[English] 日本語
Yorodumi
- PDB-2cro: STRUCTURE OF PHAGE 434 CRO PROTEIN AT 2.35 ANGSTROMS RESOLUTION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cro
TitleSTRUCTURE OF PHAGE 434 CRO PROTEIN AT 2.35 ANGSTROMS RESOLUTION
ComponentsREGULATORY PROTEIN CRO
KeywordsGENE REGULATING PROTEIN
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
Regulatory protein cro
Similarity search - Component
Biological speciesPhage 434 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.35 Å
AuthorsMondragon, A. / Wolberger, C. / Harrison, S.C.
CitationJournal: J.Mol.Biol. / Year: 1989
Title: Structure of phage 434 Cro protein at 2.35 A resolution.
Authors: Mondragon, A. / Wolberger, C. / Harrison, S.C.
History
DepositionDec 8, 1988Processing site: BNL
Revision 1.0Oct 15, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: REGULATORY PROTEIN CRO


Theoretical massNumber of molelcules
Total (without water)8,0771
Polymers8,0771
Non-polymers00
Water30617
1
A: REGULATORY PROTEIN CRO

A: REGULATORY PROTEIN CRO

A: REGULATORY PROTEIN CRO


Theoretical massNumber of molelcules
Total (without water)24,2303
Polymers24,2303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)49.820, 49.820, 154.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Atom site foot note1: SEE REMARK 5.

-
Components

#1: Protein REGULATORY PROTEIN CRO


Mass: 8076.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phage 434 (virus) / Genus: Lambda-like viruses / Species: Enterobacteria phage lambda / References: UniProt: P03036
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.74 Msodium phosphate1reservoir
20.3 M1reservoirKCl
31 %(v/v)MPD1reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 2.35 Å / Num. obs: 3055 / % possible obs: 85 % / Observed criterion σ(I): 3 / Num. measured all: 9336 / Rmerge(I) obs: 0.062

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.195 / Highest resolution: 2.35 Å
Details: DENSITY FOR THE LAST SIX CARBOXY TERMINAL RESIDUES (64 - 70) WAS NEVER SEEN IN THE MAP AT ANY STAGE OF REFINEMENT, AND THESE RESIDUES ARE PROBABLY DISORDERED.
Refinement stepCycle: LAST / Highest resolution: 2.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms520 0 0 17 537
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0250.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.152.5
X-RAY DIFFRACTIONp_mcangle_it2.015
X-RAY DIFFRACTIONp_scbond_it1.262.5
X-RAY DIFFRACTIONp_scangle_it8.175
X-RAY DIFFRACTIONp_plane_restr0.0050.02
X-RAY DIFFRACTIONp_chiral_restr0.0760.15
X-RAY DIFFRACTIONp_singtor_nbd0.2030.5
X-RAY DIFFRACTIONp_multtor_nbd0.3130.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2580.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor0.93
X-RAY DIFFRACTIONp_staggered_tor18.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 5 Å / Highest resolution: 2.35 Å / Num. reflection obs: 2709 / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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