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- PDB-3kz3: A structure of a lambda repressor fragment mutant -

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Basic information

Entry
Database: PDB / ID: 3kz3
TitleA structure of a lambda repressor fragment mutant
ComponentsRepressor protein CI
KeywordsTRANSCRIPTION / Five helix bundle / DNA-binding / Repressor / Transcription regulation
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. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) ...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. / 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
Repressor protein cI
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.64 Å
AuthorsGruebele, M. / Liu, F. / Gao, Y.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: A survey of lambda repressor fragments from two-state to downhill folding.
Authors: Liu, F. / Gao, Y.G. / Gruebele, M.
History
DepositionDec 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Repressor protein CI
B: Repressor protein CI


Theoretical massNumber of molelcules
Total (without water)17,6422
Polymers17,6422
Non-polymers00
Water5,080282
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Repressor protein CI


Theoretical massNumber of molelcules
Total (without water)8,8211
Polymers8,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Repressor protein CI


Theoretical massNumber of molelcules
Total (without water)8,8211
Polymers8,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.630, 58.710, 42.850
Angle α, β, γ (deg.)90.00, 98.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Repressor protein CI /


Mass: 8821.122 Da / Num. of mol.: 2 / Fragment: UNP Residues 8-85 / Mutation: Y22W, Q33Y, G46A, G48A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Gene: CI / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P03034
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO THE AUTHORS, THE PROTEIN WAS DERIVED FROM OAS TG'S LAMBDA REPRESSOR PROTEIN EXPRESSION ...ACCORDING TO THE AUTHORS, THE PROTEIN WAS DERIVED FROM OAS TG'S LAMBDA REPRESSOR PROTEIN EXPRESSION VECTOR WHICH CARRIES THE CHANGE OF THE FIRST N-TERM AND THE LAST C-TERM RESIDUES. THESE TWO CHANGES CAME FROM THE PREPARATION OF THE EXPRESSION SYSTEM, POSSIBLY THE RESTRICTION ENZYME DIGESTION SITE DESIGN WHEN THE DNA SEQUENCE WAS CUT FROM THE WILD-TYPE PROTEIN AND INSERTED INTO THE VECTOR

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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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-3 / Wavelength: 0.97 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.64→30 Å / Num. obs: 19544 / % possible obs: 99.1 % / Redundancy: 7.3 % / Biso Wilson estimate: 23.52 Å2 / Rmerge(I) obs: 0.067
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 6.6 % / % possible all: 90.9

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Processing

Software
NameClassification
MAR345dtbdata collection
AMoREphasing
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO / Resolution: 1.64→10 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE
RfactorNum. reflection% reflectionSelection details
Rwork0.1879 ---
obs0.1889 17329 93.8 %-
all-18248 --
Rfree---RANDOM
Refinement stepCycle: LAST / Resolution: 1.64→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 0 282 1518
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d1.957
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.022
X-RAY DIFFRACTIONs_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.043
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.07
X-RAY DIFFRACTIONs_approx_iso_adps0

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