[English] 日本語
Yorodumi
- PDB-3oqn: Structure of ccpa-hpr-ser46-p-gntr-down cre -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oqn
TitleStructure of ccpa-hpr-ser46-p-gntr-down cre
Components
  • 5'-D(*AP*TP*GP*GP*TP*AP*CP*CP*GP*CP*TP*TP*TP*CP*AP*A)-3'
  • 5'-D(*TP*TP*GP*AP*AP*AP*GP*CP*GP*GP*TP*AP*CP*CP*AP*T)-3'
  • Catabolite control protein A
  • Phosphocarrier protein HPr
KeywordsTRANSCRIPTION/TRANSFERASE/DNA / pbp fold for ccpa / transcription / hpr-ser46p- / nucleoid / TRANSCRIPTION-TRANSFERASE-DNA complex
Function / homology
Function and homology information


regulation of carbohydrate utilization / phosphoenolpyruvate-dependent sugar phosphotransferase system / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Catabolite control protein A / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site ...Catabolite control protein A / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / 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 / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Phosphocarrier protein HPr / Catabolite control protein A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSchumacher, M.A. / Sprehe, M. / Bartholomae, M. / Hillen, W. / Brennan, R.G.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators.
Authors: Schumacher, M.A. / Sprehe, M. / Bartholomae, M. / Hillen, W. / Brennan, R.G.
History
DepositionSep 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Catabolite control protein A
S: Phosphocarrier protein HPr
C: Catabolite control protein A
D: Phosphocarrier protein HPr
E: 5'-D(*TP*TP*GP*AP*AP*AP*GP*CP*GP*GP*TP*AP*CP*CP*AP*T)-3'
B: 5'-D(*AP*TP*GP*GP*TP*AP*CP*CP*GP*CP*TP*TP*TP*CP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)103,5386
Polymers103,5386
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12410 Å2
ΔGint-65 kcal/mol
Surface area37320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.930, 103.510, 175.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Catabolite control protein A / Glucose-resistance amylase regulator


Mass: 37724.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: alsA, amyR, BSU29740, ccpA, graR / Production host: Escherichia coli (E. coli) / References: UniProt: P25144
#2: Protein Phosphocarrier protein HPr / Histidine-containing protein


Mass: 9147.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU13900, hpr, ptsH / Production host: Escherichia coli (E. coli)
References: UniProt: P08877, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases
#3: DNA chain 5'-D(*TP*TP*GP*AP*AP*AP*GP*CP*GP*GP*TP*AP*CP*CP*AP*T)-3'


Mass: 4922.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)
#4: DNA chain 5'-D(*AP*TP*GP*GP*TP*AP*CP*CP*GP*CP*TP*TP*TP*CP*AP*A)-3'


Mass: 4873.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: peg 6000, citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2008
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→87.7 Å / Num. all: 20642 / Num. obs: 19982 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.3→3.56 Å / % possible all: 96.8

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FEP

2fep


Resolution: 3.3→87.7 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2272253.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1374 6.9 %RANDOM
Rwork0.222 ---
all0.222 20642 --
obs0.222 19969 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.4853 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 89 Å2
Baniso -1Baniso -2Baniso -3
1--13.89 Å20 Å20 Å2
2---11.54 Å20 Å2
3---25.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.84 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 3.3→87.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6432 650 0 0 7082
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 244 7.3 %
Rwork0.338 3088 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep-NEWSEP.param.txtprotein-NEWSEP.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna.top

+
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