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- PDB-1d1m: CRYSTAL STRUCTURE OF CRO K56-[DGEVK]-F58W MUTANT -

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Basic information

Entry
Database: PDB / ID: 1d1m
TitleCRYSTAL STRUCTURE OF CRO K56-[DGEVK]-F58W MUTANT
ComponentsLAMBDA CRO REPRESSOR
KeywordsVIRAL PROTEIN / HELIX-TURN-HELIX
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
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: 2.05 Å
AuthorsRupert, P.B. / Mollah, A.K. / Mossing, M.C. / Matthews, B.W.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The structural basis for enhanced stability and reduced DNA binding seen in engineered second-generation Cro monomers and dimers.
Authors: Rupert, P.B. / Mollah, A.K. / Mossing, M.C. / Matthews, B.W.
History
DepositionSep 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: LAMBDA CRO REPRESSOR
A: LAMBDA CRO REPRESSOR


Theoretical massNumber of molelcules
Total (without water)14,5972
Polymers14,5972
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.030, 35.660, 108.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LAMBDA CRO REPRESSOR


Mass: 7298.335 Da / Num. of mol.: 2 / Fragment: LAMBDA CRO REPRESSOR / Mutation: K56[DGEVK]-F58W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Production host: Escherichia coli (E. coli) / References: UniProt: P03040
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4.8 M SODIUM FORMATE, 0.5% BETA-OCTYLGLUCOSIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlprotein1drop
2200 mM1dropKCl
320 mMHEPES1drop
40.1 mMEDTA1drop
54.8 Msodium formate1reservoir
60.5 %(w/v)beta-octylglucoside1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jun 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 27290 / Num. obs: 9374 / % possible obs: 95 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 2.9 % / Rmerge(I) obs: 0.061
Reflection
*PLUS
Num. measured all: 27290

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
SDMSdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 2.05→20 Å / Stereochemistry target values: ENGH & HUBER / Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.298 937 -RANDOM
Rwork0.185 ---
all-9867 --
obs-9374 95 %-
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 0 30 1054
Refine LS restraints
Refine-IDTypeWeight
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg2.6
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 / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.6

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