[English] 日本語
Yorodumi
- PDB-3cro: THE PHAGE 434 CRO/OR1 COMPLEX AT 2.5 ANGSTROMS RESOLUTION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cro
TitleTHE PHAGE 434 CRO/OR1 COMPLEX AT 2.5 ANGSTROMS RESOLUTION
Components
  • DNA (5'-D(*AP*AP*GP*TP*AP*CP*AP*AP*AP*CP*TP*TP*TP*CP*TP*TP*G P*TP*AP*T)-3')
  • DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*GP*AP*AP*AP*GP*TP*TP*TP*GP*T P*AP*CP*T)-3')
  • PROTEIN (434 CRO)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Regulatory protein cro / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Regulatory protein cro
Similarity search - Component
Biological speciesPhage 434 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsMondragon, A. / Harrison, S.C.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: The phage 434 Cro/OR1 complex at 2.5 A resolution.
Authors: Mondragon, A. / Harrison, S.C.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Structure of Phage 434 Cro Protein at 2.35 Angstroms Resolution
Authors: Mondragon, A. / Wolberger, C. / Harrison, S.C.
#2: Journal: Science / Year: 1988
Title: Recognition of a DNA Operator by the Repressor of Phage 434. A View at High Resolution
Authors: Aggarwal, A.K. / Rodgers, D.W. / Drottar, M. / Ptashne, M. / Harrison, S.C.
#3: Journal: Nature / Year: 1987
Title: Structure of the Repressor-Operator Complex of Bacteriophage 434
Authors: Anderson, J.E. / Ptashne, M. / Harrison, S.C.
History
DepositionJul 6, 1990Deposition site: BNL / Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*AP*AP*GP*TP*AP*CP*AP*AP*AP*CP*TP*TP*TP*CP*TP*TP*G P*TP*AP*T)-3')
B: DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*GP*AP*AP*AP*GP*TP*TP*TP*GP*T P*AP*CP*T)-3')
L: PROTEIN (434 CRO)
R: PROTEIN (434 CRO)


Theoretical massNumber of molelcules
Total (without water)28,4164
Polymers28,4164
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.200, 47.600, 61.700
Angle α, β, γ (deg.)90.00, 109.50, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE TWO PROTEIN DOMAINS HAVE BEEN ASSIGNED CHAIN INDICATORS *L* AND *R*. THE TWO DNA CHAINS HAVE BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*. THE UNIT CELL CONTAINS TWO COMPLEXES EACH OF WHICH CONSISTS OF A PROTEIN DIMER AND TWO DIFFERENT STRANDS OF DNA.

-
Components

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


Mass: 6106.990 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*GP*AP*AP*AP*GP*TP*TP*TP*GP*T P*AP*CP*T)-3')


Mass: 6156.027 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (434 CRO)


Mass: 8076.619 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Phage 434 (virus) / Genus: Lambda-like viruses / Species: Enterobacteria phage lambda / References: UniProt: P03036
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DNA CHAINS ARE ALIGNED AS FOLLOWS *B* 5(PRIME) T-A-T-A-C-A-A-G-A-A-A-G-T-T-T-G-T-A-C-T *A* ...THE DNA CHAINS ARE ALIGNED AS FOLLOWS *B* 5(PRIME) T-A-T-A-C-A-A-G-A-A-A-G-T-T-T-G-T-A-C-T *A* 3(PRIME) T-A-T-G-T-T-C-T-T-T-C-A-A-A-C-A-T-G-A-A THE DNA CHAINS ARE NUMBERED SEQUENTIALLY. THE FOLLOWING TABLE PRESENTS THE RELATIONSHIP BETWEEN THE SEQUENTIAL DNA NUMBERING AND THAT USED IN THE PAPER CITED ON THE *JRNL* RECORDS ABOVE: PDB ENTRY PUBLISHED --------- --------- A A 1 -4R A A 2 -3R G A 3 -2R T A 4 -1R A A 5 1R C A 6 2R A A 7 3R A A 8 4R A A 9 5R C A 10 6R T A 11 7R T A 12 7'L T A 13 6'L C A 14 5'L T A 15 4'L T A 16 3'L G A 17 2'L T A 18 1'L A A 19 -1'L T A 20 -2'L T B 1 -3L A B 2 -2L T B 3 -1L A B 4 1L C B 5 2L A B 6 3L A B 7 4L G B 8 5L A B 9 6L A B 10 7L A B 11 7'R G B 12 6'R T B 13 5'R T B 14 4'R T B 15 3'R G B 16 2'R T B 17 1'R A B 18 -1'R C B 19 -2'R T B 20 -3'R

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 277 K / pH: 6.2 / Details: pH 6.20, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 350011
3MES11
4NACL11
5MGCL211
6SPERMINE11
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown / pH: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 %(w/v)PEG350012
2100 mMMES12pH6.2
3160 mM12NaCl
4120 mM12MgCl
52 mMspermine12
62 mMprotein1
71 mMDNA11

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13
DetectorType: XENTRONICS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 7232
Reflection
*PLUS
Highest resolution: 2.5 Å / Rmerge(I) obs: 0.101

-
Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.5→10 Å
Details: DENSITY FOR THE LAST SIX CARBOXY TERMINAL RESIDUES (64 - 70) WAS NOT OBSERVED IN THE MAP AT ANY STAGE OF THE REFINEMENT AND THESE RESIDUES ARE PROBABLY DISORDERED.
RfactorNum. reflection
obs0.22 5351
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 814 0 25 1881
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg2.3
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_planes0.01
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.3
X-RAY DIFFRACTIONt_plane_restr0.01

+
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