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- PDB-3h15: Crystal structure of replication initiation factor MCM10-ID bound... -

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Basic information

Entry
Database: PDB / ID: 3h15
TitleCrystal structure of replication initiation factor MCM10-ID bound to ssDNA
Components
  • 5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*C)-3'
  • Protein MCM10 homolog
KeywordsREPLICATION/DNA / OB-FOLD / ZINC FINGER / CCCH / DNA REPLICATION / ssDNA / DNA-binding / METAL-BINDING / NUCLEUS / ZINC-FINGER / REPLICATION-DNA COMPLEX
Function / homology
Function and homology information


nuclear replication fork / DNA replication origin binding / DNA replication initiation / single-stranded DNA binding / DNA damage response / zinc ion binding / nucleus
Similarity search - Function
Replication factor Mcm10, C-terminal / : / : / Mcm10, C-terminal zinc binding motif / Mcm10, CCCH-type zinc motif / Mcm10 replication factor / Zinc finger, Mcm10/DnaG-type / Minichromosome maintenance protein 10 / Primase zinc finger / MCM10 OB-fold ...Replication factor Mcm10, C-terminal / : / : / Mcm10, C-terminal zinc binding motif / Mcm10, CCCH-type zinc motif / Mcm10 replication factor / Zinc finger, Mcm10/DnaG-type / Minichromosome maintenance protein 10 / Primase zinc finger / MCM10 OB-fold / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / Protein MCM10 homolog
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsWarren, E.M. / Eichman, B.F.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Physical Interactions between Mcm10, DNA, and DNA Polymerase {alpha}.
Authors: Warren, E.M. / Huang, H. / Fanning, E. / Chazin, W.J. / Eichman, B.F.
History
DepositionApr 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Protein MCM10 homolog
B: 5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1693
Polymers25,1032
Non-polymers651
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-6 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.017, 95.017, 61.159
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein MCM10 homolog


Mass: 22545.818 Da / Num. of mol.: 1
Fragment: UNP residues 230-427, Zinc-finger domain, Internal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: mcm10 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q5EAW4
#2: DNA chain 5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*C)-3'


Mass: 2557.679 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.17 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 100mM TAPS pH 9.0, 17% PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-D10.97857
SYNCHROTRONNSLS X29A21
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDJan 7, 2008Be Lenses/Diamond Laue Mono
ADSC QUANTUM 3152CCDApr 9, 2007Si(111) Double Crystal monochrometer
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978571
211
ReflectionResolution: 2.72→50 Å / Num. all: 8882 / Num. obs: 8222 / % possible obs: 92.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 73.5 Å2 / Rsym value: 0.082 / Net I/σ(I): 11.38
Reflection shellResolution: 2.72→2.85 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.55 / Rsym value: 0.305 / % possible all: 51.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 2009_02_15_2320_3)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EBE

3ebe


Resolution: 2.72→34.138 Å / SU ML: 0.12 / σ(F): 1.34
RfactorNum. reflection% reflectionSelection details
Rfree0.232 388 4.72 %RANDOM
Rwork0.1973 ---
obs0.1991 8222 92.57 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 84.816 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 73.5 Å2
Refinement stepCycle: LAST / Resolution: 2.72→34.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 54 1 15 1450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-3.10650.31781050.27592233X-RAY DIFFRACTION80
3.1065-3.91290.28351420.19912780X-RAY DIFFRACTION100
3.9129-34.14030.19361410.17612821X-RAY DIFFRACTION98
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)
11.306-1.0275-0.96980.81360.66610.88620.41140.3055-0.2104-1.0105-0.3220.0632-0.79420.0318-0.21110.7732-0.10370.06620.7137-0.25630.377438.093814.0571-12.5387
22.19470.19641.01422.2130.04030.97670.37090.4991-0.49780.12630.2156-1.06690.00720.794-0.50730.34690.0387-0.07260.33-0.10420.47842.44216.8317-5.8935
32.154-0.9096-0.59781.0239-1.04383.4440.039-0.0111-0.2570.14740.21350.1304-0.0454-0.0259-0.24220.18650.0742-0.04680.19920.01150.309530.808524.71725.2855
41.8291-0.2717-0.01123.08860.31922.16960.0813-0.38780.21980.09360.16240.2002-0.1285-0.04110.14440.12310.0649-0.00840.2894-0.12080.18634.267932.20852.0463
53.39150.4014-0.42951.4118-0.28740.046-0.07981.1121-0.1807-0.26930.1182-0.181-0.3485-0.2038-0.02960.46460.1003-0.15840.6299-0.16060.358822.212525.913-17.8934
65.14470.7658-5.47450.77660.43878.2020.7788-1.44811.58890.36540.47780.1779-1.85730.8093-1.39551.28830.59130.69951.159-0.25531.406331.414141.95318.8052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 230:241)A230 - 241
2X-RAY DIFFRACTION2(chain A and resid 242:260)A242 - 260
3X-RAY DIFFRACTION3(chain A and resid 261:300)A261 - 300
4X-RAY DIFFRACTION4(chain A and resid 301:371)A301 - 371
5X-RAY DIFFRACTION5(chain A and resid 372:500)A372 - 500
6X-RAY DIFFRACTION6(chain B and resid 9:14)B9 - 14

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