[English] 日本語
Yorodumi
- PDB-4cro: PROTEIN-DNA CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURE OF A ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cro
TitlePROTEIN-DNA CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURE OF A LAMBDA CRO-OPERATOR COMPLEX
Components
  • DNA (5'-D(*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*A)-3')
  • PROTEIN (LAMBDA CRO)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


latency-replication decision / release from viral latency / negative regulation of transcription by competitive promoter binding / negative regulation of viral transcription / core promoter sequence-specific DNA binding / response to UV / protein homodimerization activity / DNA binding
Similarity search - Function
Regulatory protein cro superfamily / Cro / Regulatory protein cro / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Regulatory protein cro
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / Resolution: 3.9 Å
AuthorsBrennan, R.G. / Roderick, S.L. / Takeda, Y. / Matthews, B.W.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1990
Title: Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex.
Authors: Brennan, R.G. / Roderick, S.L. / Takeda, Y. / Matthews, B.W.
#1: Journal: J.Mol.Biol. / Year: 1986
Title: Crystallization of a Complex of Cro Repressor with a 17 Base-Pair Operator
Authors: Brennan, R.G. / Takeda, Y. / Kim, J. / Anderson, W.F. / Matthews, B.W.
#2: Journal: Nature / Year: 1981
Title: Structure of the Cro Repressor from Bacteriophage Lambda and its Interaction with DNA
Authors: Anderson, W.F. / Ohlendorf, D.H. / Takeda, Y. / Matthews, B.W.
History
DepositionJan 15, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 22, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Other / Refinement description
Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_radiation / diffrn_source / pdbx_database_status / refine / struct_biol
Item: _diffrn.ambient_pressure / _diffrn.ambient_temp ..._diffrn.ambient_pressure / _diffrn.ambient_temp / _diffrn_detector.details / _diffrn_detector.type / _diffrn_radiation.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.target / _pdbx_database_status.status_code_sf / _refine.details / _struct_biol.details
Revision 2.0Nov 23, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Refinement description
Category: atom_site / database_2 ...atom_site / database_2 / database_PDB_matrix / pdbx_validate_symm_contact / refine / struct_biol / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _refine.details / _struct_biol.details / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2]
Details: ORTHOGONAL X,Y,Z AXES WERE REALIGNED FROM A*,B,C TO A,B*,C CRYSTALLOGRAPHIC DIRECTIONS
Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: DNA (5'-D(*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*A)-3')
H: DNA (5'-D(*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*A)-3')
I: DNA (5'-D(*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*A)-3')
J: DNA (5'-D(*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*A)-3')
K: DNA (5'-D(*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*A)-3')
L: DNA (5'-D(*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*A)-3')
A: PROTEIN (LAMBDA CRO)
B: PROTEIN (LAMBDA CRO)
C: PROTEIN (LAMBDA CRO)
D: PROTEIN (LAMBDA CRO)
E: PROTEIN (LAMBDA CRO)
F: PROTEIN (LAMBDA CRO)


Theoretical massNumber of molelcules
Total (without water)75,61712
Polymers75,61712
Non-polymers00
Water0
1
G: DNA (5'-D(*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*A)-3')
H: DNA (5'-D(*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*A)-3')
A: PROTEIN (LAMBDA CRO)
B: PROTEIN (LAMBDA CRO)


Theoretical massNumber of molelcules
Total (without water)25,2064
Polymers25,2064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: DNA (5'-D(*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*A)-3')
J: DNA (5'-D(*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*A)-3')
C: PROTEIN (LAMBDA CRO)
D: PROTEIN (LAMBDA CRO)


Theoretical massNumber of molelcules
Total (without water)25,2064
Polymers25,2064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: DNA (5'-D(*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*A)-3')
L: DNA (5'-D(*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*A)-3')
E: PROTEIN (LAMBDA CRO)
F: PROTEIN (LAMBDA CRO)


  • defined by author
  • 25.2 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)25,2064
Polymers25,2064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.800, 154.800, 86.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Cell settingtrigonal
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.14265205, 0.48913233, 0.86043476), (0.48913233, -0.72084794, 0.49088327), (0.86043476, 0.49088327, -0.1364)-47.65808, 138.94622, -31.51
2given(0.34540109, 0.78100994, -0.52021428), (0.78100994, -0.54650108, -0.30196244), (-0.52021428, -0.30196244, -0.7989)-125.87765, 212.76648, -6.11
3given(-0.92799737, 0.040413, -0.37028759), (0.040413, -0.97720262, -0.20824308), (-0.37028759, -0.20824308, 0.9053)8.81532, 52.35142, 7.44
4given(-0.9433214, 0.03686566, -0.32976811), (0.02926566, -0.98057858, -0.19362487), (-0.33051811, -0.19232583, 0.924)-67.96615, 186.78082, 7.27
5given(0.35599807, 0.78142812, -0.51241909), (0.77822812, -0.55139807, -0.3004641), (-0.51741909, -0.29180385, -0.8045)-48.30516, 78.96699, -7.13
DetailsTHE MOLECULAR SYMMETRY IS PRESENTED ON THE *MTRIX* RECORDS BELOW. THESE TRANSFORMATIONS WERE DETERMINED FROM ELECTRON DENSITY MAP ANALYSIS. MTRIX 1 RELATES CHAINS *A* AND *B* AND IS A PSEUDO TWO-FOLD ROTATION AXIS. LIKEWISE MTRIX 2 RELATES CHAINS *C* AND *D* AND MTRIX 3 RELATES CHAINS *E* AND *F* AND BOTH ARE PSEUDO TWO-FOLD ROTATION AXES. MTRIX 4 RELATES CHAINS *A* AND *B* TO CHAINS *C* AND *D* AND IS A PSEUDO THREE-FOLD SCREW AXIS. MTRIX 5 RELATES CHAINS *A* AND *B* TO CHAINS *E* AND *F* AND IS A PSEUDO THREE-FOLD SCREW AXIS.

-
Components

#1: DNA chain
DNA (5'-D(*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*A)-3') / Coordinate model: P atoms only


Mass: 5227.397 Da / Num. of mol.: 6 / Source method: obtained synthetically
#2: Protein
PROTEIN (LAMBDA CRO) / REGULATORY PROTEIN CRO / Coordinate model: Cα atoms only


Mass: 7375.484 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / References: UniProt: P03040

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growMethod: vapor diffusion / pH: 6.9 / Details: NA CACODYLATE, NACL, pH 6.90, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11
3NACLSodium chloride11
Crystal grow
*PLUS
pH: 6.9 / Method: vapor diffusion / Details: referred to J.Mol.Biol. 188.115-118 1986
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 mg/mlcro monomer1drop
22.5 mg/mlduplex 17 base-pair fragment1drop
320 mMsodium cacodylate1drop
4100 mM1dropNaCl
53.5-4.0 M1reservoirNaCl

-
Data collection

DiffractionAmbient pressure: 101 kPa / Mean temperature: 298 K
Diffraction sourceSource: rotating-anode X-ray tube / Target: Cu
DetectorType: AREA DETECTOR / Detector: AREA DETECTOR / Details: UCSD Area Detector Facility
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 1.5418 Å
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 3.9 Å
Reflection
*PLUS
Highest resolution: 3.9 Å

-
Processing

RefinementHighest resolution: 3.9 Å
Details: THE COORDINATES CORRESPONDING TO CRO ARE GIVEN AS ALPHA CARBON POSITIONS FOR RESIDUES 3 - 66. THESE COORDINATES WERE INITIALLY TAKEN FROM THE REFINED COORDINATES OF THE UNCOMPLEXED CRO ...Details: THE COORDINATES CORRESPONDING TO CRO ARE GIVEN AS ALPHA CARBON POSITIONS FOR RESIDUES 3 - 66. THESE COORDINATES WERE INITIALLY TAKEN FROM THE REFINED COORDINATES OF THE UNCOMPLEXED CRO CRYSTAL STRUCTURE AND THEN FITTED TO THE ISOMORPHOUS REPLACEMENT MAP OF THE COMPLEX. THE COORDINATES CORRESPONDING TO DNA ARE GIVEN AS PHOSPHOROUS ATOM POSITIONS FOR BASES 2 - 17.
Refinement stepCycle: LAST / Highest resolution: 3.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms384 96 0 0 480
Refinement
*PLUS
Highest resolution: 3.9 Å
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