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- PDB-6cro: CRYSTAL STRUCTURE OF LAMBDA-CRO BOUND TO A CONSENSUS OPERATOR AT ... -

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Basic information

Entry
Database: PDB / ID: 6cro
TitleCRYSTAL STRUCTURE OF LAMBDA-CRO BOUND TO A CONSENSUS OPERATOR AT 3.0 ANGSTROM RESOLUTION
Components
  • DNA (5'-D(*AP*CP*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*AP*TP*CP*AP*CP*CP*CP*GP*CP*GP*GP*TP*GP*AP*TP*AP*G)-3')
  • LAMBDA CRO REPRESSOR
KeywordsGENE REGULATION/DNA / COMPLEX (TRANSCRIPTION REGULATION-DNA) / CRO / BACTERIOPHAGE LAMBDA / CONFORMATIONAL CHANGE / REPRESSOR / HELIX-TURN-HELIX / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


latency-replication decision / release from viral latency / negative regulation of viral transcription / negative regulation of transcription by competitive promoter binding / 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
DNA / DNA (> 10) / Regulatory protein cro
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / MIR, WITH SUBSEQUENT MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAlbright, R.A. / Matthews, B.W.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of lambda-Cro bound to a consensus operator at 3.0 A resolution.
Authors: Albright, R.A. / Matthews, B.W.
#1: Journal: Protein Sci. / Year: 1998
Title: Crystal Structure of an Engineered Cro Monomer Bound Nonspecifically to DNA: Possible Implications for Nonspecific Binding by the Wild-Type Protein
Authors: Albright, R.A. / Mossing, M.C. / Matthews, B.W.
#2: 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.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: How Cro and Lambda-Repressor Distinguish between Operators: The Structural Basis Underlying a Genetic Switch
Authors: Albright, R.A. / Matthews, B.W.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990
Title: Protein-DNA Conformational Changes in the Crystal Structure of a Lambda Cro- Operator Complex
Authors: Brennan, R.G. / Roderick, S.L. / Takeda, Y. / Matthews, B.W.
History
DepositionApr 22, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Sep 18, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: DNA (5'-D(*AP*CP*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*AP*C)-3')
U: DNA (5'-D(*TP*GP*TP*AP*TP*CP*AP*CP*CP*CP*GP*CP*GP*GP*TP*GP*AP*TP*AP*G)-3')
A: LAMBDA CRO REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0784
Polymers18,9823
Non-polymers961
Water1267
1
R: DNA (5'-D(*AP*CP*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*AP*C)-3')
U: DNA (5'-D(*TP*GP*TP*AP*TP*CP*AP*CP*CP*CP*GP*CP*GP*GP*TP*GP*AP*TP*AP*G)-3')
A: LAMBDA CRO REPRESSOR
hetero molecules

R: DNA (5'-D(*AP*CP*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*AP*C)-3')
U: DNA (5'-D(*TP*GP*TP*AP*TP*CP*AP*CP*CP*CP*GP*CP*GP*GP*TP*GP*AP*TP*AP*G)-3')
A: LAMBDA CRO REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1558
Polymers37,9636
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_566x,-y+1,-z+3/21
Unit cell
Length a, b, c (Å)102.970, 102.970, 102.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Cell settingcubic
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-400-

SO4

21A-400-

SO4

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Components

#1: DNA chain DNA (5'-D(*AP*CP*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*AP*C)-3')


Mass: 6118.968 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*GP*TP*AP*TP*CP*AP*CP*CP*CP*GP*CP*GP*GP*TP*GP*AP*TP*AP*G)-3')


Mass: 6149.979 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein LAMBDA CRO REPRESSOR / LAMBDA CRO REPRESSOR


Mass: 6712.643 Da / Num. of mol.: 1
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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS ENTRY CONTAINS THE COMPLETE ASYMMETRIC UNIT. THE PROTEIN CHAIN IS PRESENTED AS CHAIN A WITH ...THIS ENTRY CONTAINS THE COMPLETE ASYMMETRIC UNIT. THE PROTEIN CHAIN IS PRESENTED AS CHAIN A WITH OCCUPANCY 1.0. THE 10-RESIDUE LONG DNA DUPLEX IS DISORDERED WITH EACH CONFORMATION HAVING OCCUPANCY 0.5. RESIDUES 1-10 OF BOTH DNA CHAINS R AND U PRESENT ONE CONFORMATION AND RESIDUES 11-20 OF BOTH DNA CHAINS PRESENT THE OTHER CONFORMATION.

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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: 3.3 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: CRO PROTEIN WAS SUSPENDED IN 20MM SODIUM CACODYLATE PH6.9 THEN MIXED WITH A 30% EXCESS OF THE 19BP DNA FRAGMENT. THE COMPLEX WAS THEN MIXED WITH AN EQUAL VOLUME OF PRECIPITANT SOLUTION (70MM ...Details: CRO PROTEIN WAS SUSPENDED IN 20MM SODIUM CACODYLATE PH6.9 THEN MIXED WITH A 30% EXCESS OF THE 19BP DNA FRAGMENT. THE COMPLEX WAS THEN MIXED WITH AN EQUAL VOLUME OF PRECIPITANT SOLUTION (70MM AMMONIUM SULFATE, 13% PEG3350) AND ALLOWED TO EQUILIBRATE VIA THE HANGING DROP METHOD AT ROOM TEMPERATURE. COCRYSTALS TYPICALLY TAKE 3-4 MONTHS TO APPEAR., vapor diffusion - hanging drop, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2(NH4)2SO411
3PEG 335011
4(NH4)2SO412
5PEG 335012
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.0 mg/mlprotein complex1drop
250-80 mMammonium sulfate1drop
311-14 %PEG33501drop
4100-160 mMammonium sulfate1reservoir
522-28 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Feb 15, 1993 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 3758 / Num. obs: 3758 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.7 % / Biso Wilson estimate: 40.8 Å2 / Rsym value: 0.072
Reflection shellHighest resolution: 3 Å
Reflection
*PLUS
Num. all: 3760 / Num. measured all: 132786 / Rmerge(I) obs: 0.072

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Processing

Software
NameVersionClassification
VERIFY(RODERICK)model building
EDPDB(ZHANG)model building
TNT5EBrefinement
SDMSdata reduction
SDMSdata scaling
VERIFY(RODERICK)phasing
EDPDB(ZHANG)phasing
RefinementMethod to determine structure: MIR, WITH SUBSEQUENT MOLECULAR REPLACEMENT
Starting model: TRUNCATED VERSION OF THE PREVIOUS LOW-RESOLUTION COMPLEX STRUCTURE

Resolution: 3→20 Å / σ(F): 0
Stereochemistry target values: TNT PROTGEO & NUCLGEO ISOTROPIC THERMAL FACTOR RESTRAINTS: TNT BCORREL (MODIFIED TO INCLUDE DNA)
Details: THIS MODEL UNDERWENT ONE FINAL ROUND OF REFINEMENT AFTER THE MANUSCRIPT WAS SUBMITTED. THE PSEUDO-DYAD OF THE COMPLEX IS COINCIDENT WITH A CRYSTALLOGRAPHIC TWO-FOLD AXIS, SUCH THAT THE ...Details: THIS MODEL UNDERWENT ONE FINAL ROUND OF REFINEMENT AFTER THE MANUSCRIPT WAS SUBMITTED. THE PSEUDO-DYAD OF THE COMPLEX IS COINCIDENT WITH A CRYSTALLOGRAPHIC TWO-FOLD AXIS, SUCH THAT THE COMPLEX IS EVENLY-DISTRIBUTED BETWEEN TWO ORIENTATIONS RELATED BY A 180-DEGREE ROTATION. THE SPACE GROUP IS I 21 3 WITH A SINGLE CRO SUBUNIT AND AN "AVERAGED" DNA HALF-FRAGMENT PER ASU. THIS AVERAGING AFFECTED ONLY THOSE BP IDENTITIES WHERE THE SEQUENCE PALINDROME BREAKS DOWN, WHICH OCCURS ONLY IN REGIONS NOT CONTACTED BY CRO. THE PROTEIN, DNA BACKBONE, AND THOSE BPS DIRECTLY CONTACTED BY CRO ARE EVERYWHERE "NORMAL". THE AVERAGED BASES CONSISTED OF THE TWO COMPONENT BASES AT A GIVEN POSITION, EACH BONDED TO THE SAME RIBOSE, BUT ALLOWED TO IGNORE THE PRESENCE OF EACH OTHER DURING REFINEMENT.
RfactorNum. reflection% reflection
Rwork0.194 --
all-3758 -
obs-3758 99.9 %
Solvent computationSolvent model: BABINET / Bsol: 160 Å2 / ksol: 0.5 e/Å3
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms472 814 5 7 1298
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01410061.6
X-RAY DIFFRACTIONt_angle_deg2.58714562.3
X-RAY DIFFRACTIONt_dihedral_angle_d23.2445310.2
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011122.2
X-RAY DIFFRACTIONt_gen_planes0.016956.6
X-RAY DIFFRACTIONt_it1.811105834
X-RAY DIFFRACTIONt_nbd0.0335110
Software
*PLUS
Name: TNT / Version: 5EB / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg23.2440.2
X-RAY DIFFRACTIONt_planar_d0.0112.2
X-RAY DIFFRACTIONt_plane_restr0.0166.6

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