CRYSTAL STRUCTURE OF THE COMPLEX OF HMG-D AND DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qrv
TitleCRYSTAL STRUCTURE OF THE COMPLEX OF HMG-D AND DNA
Components
  • DNA (5'-D(*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3')
  • HIGH MOBILITY GROUP PROTEIN DHigh-mobility group
KeywordsGENE REGULATION/DNA / PROTEIN-DNA COMPLEX / HMG DOMAIN / NON-SEQUENCE SPECIFIC CHROMOSOMAL PROTEIN HMG-D / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / chromatin organization / transcription cis-regulatory region binding / chromatin / DNA binding / nucleus
Similarity search - Function
High mobility group box domain / DNA Binding (I), subunit A / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / High mobility group protein D
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsMurphy IV, F.V. / Sweet, R.M. / Churchill, M.E.A.
CitationJournal: EMBO J. / Year: 1999
Title: The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition.
Authors: Murphy IV, F.V. / Sweet, R.M. / Churchill, M.E.
History
DepositionJun 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
C: DNA (5'-D(*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3')
D: DNA (5'-D(*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3')
A: HIGH MOBILITY GROUP PROTEIN D
B: HIGH MOBILITY GROUP PROTEIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8545
Polymers22,8314
Non-polymers231
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.740, 53.797, 86.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

-
Components

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


Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein HIGH MOBILITY GROUP PROTEIN D / High-mobility group / HMG-D


Mass: 8370.515 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: PET13A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: Q05783
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.85
Details: PEG 3350, TRIZMA-CL, NACL, pH 7.85, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 3350,11
2TRIZMA-CL11
3NACLSodium chloride11
4PEG 3350,12
5TRIZMA-CL12
6NACLSodium chloride12
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion / Details: Murphy, F.V., (1999) Acta Crystallogr. D55, 1594.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mMprotein solution1drop
223 %PEG40001reservoir
310 mMHEPES1reservoir
41
51
61

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)Wavelength
SYNCHROTRONNSLS X12C10.9000,0.9211,0.92157,1.05
ROTATING ANODERIGAKU RU30021.54181.5418
Detector
TypeIDDetectorDate
BRANDEIS - B41CCDAug 15, 1998
RIGAKU RAXIS IIC2IMAGE PLATEJul 2, 1996
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.92111
30.921571
41.051
51.54181
ReflectionResolution: 2.2→20 Å / Num. all: 10672 / Num. obs: 10672 / % possible obs: 98 % / Observed criterion σ(F): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 24.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.198 / % possible all: 97.9
Reflection
*PLUS
Num. measured all: 94446
Reflection shell
*PLUS
% possible obs: 97.9 %

-
Processing

Software
NameVersionClassification
SOLVEphasing
SHARPphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 931772.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: PROTEIN: ENGH & HUBER, DNA: PARKINSON ET AL.
Details: USED CROSS VALIDATED MAXIMUM LIKELIHOOD PROCEDURE INSTITUTED IN CNS 0.5.
RfactorNum. reflection% reflection
Rfree0.288 560 5.2 %
Rwork0.238 --
obs0.238 10672 97.9 %
all-10672 -
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.39 Å2 / ksol: 0.294 e/Å3
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.56 Å20 Å20 Å2
2---4.17 Å20 Å2
3----4.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 423 1 116 1700
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.181.5
X-RAY DIFFRACTIONc_mcangle_it3.322
X-RAY DIFFRACTIONc_scbond_it3.342
X-RAY DIFFRACTIONc_scangle_it4.642.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 87 5 %
Rwork0.266 1648 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PADNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.332 / % reflection Rfree: 5 % / Rfactor Rwork: 0.266

+
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