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- PDB-1lrp: COMPARISON OF THE STRUCTURES OF CRO AND LAMBDA REPRESSOR PROTEINS... -

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Basic information

Entry
Database: PDB / ID: 1lrp
TitleCOMPARISON OF THE STRUCTURES OF CRO AND LAMBDA REPRESSOR PROTEINS FROM BACTERIOPHAGE LAMBDA
ComponentsLAMBDA REPRESSOR
KeywordsDNA BINDING REGULATORY PROTEIN
Function / homology
Function and homology information


maintenance of viral latency / latency-replication decision / positive regulation of viral transcription / negative regulation of transcription by competitive promoter binding / core promoter sequence-specific DNA binding / identical protein binding
Similarity search - Function
: / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
Repressor protein cI
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsPabo, C. / Lewis, M.
Citation
Journal: J.Mol.Biol. / Year: 1983
Title: Comparison of the structures of cro and lambda repressor proteins from bacteriophage lambda.
Authors: Ohlendorf, D.H. / Anderson, W.F. / Lewis, M. / Pabo, C.O. / Matthews, B.W.
#1: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1983
Title: Structure of the Operator-Binding Domain of Bacteriophage Lambda Repressor. Implications for DNA Recognition and Gene Regulation
Authors: Lewis, M. / Jeffrey, A. / Wang, J. / Ladner, R. / Ptashne, M. / Pabo, C.O.
#2: Journal: Nature / Year: 1982
Title: Homology Among DNA-Binding Proteins Suggests Use of a Conserved Super-Secondary Structure
Authors: Sauer, R.T. / Yocum, R.R. / Doolittle, R.F. / Lewis, M. / Pabo, C.O.
#3: Journal: Nature / Year: 1982
Title: The Operator-Binding Domain of Lambda Repressor. Structure and DNA Recognition
Authors: Pabo, C.O. / Lewis, M.
#4: Journal: Nature / Year: 1982
Title: The N-Terminal Arms of Lambda Repressor Wrap Around the Operator DNA
Authors: Pabo, C.O. / Krovatin, W. / Jeffrey, A. / Sauer, R.T.
History
DepositionDec 4, 1987Processing site: BNL
Revision 1.0Jan 9, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_struct_oper_list / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _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[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _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.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3]
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LAMBDA REPRESSOR
B: LAMBDA REPRESSOR
C: LAMBDA REPRESSOR


Theoretical massNumber of molelcules
Total (without water)30,4103
Polymers30,4103
Non-polymers00
Water00
1
A: LAMBDA REPRESSOR

A: LAMBDA REPRESSOR


Theoretical massNumber of molelcules
Total (without water)20,2732
Polymers20,2732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
2
B: LAMBDA REPRESSOR
C: LAMBDA REPRESSOR


Theoretical massNumber of molelcules
Total (without water)20,2732
Polymers20,2732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.000, 65.000, 149.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.4992519, 0.8668697, -0.00152157), (-0.86305728, -0.4970783, -0.08607109), (-0.07563217, -0.04175575, 0.99635719)-32.72378, -76.04117, -4.09961
2given(-0.49886057, -0.86360024, -0.07534558), (0.86632184, -0.49751575, -0.04164961), (-0.0016472, -0.08620035, 0.99630031)-82.29823, -9.65392, -2.53322
DetailsTHE REPRESSOR MOLECULE CONSISTS OF A DIMER, AND COORDINATES FOR THE SYMMETRY RELATED CHAIN CAN BE GENERATED FROM THE CHAIN PRESENTED IN THIS ENTRY BY 1.0 0.0 0.0 0.0 0.0 -1.0 0.0 0.0 0.0 0.0 -1.0 0.0

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Components

#1: Protein LAMBDA REPRESSOR / Coordinate model: Cα atoms only


Mass: 10136.613 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / References: UniProt: P03034

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.99 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 3.2 Å
Refinement stepCycle: LAST / Highest resolution: 3.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms267 0 0 0 267
Refinement
*PLUS
Highest resolution: 3.2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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