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- PDB-5c8h: Crystal structure of ORC2 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 5c8h
TitleCrystal structure of ORC2 C-terminal domain
ComponentsOrigin recognition complex subunit 2
KeywordsREPLICATION / Structural Genomics / DNA replication / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / inner kinetochore / DNA replication origin binding / Activation of the pre-replicative complex / DNA replication initiation / heterochromatin / Activation of ATR in response to replication stress ...CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / inner kinetochore / DNA replication origin binding / Activation of the pre-replicative complex / DNA replication initiation / heterochromatin / Activation of ATR in response to replication stress / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / Orc1 removal from chromatin / chromosome, telomeric region / centrosome / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / membrane
Similarity search - Function
Origin recognition complex subunit 2 RecA-like domain / Origin recognition complex, subunit 2
Similarity search - Domain/homology
Origin recognition complex subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsTempel, W. / Xu, C. / Dong, A. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of ORC2 C-terminal domain
Authors: Tempel, W. / Xu, C. / Dong, A. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Origin recognition complex subunit 2


Theoretical massNumber of molelcules
Total (without water)13,8134
Polymers13,8131
Non-polymers03
Water43224
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.038, 55.038, 75.629
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
DetailsThe extent of the biological unit was not examined in this experiment.

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Components

#1: Protein Origin recognition complex subunit 2


Mass: 13813.487 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 458-577)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORC2, ORC2L / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q13416
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG-3350, 0.2 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792604 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792604 Å / Relative weight: 1
ReflectionResolution: 2.01→47.66 Å / Num. obs: 8700 / % possible obs: 99.8 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.024 / Net I/σ(I): 21.5 / Num. measured all: 96076
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.01-2.0610.61.032.267176320.8010.32798.1
9-47.669.40.0363.810111070.9990.00998.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.7data scaling
PHASERphasing
REFMAC5.8.0123refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
PHENIXrefinement
ARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: polyalanine coordinates derived from PDB entry 4XGC.

4xgc


Resolution: 2.01→47.66 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2429 / WRfactor Rwork: 0.1825 / FOM work R set: 0.8216 / SU B: 9.777 / SU ML: 0.132 / SU R Cruickshank DPI: 0.1792 / SU Rfree: 0.1801 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Data were reduced with HKL3000 for structure solution and early refinement. Molecular replacement was followed by simulated annealing refinement with PHENIX, subsequent phase improvement and ...Details: Data were reduced with HKL3000 for structure solution and early refinement. Molecular replacement was followed by simulated annealing refinement with PHENIX, subsequent phase improvement and automated model buidling with ARP/WARP. Diffraction data were reduced with XDS/AIMLESS for later refinement steps.
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 837 9.7 %RANDOM
Rwork0.1896 7833 --
obs0.196 8670 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.98 Å2 / Biso mean: 39.091 Å2 / Biso min: 26.46 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20.56 Å20 Å2
2--1.11 Å2-0 Å2
3----3.61 Å2
Refinement stepCycle: final / Resolution: 2.01→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms835 0 3 24 862
Biso mean--32.48 36.94 -
Num. residues----105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.019877
X-RAY DIFFRACTIONr_bond_other_d0.0020.02830
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9741195
X-RAY DIFFRACTIONr_angle_other_deg0.97531904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0555110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76423.77845
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09115152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.502158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021010
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
X-RAY DIFFRACTIONr_mcbond_it1.8742.758428
X-RAY DIFFRACTIONr_mcbond_other1.8222.752427
X-RAY DIFFRACTIONr_mcangle_it2.6834.118534
LS refinement shellResolution: 2.012→2.064 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 54 -
Rwork0.263 576 -
all-630 -
obs--98.59 %
Refinement TLS params.Method: refined / Origin x: 35.851 Å / Origin y: 13.1035 Å / Origin z: -5.9789 Å
111213212223313233
T0.0187 Å20.0115 Å20.0242 Å2-0.0169 Å20.0315 Å2--0.112 Å2
L2.482 °2-0.2884 °2-0.4876 °2-1.874 °20.8408 °2--3.5791 °2
S0.0466 Å °-0.0734 Å °-0.0188 Å °0.0039 Å °-0.06 Å °0.0235 Å °-0.2026 Å °-0.1148 Å °0.0134 Å °

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