[English] 日本語
Yorodumi
- PDB-1zvv: Crystal structure of a ccpa-crh-dna complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zvv
TitleCrystal structure of a ccpa-crh-dna complex
Components
  • DNA recognition strand CRE
  • Glucose-resistance amylase regulator
  • HPr-like protein crh
KeywordsTRANSCRIPTION/DNA / ccpa / crh / dna / complex / lacI member / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


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
Similarity search - Function
Catabolite control protein A / 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 ...Catabolite control protein A / 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
IODIDE ION / DNA / DNA (> 10) / HPr-like protein Crh / Catabolite control protein A / Catabolite control protein A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsSchumacher, M.A. / Brennan, R.G. / Hillen, W. / Seidel, G.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Phosphoprotein Crh-Ser46-P displays altered binding to CcpA to effect carbon catabolite regulation.
Authors: Schumacher, M.A. / Seidel, G. / Hillen, W. / Brennan, R.G.
History
DepositionJun 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 22, 2012Group: Other
Revision 1.4Jan 11, 2017Group: Other
Revision 1.5Feb 22, 2023Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / 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 / _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.oper_expression / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
O: DNA recognition strand CRE
T: DNA recognition strand CRE
R: DNA recognition strand CRE
A: Glucose-resistance amylase regulator
W: HPr-like protein crh
B: Glucose-resistance amylase regulator
P: HPr-like protein crh
G: Glucose-resistance amylase regulator
J: HPr-like protein crh
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,50920
Polymers153,1139
Non-polymers1,39611
Water82946
1
O: DNA recognition strand CRE
A: Glucose-resistance amylase regulator
W: HPr-like protein crh
hetero molecules

O: DNA recognition strand CRE
A: Glucose-resistance amylase regulator
W: HPr-like protein crh
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,34416
Polymers102,0756
Non-polymers1,26910
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area14040 Å2
ΔGint-69 kcal/mol
Surface area37370 Å2
MethodPISA
2
T: DNA recognition strand CRE
B: Glucose-resistance amylase regulator
P: HPr-like protein crh
hetero molecules

R: DNA recognition strand CRE
G: Glucose-resistance amylase regulator
J: HPr-like protein crh
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,83712
Polymers102,0756
Non-polymers7616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
Buried area13230 Å2
ΔGint-65 kcal/mol
Surface area37640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.690, 158.100, 125.470
Angle α, β, γ (deg.)90.00, 100.73, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

-
Components

#1: DNA chain DNA recognition strand CRE


Mass: 4907.206 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Glucose-resistance amylase regulator / ccpa / Catabolite control protein A


Mass: 36671.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ccpA / Plasmid: pet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46828, UniProt: P25144*PLUS
#3: Protein HPr-like protein crh / crh / Catabolite repression HPr


Mass: 9458.728 Da / Num. of mol.: 3 / Mutation: phosphorylated at Ser46
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: crh / Plasmid: pet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O06976
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.68 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, sodium iodide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2PEG 335012
3NaI12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.998 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 23, 2004 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.998 Å / Relative weight: 1
ReflectionResolution: 2.98→79.1 Å / Num. all: 32560 / Num. obs: 32545 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 0.1 Å2 / Rsym value: 0.106 / Net I/σ(I): 6
Reflection shellResolution: 2.98→3.12 Å / Redundancy: 2 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2 / Num. unique all: 4128 / % possible all: 92

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RZR

1rzr


Resolution: 2.98→79.05 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1931353.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 2450 8 %RANDOM
Rwork0.235 ---
obs0.235 30499 93.2 %-
all-30499 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.9262 Å2 / ksol: 0.269566 e/Å3
Displacement parametersBiso mean: 67.5 Å2
Baniso -1Baniso -2Baniso -3
1-13.22 Å20 Å20.36 Å2
2--7.49 Å20 Å2
3----20.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 2.98→79.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9626 978 11 46 10661
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it2.71.5
X-RAY DIFFRACTIONc_mcangle_it4.552
X-RAY DIFFRACTIONc_scbond_it3.652
X-RAY DIFFRACTIONc_scangle_it5.742.5
LS refinement shellResolution: 2.98→3.17 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.447 386 7.8 %
Rwork0.403 4570 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep-NEWSEP.paramprotein-NEWSEP.top
X-RAY DIFFRACTION2water_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4dna-rna_rep.paramion.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