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- PDB-4dov: Structure of free mouse ORC1 BAH domain -

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Basic information

Entry
Database: PDB / ID: 4dov
TitleStructure of free mouse ORC1 BAH domain
ComponentsOrigin recognition complex subunit 1
KeywordsREPLICATION / DNA replication
Function / homology
Function and homology information


CDC6 association with the ORC:origin complex / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / Assembly of the ORC complex at the origin of replication / origin recognition complex / Orc1 removal from chromatin / positive regulation of G0 to G1 transition / nuclear origin of replication recognition complex / mitotic DNA replication checkpoint signaling / DNA replication initiation ...CDC6 association with the ORC:origin complex / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / Assembly of the ORC complex at the origin of replication / origin recognition complex / Orc1 removal from chromatin / positive regulation of G0 to G1 transition / nuclear origin of replication recognition complex / mitotic DNA replication checkpoint signaling / DNA replication initiation / positive regulation of smooth muscle cell proliferation / DNA replication / chromosome, telomeric region / chromatin binding / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus
Similarity search - Function
Bromo adjacent homology (BAH) domain / Cdc6, C-terminal / CDC6, C terminal / CDC6, C terminal winged helix domain / AAA lid domain / AAA lid domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain ...Bromo adjacent homology (BAH) domain / Cdc6, C-terminal / CDC6, C terminal / CDC6, C terminal winged helix domain / AAA lid domain / AAA lid domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / SH3 type barrels. / Roll / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Origin recognition complex subunit 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.696 Å
AuthorsSong, J. / Patel, D.J.
CitationJournal: Nature / Year: 2012
Title: The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier-Gorlin syndrome.
Authors: Kuo, A.J. / Song, J. / Cheung, P. / Ishibe-Murakami, S. / Yamazoe, S. / Chen, J.K. / Patel, D.J. / Gozani, O.
History
DepositionFeb 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Apr 11, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Origin recognition complex subunit 1
C: Origin recognition complex subunit 1


Theoretical massNumber of molelcules
Total (without water)38,0792
Polymers38,0792
Non-polymers00
Water4,324240
1
A: Origin recognition complex subunit 1


Theoretical massNumber of molelcules
Total (without water)19,0401
Polymers19,0401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Origin recognition complex subunit 1


Theoretical massNumber of molelcules
Total (without water)19,0401
Polymers19,0401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.922, 53.916, 71.971
Angle α, β, γ (deg.)90.00, 102.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Origin recognition complex subunit 1 / / ORC1


Mass: 19039.691 Da / Num. of mol.: 2 / Fragment: BAH domain (UNP residues 9-170)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Orc1, Orc1l / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9Z1N2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M 3-(1-pyridino)-1-propane sulfonate, 0.2 M sodium bromide, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2011
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.696→30 Å / Num. all: 41317 / Num. obs: 41079 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.064 / Net I/σ(I): 24.3
Reflection shellResolution: 1.696→1.76 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.85 / Num. unique all: 4090 / Rsym value: 0.445 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.696→22.414 Å / SU ML: 0.46 / σ(F): 1.35 / Phase error: 25.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 1997 4.87 %RANDOM
Rwork0.2146 ---
obs0.2159 41016 96.9 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.021 Å2 / ksol: 0.412 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.601 Å20 Å20.9148 Å2
2--1.1495 Å20 Å2
3---6.4515 Å2
Refinement stepCycle: LAST / Resolution: 1.696→22.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 0 240 2707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072538
X-RAY DIFFRACTIONf_angle_d1.123455
X-RAY DIFFRACTIONf_dihedral_angle_d16.956931
X-RAY DIFFRACTIONf_chiral_restr0.085376
X-RAY DIFFRACTIONf_plane_restr0.005444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.696-1.73850.3151280.28642536X-RAY DIFFRACTION90
1.7385-1.78550.31961450.2642803X-RAY DIFFRACTION100
1.7855-1.8380.30191420.25332792X-RAY DIFFRACTION100
1.838-1.89730.25881450.23372795X-RAY DIFFRACTION100
1.8973-1.96510.26181430.22242796X-RAY DIFFRACTION100
1.9651-2.04370.25531450.21662822X-RAY DIFFRACTION100
2.0437-2.13660.25541430.21162801X-RAY DIFFRACTION100
2.1366-2.24920.25831440.21282825X-RAY DIFFRACTION100
2.2492-2.38990.25041440.22162801X-RAY DIFFRACTION100
2.3899-2.57420.30381440.23652831X-RAY DIFFRACTION100
2.5742-2.83280.27931460.23742832X-RAY DIFFRACTION100
2.8328-3.24170.27231440.2212820X-RAY DIFFRACTION100
3.2417-4.08020.21421460.19012858X-RAY DIFFRACTION100
4.0802-22.41560.19151380.20082707X-RAY DIFFRACTION93

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