[English] 日本語
Yorodumi
- PDB-1qp4: PURINE REPRESSOR-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qp4
TitlePURINE REPRESSOR-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX
Components
  • DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*TP*CP*GP*AP*TP*TP*GP*CP*GP*T)-3')
  • PROTEIN (PURINE NUCLEOTIDE SYNTHESIS REPRESSOR)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / DNA-BINDING / REPRESSOR / PURINE BIOSYNTHESIS / COMPLEX (DNA-BINDING PROTEIN-DNA) / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


guanine binding / negative regulation of purine nucleotide biosynthetic process / purine nucleotide biosynthetic process / DNA-binding transcription repressor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / cytosol
Similarity search - Function
Transcription regulator HTH, PurR / Transcriptional regulator LacI/GalR-like, sensor domain / LacI-type HTH domain signature. / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) ...Transcription regulator HTH, PurR / Transcriptional regulator LacI/GalR-like, sensor domain / LacI-type HTH domain signature. / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HYPOXANTHINE / DNA / DNA (> 10) / HTH-type transcriptional repressor PurR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsGlasfeld, A. / Koehler, A.N. / Schumacher, M.A. / Brennan, R.G.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions.
Authors: Glasfeld, A. / Koehler, A.N. / Schumacher, M.A. / Brennan, R.G.
#1: Journal: Science / Year: 1994
Title: Crystal Structure of LacI Member, PurR, Bound to DNA: Minor Groove Binding by Alpha Helices
Authors: Schumacher, M.A. / Choi, K.Y. / Zalkin, H. / Brennan, R.G.
History
DepositionJun 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.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
M: DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*TP*CP*GP*AP*TP*TP*GP*CP*GP*T)-3')
A: PROTEIN (PURINE NUCLEOTIDE SYNTHESIS REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4303
Polymers43,2942
Non-polymers1361
Water362
1
M: DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*TP*CP*GP*AP*TP*TP*GP*CP*GP*T)-3')
A: PROTEIN (PURINE NUCLEOTIDE SYNTHESIS REPRESSOR)
hetero molecules

M: DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*TP*CP*GP*AP*TP*TP*GP*CP*GP*T)-3')
A: PROTEIN (PURINE NUCLEOTIDE SYNTHESIS REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8606
Polymers86,5884
Non-polymers2722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)176.480, 95.260, 81.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: DNA chain DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*TP*CP*GP*AP*TP*TP*GP*CP*GP*T)-3') / PURA


Mass: 5202.384 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (PURINE NUCLEOTIDE SYNTHESIS REPRESSOR)


Mass: 38091.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURR / Plasmid: PDNA100\:K55A / Gene (production host): PURR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 LAMBDA DE3 / References: UniProt: P0ACP7
#3: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.92 Å3/Da / Density % sol: 68.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, (NH4)2SO4, [CO(NH3)6]CL3, NA2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1[CO(NH3)6]CL311
2(NH4)2SO411
3NA2SO411
4PEG 400011
5(NH4)2SO412
6NA2SO412
7PEG 400012
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mMprotein1drop
21.0 mMdithiothreitol1drop
3160 mMsodium potassium phosphate1drop
40.6 mMDNA1drop
550 mMsodium cacodylate1drop
625 %PEG40001drop
70.4 %ammonium sulfate1drop
850 mMcobalt hexammine1drop
90.1 Mammonium phosphate1drop
1025 %PEG40001reservoir
110.4 Mammonium sulphate1reservoir
1250 mMcobalt hexammine1reservoir
130.1 Mammonium phosphate1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: UCSD MARK III / Detector: AREA DETECTOR / Date: Feb 14, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→10 Å / Num. obs: 13547 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 41 Å2 / Rsym value: 7.97 / Net I/σ(I): 9.32
Reflection shellResolution: 3→3.23 Å / Redundancy: 1.8 % / % possible all: 89.6
Reflection
*PLUS
Num. measured all: 58105 / Rmerge(I) obs: 0.0797
Reflection shell
*PLUS
% possible obs: 89.6 %

-
Processing

Software
NameClassification
TNTrefinement
UCSD-systemdata reduction
UCSD-systemdata scaling
RefinementResolution: 3→10 Å / σ(I): 2
Stereochemistry target values: DNA BASE GEOMETRIES TAKEN FROM CLOWNEY ET AL. (1996) J. AM. CHEM. SOC., VOL. 118, PP. 509-518. SUGAR PHOSPHATE GEOMETRIES TAKEN FROM GELBIN ET AL. (1996) J. AM. CHEM. ...Stereochemistry target values: DNA BASE GEOMETRIES TAKEN FROM CLOWNEY ET AL. (1996) J. AM. CHEM. SOC., VOL. 118, PP. 509-518. SUGAR PHOSPHATE GEOMETRIES TAKEN FROM GELBIN ET AL. (1996) J. AM. CHEM. SOC., VOL. 118, PP. 519-529.
RfactorNum. reflection
all0.157 -
obs-13547
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 345 10 2 3009
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0152.1
X-RAY DIFFRACTIONt_angle_deg1.81.8
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

+
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