[English] 日本語
Yorodumi
- PDB-1orc: CRO REPRESSOR INSERTION MUTANT K56-[DGEVK] -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1orc
TitleCRO REPRESSOR INSERTION MUTANT K56-[DGEVK]
ComponentsCRO REPRESSOR INSERTION MUTANT K56-[DGEVK]
KeywordsGENE REGULATING PROTEIN
Function / homology
Function and homology information


latency-replication decision / release from viral latency / negative regulation of viral transcription / negative regulation of transcription by competitive promoter binding / core promoter sequence-specific DNA binding / response to UV / protein homodimerization activity / DNA binding
Similarity search - Function
CRO Repressor / Regulatory protein cro superfamily / Cro / Regulatory protein cro / CRO Repressor / Lambda repressor-like, DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Regulatory protein cro
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.54 Å
AuthorsAlbright, R.A. / Mossing, M.C. / Matthews, B.W.
Citation
Journal: Biochemistry / Year: 1996
Title: High-resolution structure of an engineered Cro monomer shows changes in conformation relative to the native dimer.
Authors: Albright, R.A. / Mossing, M.C. / Matthews, B.W.
#1: Journal: Science / Year: 1990
Title: Stable, Monomeric Variants of Lambda Cro Obtained by Insertion of a Designed Beta-Hairpin Sequence
Authors: Mossing, M.C. / Sauer, R.T.
History
DepositionOct 30, 1995Processing site: BNL
Revision 1.0Dec 23, 1996Provider: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRO REPRESSOR INSERTION MUTANT K56-[DGEVK]


Theoretical massNumber of molelcules
Total (without water)7,9051
Polymers7,9051
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.770, 39.170, 48.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CRO REPRESSOR INSERTION MUTANT K56-[DGEVK]


Mass: 7905.048 Da / Num. of mol.: 1 / Mutation: INS(K56-DGEVK)
Source method: isolated from a genetically manipulated source
Details: RESULTS IN A 71-RESIDUE STABLE "MONOMER" MUTANT / Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Gene: CRO MUTANT K56-[DGEVK] / Gene (production host): CRO MUTANT K56-[DGEVK] / Production host: Escherichia coli (E. coli) / References: UniProt: P03040
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mM1dropK2HPO4
20.1 mMEDTA1drop
316 mg/mlprotein1drop
44.2-4.8 Msodium formate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Sep 26, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 9834 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.029
Reflection
*PLUS
Highest resolution: 1.54 Å / Num. measured all: 45435

-
Processing

Software
NameClassification
TNTrefinement
SDMSdata reduction
RefinementResolution: 1.54→20 Å / σ(F): 0
Details: BOTH TERMINI OF CRO K56-[DGEVK]ARE DISORDERED. RESIDUES 1, 2, 62, 63, 64, 65, AND 66 HAVE NO INTERPRETABLE DENSITY AND ARE NOT INCLUDED IN THE MODEL. RESIDUES 3 AND 61 EXTEN AWAY FROM THE ...Details: BOTH TERMINI OF CRO K56-[DGEVK]ARE DISORDERED. RESIDUES 1, 2, 62, 63, 64, 65, AND 66 HAVE NO INTERPRETABLE DENSITY AND ARE NOT INCLUDED IN THE MODEL. RESIDUES 3 AND 61 EXTEN AWAY FROM THE GLOBULAR PORTION OF THE MOLECULE AND ARE MOST PROBABLY IN MULTIPLE CONFORMATIONS. THE GLOBULAR PORTION OF THE MOLECULE (RESIDUES 4 - 59) IS EXCEPTIONALLY WELL-DEFINED IN THE DENSITY.
RfactorNum. reflection
Rwork0.178 -
all-9834
obs-9834
Refinement stepCycle: LAST / Resolution: 1.54→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms500 0 0 59 559
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
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_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.178
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://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