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- PDB-2qby: Crystal structure of a heterodimer of Cdc6/Orc1 initiators bound ... -

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Basic information

Entry
Database: PDB / ID: 2qby
TitleCrystal structure of a heterodimer of Cdc6/Orc1 initiators bound to origin DNA (from S. solfataricus)
Components
  • (Cell division control protein 6 homolog ...) x 2
  • (DNA (33-MER)) x 2
KeywordsREPLICATION/DNA / winged-helix domain / helix-turn-helix / AAA+ ATPase domain / protein-DNA complex / double helix / REPLICATION-DNA COMPLEX
Function / homology
Function and homology information


DNA replication origin binding / DNA replication / ATP binding
Similarity search - Function
Orc1/Cdc6-type DNA replication protein, archaea / Cdc6, C-terminal / CDC6, C terminal / CDC6, C terminal winged helix domain / AAA domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases ...Orc1/Cdc6-type DNA replication protein, archaea / Cdc6, C-terminal / CDC6, C terminal / CDC6, C terminal winged helix domain / AAA domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / SPERMIDINE / DNA / DNA (> 10) / ORC1-type DNA replication protein 3 / ORC1-type DNA replication protein 1
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.35 Å
AuthorsCunningham Dueber, E.L. / Corn, J.E. / Bell, S.D. / Berger, J.M.
CitationJournal: Science / Year: 2007
Title: Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex.
Authors: Dueber, E.L. / Corn, J.E. / Bell, S.D. / Berger, J.M.
History
DepositionJun 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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
C: DNA (33-MER)
D: DNA (33-MER)
A: Cell division control protein 6 homolog 1
B: Cell division control protein 6 homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,91811
Polymers107,6854
Non-polymers1,2337
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.649, 199.143, 213.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsheterodimer of Orc1-1 and Orc1-3 bound to a 33bp DNA per asymmetric unit

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Components

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DNA chain , 2 types, 2 molecules CD

#1: DNA chain DNA (33-MER)


Mass: 10200.622 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (33-MER)


Mass: 10093.530 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Cell division control protein 6 homolog ... , 2 types, 2 molecules AB

#3: Protein Cell division control protein 6 homolog 1 / CDC6 homolog 1


Mass: 43922.883 Da / Num. of mol.: 1 / Fragment: Residues 15-397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: cdc6-1 / Plasmid: pSV271 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+ / References: UniProt: Q980N4
#4: Protein Cell division control protein 6 homolog 3 / CDC6 homolog 3


Mass: 43468.004 Da / Num. of mol.: 1 / Fragment: Residues 14-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: cdc6-3 / Plasmid: pSV271 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+ / References: UniProt: Q97WM8

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Non-polymers , 5 types, 11 molecules

#5: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.81 Å3/Da / Density % sol: 67.68 %
Crystal growTemperature: 292 K / Method: microbatch / pH: 5
Details: 25mM HEPES pH 7.5, 50mM sodium chloride, 5% glycerol, 0.5mM TCEP, 15mM spermidine, 15mM sodium cacodylate pH 5.0, 4.4% (w/v) PEG 3350 and 25mM potassium thiocyanate, microbatch, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2HEPES12
3sodium chloride11
4sodium chloride12
5TCEP11
6TCEP12
7spermidine11
8sodium cacodylate11
9sodium cacodylate12
10PEG 335011
11PEG 335012
12potassium thiocyanate11
13potassium thiocyanate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11111, 0.979578, 0.979733, 0.987379
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 20, 2006
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.111111
20.9795781
30.9797331
40.9873791
ReflectionResolution: 3.35→50 Å / Num. all: 24607 / Num. obs: 24287 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 119 Å2 / Net I/σ(I): 25.4
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.835 / Mean I/σ(I) obs: 1.93 / Num. unique all: 2385 / % possible all: 99

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Processing

Software
NameClassification
HKL-2000data collection
MLPHAREphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD
Starting model: PDB entry 1FNN

1fnn


Resolution: 3.35→30 Å / Isotropic thermal model: ISOTROPIC GROUPED B FACTOR / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: The authors state that the ANISOU lines in the pdb refer to TLS parameters, not anisotropic B factors.
RfactorNum. reflection% reflectionSelection details
Rfree0.2692 1215 -random
Rwork0.2262 ---
obs0.2262 22548 98 %-
all-23763 --
Refinement stepCycle: LAST / Resolution: 3.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5881 1347 77 4 7309
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_deg0.837
LS refinement shellResolution: 3.35→3.48 Å
RfactorNum. reflection% reflection
Rfree0.4376 148 -
Rwork0.3705 --
obs-2533 99 %

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