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- PDB-1w5s: Structure of the Aeropyrum Pernix ORC2 protein (ADP form) -

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Basic information

Entry
Database: PDB / ID: 1w5s
TitleStructure of the Aeropyrum Pernix ORC2 protein (ADP form)
ComponentsORIGIN RECOGNITION COMPLEX SUBUNIT 2 ORC2
KeywordsREPLICATION / ORC / CDC6 / DNA REPLICATION INITIATION / DNA BINDING PROTEIN / AAA+ ATPASE
Function / homology
Function and homology information


DNA replication origin binding / DNA replication / ATP hydrolysis activity / 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 / 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 / ORC1-type DNA replication protein 2
Similarity search - Component
Biological speciesAEROPYRUM PERNIX (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.4 Å
AuthorsSingleton, M.R. / Morales, R. / Grainge, I. / Cook, N. / Isupov, M.N. / Wigley, D.B.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Conformational Changes Induced by Nucleotide Binding in Cdc6/Orc from Aeropyrum Pernix
Authors: Singleton, M.R. / Morales, R. / Grainge, I. / Cook, N. / Isupov, M.N. / Wigley, D.B.
History
DepositionAug 9, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORIGIN RECOGNITION COMPLEX SUBUNIT 2 ORC2
B: ORIGIN RECOGNITION COMPLEX SUBUNIT 2 ORC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8298
Polymers92,5912
Non-polymers1,2396
Water2,054114
1
A: ORIGIN RECOGNITION COMPLEX SUBUNIT 2 ORC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9154
Polymers46,2951
Non-polymers6193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ORIGIN RECOGNITION COMPLEX SUBUNIT 2 ORC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9154
Polymers46,2951
Non-polymers6193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.495, 101.911, 255.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ORIGIN RECOGNITION COMPLEX SUBUNIT 2 ORC2 / HYPOTHETICAL PROTEIN APE0152 / ORC2


Mass: 46295.398 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AEROPYRUM PERNIX (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): K1 / References: UniProt: Q9YFU8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.46 Å3/Da / Density % sol: 49.58 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9599
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9599 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 34887 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 11 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 19.2

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.4→129.1 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.856 / SU B: 18.587 / SU ML: 0.228 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.494 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1735 5 %RANDOM
Rwork0.212 ---
obs0.216 32664 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å20 Å20 Å2
2---1.67 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.4→129.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 74 114 6390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226377
X-RAY DIFFRACTIONr_bond_other_d0.0020.026053
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.9988638
X-RAY DIFFRACTIONr_angle_other_deg1.004313978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2795781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35222.979282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.965151139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8591562
X-RAY DIFFRACTIONr_chiral_restr0.1160.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026963
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021293
X-RAY DIFFRACTIONr_nbd_refined0.2330.21481
X-RAY DIFFRACTIONr_nbd_other0.2090.26213
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22999
X-RAY DIFFRACTIONr_nbtor_other0.0950.23937
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.2133
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0251.55025
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23926272
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17832807
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1954.52366
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: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 111
Rwork0.233 2417
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)
12.50171.6196-0.76812.9877-0.76121.7236-0.02050.0155-0.0928-0.0195-0.0223-0.0050.10370.15180.0428-0.1803-0.03520.005-0.1211-0.0111-0.21198.035462.572146.4406
23.97771.3819-1.18164.19541.65594.79650.0382-0.22580.26150.0595-0.05650.2287-0.29380.08360.0183-0.1497-0.097-0.0108-0.166-0.0028-0.113714.634392.618150.8585
32.6917-1.11821.48414.7042-1.37720.9548-0.1399-0.40760.10840.41920.07630.2268-0.5079-0.01120.06350.4619-0.07080.04820.55590.01260.438340.356973.413333.9847
42.02021.5580.10075.3253-0.7871.2612-0.22980.09980.1162-0.60190.1672-0.12790.08190.11690.06260.0063-0.09560.0034-0.0949-0.003-0.198410.437973.435617.5365
55.09391.19471.1355.49430.06333.1664-0.10420.29660.1877-0.57150.12730.58380.0189-0.2505-0.0231-0.0512-0.1181-0.067-0.12610.043-0.0753-14.992355.922616.0508
65.7721-0.47890.35087.4073-1.40933.8990.04810.1259-0.02110.0476-0.12730.316-0.0203-0.04560.0793-0.0451-0.0495-0.0051-0.0396-0.0453-0.056418.123839.777212.7796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 214
2X-RAY DIFFRACTION2A215 - 293
3X-RAY DIFFRACTION3A300 - 409
4X-RAY DIFFRACTION4B7 - 214
5X-RAY DIFFRACTION5B215 - 296
6X-RAY DIFFRACTION6B300 - 409

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