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- PDB-1kca: Crystal Structure of the lambda Repressor C-terminal Domain Octamer -

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Basic information

Entry
Database: PDB / ID: 1kca
TitleCrystal Structure of the lambda Repressor C-terminal Domain Octamer
ComponentsREPRESSOR PROTEIN CI
KeywordsGENE REGULATION / dna-binding / lambda repressor / protein oligomerization / dna-looping
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
Umud Fragment, subunit A / Umud Fragment, subunit A / : / 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. ...Umud Fragment, subunit A / Umud Fragment, subunit A / : / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Repressor protein cI
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsBell, C.E. / Lewis, M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the lambda repressor C-terminal domain octamer.
Authors: Bell, C.E. / Lewis, M.
History
DepositionNov 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE SEQUENCE GSHM (128-131) IS FROM THE EXPRESSION VECTOR (GS FROM THE THROMBIN SITE, AND ...SEQUENCE THE SEQUENCE GSHM (128-131) IS FROM THE EXPRESSION VECTOR (GS FROM THE THROMBIN SITE, AND HIS MET FROM THE NDEI SITE).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REPRESSOR PROTEIN CI
B: REPRESSOR PROTEIN CI
C: REPRESSOR PROTEIN CI
D: REPRESSOR PROTEIN CI
E: REPRESSOR PROTEIN CI
F: REPRESSOR PROTEIN CI
G: REPRESSOR PROTEIN CI
H: REPRESSOR PROTEIN CI


Theoretical massNumber of molelcules
Total (without water)94,7958
Polymers94,7958
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13310 Å2
ΔGint-66 kcal/mol
Surface area35190 Å2
MethodPISA
2
A: REPRESSOR PROTEIN CI
B: REPRESSOR PROTEIN CI
C: REPRESSOR PROTEIN CI
D: REPRESSOR PROTEIN CI
E: REPRESSOR PROTEIN CI
F: REPRESSOR PROTEIN CI
G: REPRESSOR PROTEIN CI
H: REPRESSOR PROTEIN CI

A: REPRESSOR PROTEIN CI
B: REPRESSOR PROTEIN CI
C: REPRESSOR PROTEIN CI
D: REPRESSOR PROTEIN CI
E: REPRESSOR PROTEIN CI
F: REPRESSOR PROTEIN CI
G: REPRESSOR PROTEIN CI
H: REPRESSOR PROTEIN CI


Theoretical massNumber of molelcules
Total (without water)189,59016
Polymers189,59016
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area28990 Å2
ΔGint-142 kcal/mol
Surface area68000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.090, 113.720, 95.730
Angle α, β, γ (deg.)90.00, 110.26, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is the octamer that is in the asmmetric unit

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Components

#1: Protein
REPRESSOR PROTEIN CI


Mass: 11849.380 Da / Num. of mol.: 8 / Fragment: C-terminal domain (residues 132-236)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Plasmid: pET-14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03034
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.04 Å3/Da / Density % sol: 69.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium formate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21.69 Msodium formate1reservoir
30.05 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→23.5 Å / Num. obs: 33013 / % possible obs: 99.2 % / Observed criterion σ(I): -2 / Redundancy: 1.6 % / Biso Wilson estimate: 58.1 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 4.5
Reflection shellHighest resolution: 2.9 Å / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 1.8 / % possible all: 95
Reflection
*PLUS
Num. measured all: 53445
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F39

1f39


Resolution: 2.91→23.53 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 893314.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3299 10 %RANDOM
Rwork0.227 ---
obs-33013 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.0074 Å2 / ksol: 0.372394 e/Å3
Displacement parametersBiso mean: 46.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å25.56 Å2
2---2.6 Å20 Å2
3---1.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.91→23.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6160 0 0 0 6160
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shellResolution: 2.91→3.08 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 502 9.8 %
Rwork0.339 4600 -
obs--91.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 46.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.384 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.339

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