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- PDB-3ebe: Crystal structure of xenopus laevis replication initiation factor... -

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Basic information

Entry
Database: PDB / ID: 3ebe
TitleCrystal structure of xenopus laevis replication initiation factor MCM10 internal domain
ComponentsProtein MCM10 homolog
KeywordsREPLICATION / OB-FOLD / ZINC FINGER / CCCH / DNA replication / Metal-binding / Nucleus / Zinc-finger
Function / homology
Function and homology information


DNA replication initiation / single-stranded DNA binding / double-stranded DNA binding / DNA damage response / metal ion binding / nucleus
Similarity search - Function
Replication factor Mcm10, C-terminal / Mcm10 replication factor / Mcm10 replication factor / Zinc finger, Mcm10/DnaG-type / Minichromosome maintenance protein 10 / Primase zinc finger / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Protein MCM10 homolog
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsWarren, E.M. / Eichman, B.F.
CitationJournal: Structure / Year: 2008
Title: Structural basis for DNA binding by replication initiator mcm10.
Authors: Warren, E.M. / Vaithiyalingam, S. / Haworth, J. / Greer, B. / Bielinsky, A.K. / Chazin, W.J. / Eichman, B.F.
History
DepositionAug 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Protein MCM10 homolog
B: Protein MCM10 homolog
C: Protein MCM10 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2966
Polymers68,1003
Non-polymers1963
Water2,684149
1
A: Protein MCM10 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7652
Polymers22,7001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein MCM10 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7652
Polymers22,7001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein MCM10 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7652
Polymers22,7001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.565, 94.414, 69.775
Angle α, β, γ (deg.)90.00, 112.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein MCM10 homolog


Mass: 22699.984 Da / Num. of mol.: 3 / Fragment: UNP residues 230-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: mcm10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5EAW4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, TRIS, KSCN, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 22-ID111
SYNCHROTRONAPS 22-ID21.0388, 1.0311, 1.0370
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDMar 10, 2007
MARMOSAIC 300 mm CCD2CCDJun 10, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.03881
31.03111
41.0371
ReflectionResolution: 2.3→50 Å / Num. obs: 29404 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 48.4 Å2 / Rsym value: 0.074 / Net I/σ(I): 27.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2882 / Rsym value: 0.425 / % possible all: 97

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→44.4 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.508 / SU ML: 0.178 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2471 1481 5.1 %RANDOM
Rwork0.2023 ---
all0.2046 ---
obs0.2046 28929 99.73 %-
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: 55.685 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å2-0.73 Å2
2--0.71 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4123 0 3 149 4275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224199
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9615644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9195508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58424.948192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.02615821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4881523
X-RAY DIFFRACTIONr_chiral_restr0.1230.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023068
X-RAY DIFFRACTIONr_nbd_refined0.2190.21741
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22762
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2210
X-RAY DIFFRACTIONr_metal_ion_refined0.0420.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.221
X-RAY DIFFRACTIONr_mcbond_it0.7811.52646
X-RAY DIFFRACTIONr_mcangle_it1.36924126
X-RAY DIFFRACTIONr_scbond_it1.81431771
X-RAY DIFFRACTIONr_scangle_it2.9734.51518
LS refinement shellResolution: 2.3→2.424 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.319 221 -
Rwork0.253 3896 -
obs-4117 98.23 %
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)
12.4409-0.39430.53451.537-0.27181.5174-0.10630.1207-0.0345-0.00680.0106-0.0127-0.0821-0.1240.0957-0.0306-0.04280.0039-0.10080.0074-0.0838-22.6457-43.028716.6471
26.18780.36491.20240.5035-0.00232.07130.0358-0.0152-0.16690.03320.0949-0.0291-0.01530.0441-0.1307-0.12540.00690.006-0.1462-0.0453-0.1278-41.3084-68.40556.865
32.4701-0.3639-0.64772.35431.03852.76450.00840.01790.0308-0.058-0.1613-0.05-0.022-0.23090.1529-0.1059-0.05350.0052-0.1059-0.0365-0.1372-20.758-20.18129.7032
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA235 - 2978 - 70
2X-RAY DIFFRACTION1AA305 - 41378 - 186
3X-RAY DIFFRACTION1A500
4X-RAY DIFFRACTION2BB235 - 2968 - 69
5X-RAY DIFFRACTION2BB305 - 40878 - 181
6X-RAY DIFFRACTION2B501
7X-RAY DIFFRACTION3CC231 - 2974 - 70
8X-RAY DIFFRACTION3CC306 - 35079 - 123
9X-RAY DIFFRACTION3CC355 - 419128 - 192
10X-RAY DIFFRACTION3C502

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