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- PDB-5cro: REFINED STRUCTURE OF CRO REPRESSOR PROTEIN FROM BACTERIOPHAGE LAMBDA -

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Basic information

Entry
Database: PDB / ID: 5cro
TitleREFINED STRUCTURE OF CRO REPRESSOR PROTEIN FROM BACTERIOPHAGE LAMBDA
ComponentsCRO REPRESSOR PROTEIN
KeywordsGENE REGULATING PROTEIN / TRANSCRIPTION REGULATION
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
PHOSPHATE ION / Regulatory protein cro
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsOhlendorf, D.H. / Tronrud, D.E. / Matthews, B.W.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Refined structure of Cro repressor protein from bacteriophage lambda suggests both flexibility and plasticity.
Authors: Ohlendorf, D.H. / Tronrud, D.E. / Matthews, B.W.
#1: Journal: J.Biol.Chem. / Year: 1986
Title: Different Interactions Used by Cro Repressor in Specific and Nonspecific DNA Binding
Authors: Takeda, Y. / Kim, J.G. / Caday, C.G. / Steers Junior, E. / Ohlendorf, D.H. / Anderson, W.F. / Matthews, B.W.
#2: Journal: Chem.Scr. / Year: 1986
Title: Use of Protein Sequence and Structure to Infer Distant Evolutionary Relationships
Authors: Brennan, R.G. / Weaver, L.H. / Matthews, B.W.
#3: Journal: Biological Macromolecules and Assemblies. V.2: Nucleic Acids and Interactive Proteins
Year: 1985
Title: The Structure of Cro Repressor Protein
Authors: Takeda, Y. / Ohlendorf, D.H. / Anderson, W.F. / Matthews, B.W.
#4: Journal: J.Biomol.Struct.Dyn. / Year: 1983
Title: High Resolution Structural Studies of Cro Repressor Protein and Implications for DNA Recognition
Authors: Ohlendorf, D.H. / Anderson, W.F. / Takeda, Y. / Matthews, B.W.
#5: Journal: Science / Year: 1983
Title: DNA-Binding Proteins
Authors: Takeda, Y. / Ohlendorf, D.H. / Anderson, W.F. / Matthews, B.W.
#6: 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.
#7: Journal: J.Mol.Biol. / Year: 1983
Title: Crystallographic Data for Complexes of the Cro Repressor with DNA
Authors: Anderson, W.F. / Cygler, M. / Vandonselaar, M. / Ohlendorf, D.H. / Matthews, B.W. / Kim, J. / Takeda, Y.
#8: Journal: Annu.Rev.Biophys.Bioeng. / Year: 1983
Title: Structural Studies of Protein-Nucleic Acid Interactions
Authors: Ohlendorf, D.H. / Matthews, B.W.
#9: Journal: Trends Biochem.Sci. / Year: 1983
Title: How Does Cro Repressor Recognize its DNA Target Sites?
Authors: Matthews, B.W. / Ohlendorf, D.H. / Anderson, W.F. / Fisher, R.G. / Takeda, Y.
#10: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1983
Title: Cro Repressor Protein and its Interaction with DNA
Authors: Matthews, B.W. / Ohlendorf, D.H. / Anderson, W.F. / Fisher, R.G. / Takeda, Y.
#11: Journal: J.Mol.Evol. / Year: 1983
Title: Many Gene-Regulatory Proteins Appear to Have a Similar Alpha-Helical Fold that Binds DNA and Evolved from a Common Precursor
Authors: Ohlendorf, D.H. / Anderson, W.F. / Matthews, B.W.
#12: Journal: Nature / Year: 1982
Title: The Molecular Basis of DNA-Protein Recognition Inferred from the Structure of Cro Repressor
Authors: Ohlendorf, D.H. / Anderson, W.F. / Fisher, R.G. / Takeda, Y. / Matthews, B.W.
#13: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Structural Similarity in the DNA-Binding Domains of Catabolite Gene Activator and Cro Repressor Proteins
Authors: Steitz, T.A. / Ohlendorf, D.H. / Mckay, D.B. / Anderson, W.F. / Matthews, B.W.
#14: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Structure of the DNA-Binding Region of Lac Repressor Inferred from its Homology with Cro Repressor
Authors: Matthews, B.W. / Ohlendorf, D.H. / Anderson, W.F. / Takeda, Y.
#15: Journal: J.Mol.Biol. / Year: 1982
Title: Proposed Alpha-Helical Super-Secondary Structure Associated with Protein-DNA Recognition
Authors: Anderson, W.F. / Takeda, Y. / Ohlendorf, D.H. / Matthews, B.W.
#16: Journal: Nature / Year: 1981
Title: Structure of the Cro Repressor from Bacteriophage Lambda and its Interaction with DNA
Authors: Anderson, W.F. / Ohlendorf, D.H. / Takeda, Y. / Matthews, B.W.
#17: Journal: J.Mol.Biol. / Year: 1979
Title: The Structure of a Repressor. Crystallographic Data for the Cro Regulatory Protein of Bacteriophage Lambda
Authors: Anderson, W.F. / Matthews, B.W. / Takeda, Y. / Echols, H.
#18: Journal: Nature / Year: 1977
Title: Amino Acid Sequence of Cro Regulatory Protein of Bacteriophage Lambda
Authors: Hsiang, M.W. / Cole, R.D. / Takeda, Y. / Echols, H.
History
DepositionApr 17, 1998Processing site: BNL
SupersessionJun 17, 1998ID: 1CRO
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: CRO REPRESSOR PROTEIN
A: CRO REPRESSOR PROTEIN
B: CRO REPRESSOR PROTEIN
C: CRO REPRESSOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6926
Polymers29,5024
Non-polymers1902
Water59433
1
O: CRO REPRESSOR PROTEIN
B: CRO REPRESSOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9414
Polymers14,7512
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-9 kcal/mol
Surface area7960 Å2
MethodPISA
2
A: CRO REPRESSOR PROTEIN
C: CRO REPRESSOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,7512
Polymers14,7512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-10 kcal/mol
Surface area8010 Å2
MethodPISA
3
O: CRO REPRESSOR PROTEIN
A: CRO REPRESSOR PROTEIN
B: CRO REPRESSOR PROTEIN
C: CRO REPRESSOR PROTEIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)178,15136
Polymers177,01224
Non-polymers1,14012
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation17_434x-y-2/3,-y-4/3,-z-1/31
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area44270 Å2
ΔGint-175 kcal/mol
Surface area66830 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-21 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.600, 91.600, 268.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11O-100-

PO4

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99383, 0.0516, -0.02407), (0.05397, 0.99229, -0.1116), (0.01812, -0.11272, -0.99346)-27.083, -1.7302, -48.907
2given(0.31092, -0.02396, 0.95013), (0.02281, -0.99921, -0.03266), (0.95016, 0.03183, -0.31013)10.4738, -73.83, -14.8488
3given(-0.31067, -0.12332, -0.94248), (-0.08774, -0.98359, 0.15763), (-0.94646, 0.13167, 0.29475)-44.5491, -70.7468, -24.4876
DetailsTHE DIMER OF CRO THAT EXISTS IN SOLUTION IS PRESUMED TO BE THE O-B DIMER WHICH IS GENERALLY USED AS THE MODEL OF THE DIMER WHICH BINDS DNA.

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Components

#1: Protein
CRO REPRESSOR PROTEIN


Mass: 7375.484 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: WATER MOLECULES AND TWO PHOSPHATE RADICALS / Source: (natural) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / References: UniProt: P03040
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 4

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 67 % / Description: THE DATA WERE COLLECTED IN THE EARLY 1980'S.
Crystal growMethod: microdialysis or batch / pH: 7.5
Details: CRYSTALS WERE OBTAINED IN THE PRESENCE OF ABOUT 1.2M PHOSPHATE BY MICRODIALYSIS OR BATCH TECHNIQUES., pH 7.5, microdialysis or batch
Crystal grow
*PLUS
Method: microdialysis / Details: or batch / PH range low: 7.7 / PH range high: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
142 %satammonium sulfate11
21.2 Mphosphate11

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: FILM / Detector: FILM
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 17141 / % possible obs: 84 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.096

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Processing

Software
NameVersionClassification
LYNNTEN EYCK'S NEWREFmodel building
TNT1refinement
OSCTSTdata reduction
VENUSdata reduction
CCP4(ROTAVATA)data scaling
ODPROCdata scaling
NEWREF(LYNN TEN EYCK)phasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO V1.0
RfactorNum. reflection% reflection
Rwork0.193 --
all-17141 -
obs-17141 84 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 120 Å2 / ksol: 0.749 e/Å3
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 10 33 1940
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01919370.8
X-RAY DIFFRACTIONt_angle_deg3.27125931.3
X-RAY DIFFRACTIONt_dihedral_angle_d19.57811680
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle25.35981
X-RAY DIFFRACTIONt_trig_c_planes0.008442
X-RAY DIFFRACTIONt_gen_planes0.0142795
X-RAY DIFFRACTIONt_it7.32319371
X-RAY DIFFRACTIONt_nbd0.0213510
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19.5780
X-RAY DIFFRACTIONt_plane_restr0.0145

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