[English] 日本語
Yorodumi
- PDB-2zny: Crystal structure of the FFRP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zny
TitleCrystal structure of the FFRP
ComponentsUncharacterized HTH-type transcriptional regulator PH1519
KeywordsDNA BINDING PROTEIN / transcription / DNA-binding / Transcription regulation
Function / homology
Function and homology information


response to amino acid / sequence-specific DNA binding / identical protein binding / cytosol
Similarity search - Function
AsnC-type helix-turn-helix domain / AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / AsnC-type HTH domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel ...AsnC-type helix-turn-helix domain / AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / AsnC-type HTH domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ARGININE / HTH-type transcriptional regulator FL11
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsYamada, M. / Suzuki, M.
CitationJournal: Proteins / Year: 2009
Title: Interactions between the archaeal transcription repressor FL11 and its coregulators lysine and arginine.
Authors: Yamada, M. / Ishijima, S.A. / Suzuki, M.
History
DepositionMay 2, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
A: Uncharacterized HTH-type transcriptional regulator PH1519
B: Uncharacterized HTH-type transcriptional regulator PH1519
C: Uncharacterized HTH-type transcriptional regulator PH1519
D: Uncharacterized HTH-type transcriptional regulator PH1519
E: Uncharacterized HTH-type transcriptional regulator PH1519
F: Uncharacterized HTH-type transcriptional regulator PH1519
G: Uncharacterized HTH-type transcriptional regulator PH1519
H: Uncharacterized HTH-type transcriptional regulator PH1519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,26114
Polymers153,2108
Non-polymers1,0516
Water4,234235
1
A: Uncharacterized HTH-type transcriptional regulator PH1519
B: Uncharacterized HTH-type transcriptional regulator PH1519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4783
Polymers38,3022
Non-polymers1751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-35 kcal/mol
Surface area14150 Å2
MethodPISA
2
C: Uncharacterized HTH-type transcriptional regulator PH1519
D: Uncharacterized HTH-type transcriptional regulator PH1519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6534
Polymers38,3022
Non-polymers3502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-35 kcal/mol
Surface area14290 Å2
MethodPISA
3
E: Uncharacterized HTH-type transcriptional regulator PH1519
F: Uncharacterized HTH-type transcriptional regulator PH1519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6534
Polymers38,3022
Non-polymers3502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-37 kcal/mol
Surface area14210 Å2
MethodPISA
4
G: Uncharacterized HTH-type transcriptional regulator PH1519
H: Uncharacterized HTH-type transcriptional regulator PH1519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4783
Polymers38,3022
Non-polymers1751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-34 kcal/mol
Surface area14420 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.310, 73.500, 103.060
Angle α, β, γ (deg.)90.00, 98.47, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Uncharacterized HTH-type transcriptional regulator PH1519 / archaeal transcription repressor


Mass: 19151.221 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1519 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O59188
#2: Chemical
ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% PEG 3350, 0.3M CaCl2, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. all: 49860 / Num. obs: 47467 / % possible obs: 95.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.1
Reflection shellResolution: 2.59→2.68 Å / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 4.8 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RI7

1ri7


Resolution: 2.59→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 4746 -random
Rwork0.254 ---
obs0.254 47467 95.2 %-
all-49860 --
Refinement stepCycle: LAST / Resolution: 2.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9184 0 72 235 9491

+
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