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- PDB-2v1u: STRUCTURE OF THE AEROPYRUM PERNIX ORC1 PROTEIN IN COMPLEX WITH DNA -

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Basic information

Entry
Database: PDB / ID: 2v1u
TitleSTRUCTURE OF THE AEROPYRUM PERNIX ORC1 PROTEIN IN COMPLEX WITH DNA
Components
  • 5'-D(*AP*CP*CP*CP*CP*TP*CP*CP*GP*TP *TP*TP*CP*CP*TP*GP*TP*GP*GP*AP*GP*A)-3'
  • 5'-D(*TP*CP*TP*CP*CP*AP*CP*AP*GP*GP *AP*AP*AP*CP*GP*GP*AP*GP*GP*GP*GP*T)-3'
  • CELL DIVISION CONTROL PROTEIN 6 HOMOLOG
KeywordsREPLICATION / DNA REPLICATION / NUCLEOTIDE-BINDING / ARCHAEA / ATP-BINDING / PHOSPHORYLATION / DNA REPLICATION INITIATION
Function / homology
Function and homology information


DNA replication / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
: / Cdc6 AAA+ ATPase-type lid domain / Orc1/Cdc6-type DNA replication protein, archaea / CDC6, C terminal / Cdc6, C-terminal / CDC6, C terminal winged helix domain / : / AAA domain / AAA ATPase domain / : ...: / Cdc6 AAA+ ATPase-type lid domain / Orc1/Cdc6-type DNA replication protein, archaea / CDC6, C terminal / Cdc6, C-terminal / CDC6, C terminal winged helix domain / : / AAA domain / AAA ATPase 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 / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / ORC1-type DNA replication protein 1
Similarity search - Component
Biological speciesAEROPYRUM PERNIX (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsGaudier, M. / Schuwirth, B.S. / Westcott, S.L. / Wigley, D.B.
CitationJournal: Science / Year: 2007
Title: Structural Basis of DNA Replication Origin Recognition by an Orc Protein.
Authors: Gaudier, M. / Schuwirth, B.S. / Westcott, S.L. / Wigley, D.B.
History
DepositionMay 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELL DIVISION CONTROL PROTEIN 6 HOMOLOG
B: 5'-D(*TP*CP*TP*CP*CP*AP*CP*AP*GP*GP *AP*AP*AP*CP*GP*GP*AP*GP*GP*GP*GP*T)-3'
C: 5'-D(*AP*CP*CP*CP*CP*TP*CP*CP*GP*TP *TP*TP*CP*CP*TP*GP*TP*GP*GP*AP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4595
Polymers57,0073
Non-polymers4522
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
MethodPQS
Unit cell
Length a, b, c (Å)75.700, 75.700, 395.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CELL DIVISION CONTROL PROTEIN 6 HOMOLOG / CDC6 HOMOLOG / ORC1


Mass: 43501.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) AEROPYRUM PERNIX (archaea) / References: UniProt: Q9YEV6

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 5'-D(*TP*CP*TP*CP*CP*AP*CP*AP*GP*GP *AP*AP*AP*CP*GP*GP*AP*GP*GP*GP*GP*T)-3' / 22BP ORB4 ELEMENT


Mass: 6826.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) AEROPYRUM PERNIX (archaea)
#3: DNA chain 5'-D(*AP*CP*CP*CP*CP*TP*CP*CP*GP*TP *TP*TP*CP*CP*TP*GP*TP*GP*GP*AP*GP*A)-3' / 22BP ORB4 ELEMENT


Mass: 6679.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) AEROPYRUM PERNIX (archaea)

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Non-polymers , 3 types, 10 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.74 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.97295
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97295 Å / Relative weight: 1
ReflectionResolution: 3.1→15 Å / Num. obs: 12348 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.41
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.52 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
autoSHARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3.1→15 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.889 / SU B: 63.427 / SU ML: 0.515 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.531 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.297 636 4.9 %RANDOM
Rwork0.254 ---
obs0.257 12348 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 102.61 Å2
Baniso -1Baniso -2Baniso -3
1-5.07 Å22.54 Å20 Å2
2--5.07 Å20 Å2
3----7.61 Å2
Refinement stepCycle: LAST / Resolution: 3.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 896 28 8 3951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0224096
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1472.285737
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.515380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33321.095137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg27.54515554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3471548
X-RAY DIFFRACTIONr_chiral_restr0.1010.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022760
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3570.22268
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3390.22621
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2850.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2850.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.51551927
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.89353078
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it12.113202710
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it14.822202659
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.457 53
Rwork0.368 868
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.31843.124-0.28571.9018-0.96391.90750.1065-0.0241-0.64620.3369-0.0234-0.211.1832-0.0353-0.08310.63510.2851-0.1588-0.3849-0.11010.0985-16.447-30.378-27.959
25.3309-4.0071-1.54738.26221.38549.740.6358-0.16110.4330.8094-0.3226-0.4301-0.11270.9461-0.3132-0.0488-0.0188-0.017-0.5336-0.0088-0.3356-7.749-3.612-17.413
33.19673.2697-1.07445.2492-1.84063.00630.2316-0.13970.24990.44340.06040.2276-0.0884-0.2828-0.2920.1533-0.0768-0.0191-0.456-0.1201-0.2982-31.194-14.9772.545
41.79380.05210.80161.72280.65275.74360.3773-0.0337-0.5631-0.0304-0.06070.18420.2179-0.6006-0.31660.2581-0.1884-0.2227-0.39270.0645-0.2173-35.446-35.76-3.147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 211
2X-RAY DIFFRACTION2A13 - 36
3X-RAY DIFFRACTION2A212 - 278
4X-RAY DIFFRACTION3A279 - 399
5X-RAY DIFFRACTION4B1 - 22
6X-RAY DIFFRACTION4C1 - 22

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