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- PDB-1orc: CRO REPRESSOR INSERTION MUTANT K56-[DGEVK] -

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Basic information

Entry
Database: PDB / ID: 1orc
TitleCRO REPRESSOR INSERTION MUTANT K56-[DGEVK]
ComponentsCRO REPRESSOR INSERTION MUTANT K56-[DGEVK]
KeywordsGENE REGULATING PROTEIN
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: 1.54 Å
AuthorsAlbright, R.A. / Mossing, M.C. / Matthews, B.W.
Citation
Journal: Biochemistry / Year: 1996
Title: High-resolution structure of an engineered Cro monomer shows changes in conformation relative to the native dimer.
Authors: Albright, R.A. / Mossing, M.C. / Matthews, B.W.
#1: Journal: Science / Year: 1990
Title: Stable, Monomeric Variants of Lambda Cro Obtained by Insertion of a Designed Beta-Hairpin Sequence
Authors: Mossing, M.C. / Sauer, R.T.
History
DepositionOct 30, 1995Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRO REPRESSOR INSERTION MUTANT K56-[DGEVK]


Theoretical massNumber of molelcules
Total (without water)7,9051
Polymers7,9051
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.770, 39.170, 48.310
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 CRO REPRESSOR INSERTION MUTANT K56-[DGEVK]


Mass: 7905.048 Da / Num. of mol.: 1 / Mutation: INS(K56-DGEVK)
Source method: isolated from a genetically manipulated source
Details: RESULTS IN A 71-RESIDUE STABLE "MONOMER" MUTANT / Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Gene: CRO MUTANT K56-[DGEVK] / Gene (production host): CRO MUTANT K56-[DGEVK] / Production host: Escherichia coli (E. coli) / References: UniProt: P03040
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mM1dropK2HPO4
20.1 mMEDTA1drop
316 mg/mlprotein1drop
44.2-4.8 Msodium formate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Sep 26, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 9834 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.029
Reflection
*PLUS
Highest resolution: 1.54 Å / Num. measured all: 45435

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Processing

Software
NameClassification
TNTrefinement
SDMSdata reduction
RefinementResolution: 1.54→20 Å / σ(F): 0
Details: BOTH TERMINI OF CRO K56-[DGEVK]ARE DISORDERED. RESIDUES 1, 2, 62, 63, 64, 65, AND 66 HAVE NO INTERPRETABLE DENSITY AND ARE NOT INCLUDED IN THE MODEL. RESIDUES 3 AND 61 EXTEN AWAY FROM THE ...Details: BOTH TERMINI OF CRO K56-[DGEVK]ARE DISORDERED. RESIDUES 1, 2, 62, 63, 64, 65, AND 66 HAVE NO INTERPRETABLE DENSITY AND ARE NOT INCLUDED IN THE MODEL. RESIDUES 3 AND 61 EXTEN AWAY FROM THE GLOBULAR PORTION OF THE MOLECULE AND ARE MOST PROBABLY IN MULTIPLE CONFORMATIONS. THE GLOBULAR PORTION OF THE MOLECULE (RESIDUES 4 - 59) IS EXCEPTIONALLY WELL-DEFINED IN THE DENSITY.
RfactorNum. reflection
Rwork0.178 -
all-9834
obs-9834
Refinement stepCycle: LAST / Resolution: 1.54→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms500 0 0 59 559
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2.3
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 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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