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- PDB-7y01: Crystal structure of ZmMCM10 in complex with 16nt ssDNA at 2.8. A... -

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Basic information

Entry
Database: PDB / ID: 7y01
TitleCrystal structure of ZmMCM10 in complex with 16nt ssDNA at 2.8. Angstrom resolution
Components
  • DNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')
  • MCM10 minichromosome maintenance deficient 10
KeywordsPLANT PROTEIN/DNA / DNA binding / maintain genome stability / maintain epigenetic modifications / PLANT PROTEIN / PLANT PROTEIN-DNA complex
Function / homology
Function and homology information


nuclear replication fork / DNA replication origin binding / DNA replication initiation / single-stranded DNA binding
Similarity search - Function
Zinc finger, Mcm10/DnaG-type / Minichromosome maintenance protein 10 / Primase zinc finger / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / MCM10 minichromosome maintenance deficient 10
Similarity search - Component
Biological speciesZea mays (maize)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDu, X. / Du, J.
CitationJournal: J Integr Plant Biol / Year: 2023
Title: AtMCM10 promotes DNA replication-coupled nucleosome assembly in Arabidopsis.
Authors: Zhao, X. / Wang, J. / Jin, D. / Cheng, J. / Chen, H. / Li, Z. / Wang, Y. / Lou, H. / Zhu, J.K. / Du, X. / Gong, Z.
History
DepositionJun 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MCM10 minichromosome maintenance deficient 10
B: DNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9183
Polymers24,8522
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.180, 85.180, 103.912
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein MCM10 minichromosome maintenance deficient 10 / Minichromosome maintenance 10


Mass: 20270.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100279993, ZEAMMB73_Zm00001d022619
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B6TE84
#2: DNA chain DNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')


Mass: 4581.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 4.38 Å3/Da / Density % sol: 71.91 %
Crystal growTemperature: 293.15 K / Method: evaporation, recrystallization / Details: 0.2M lithium citrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 11121 / % possible obs: 99.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 14.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 60687 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EBE

3ebe


Resolution: 2.8→36.88 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.65
RfactorNum. reflection% reflection
Rfree0.243 532 4.79 %
Rwork0.199 10565 -
obs0.201 11097 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.55 Å2 / Biso mean: 61.3436 Å2 / Biso min: 33.06 Å2
Refinement stepCycle: final / Resolution: 2.8→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 202 1 0 1485
Biso mean--56.44 --
Num. residues----183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8002-3.08190.29291070.2651261199
3.0819-3.52760.27441500.23532600100
3.5276-4.44310.19831430.18642608100
4.4431-36.880.25381320.175274699
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)
10.68280.0896-0.02981.53460.68980.6991-0.3049-0.15750.90040.04-0.16510.0241-0.1924-0.6201-0.05170.5976-0.05440.0390.627-0.0410.432241.1517-27.3023-17.3901
22.1541-0.30040.54781.76960.18222.51690.53990.0401-0.2855-0.4274-0.48560.0173-0.4092-0.7559-0.01540.6787-0.05020.0750.6008-0.02490.435236.4404-26.2056-16.6165
31.2493-0.3397-0.14132.2476-1.19274.7177-0.00260.07890.5154-0.00420.5774-0.8028-1.58190.7515-0.05530.6634-0.22180.19030.5538-0.0330.597644.459-17.0353-10.058
42.0547-0.96530.44810.4408-0.05381.9628-0.31890.0819-0.15190.4520.2226-0.8589-0.26250.9943-0.08350.4763-0.03160.00360.6967-0.06540.541145.5518-21.61764.3376
52.3494-0.753-0.67491.90180.67281.8708-0.12410.0110.26650.2081-0.1640.85720.3591-1.12960.13690.5754-0.19210.1690.7314-0.15440.635225.0453-22.47563.0501
63.8573-0.9369-2.15332.94712.50722.6675-0.7903-0.16470.29161.90570.2409-0.81741.53480.16970.02880.6556-0.02070.01360.4382-0.04570.500833.1412-30.3422-0.4018
72.49671.325-0.77151.98831.34072.4672-0.08090.42190.09110.3893-0.16430.5864-0.2535-0.55760.02970.5156-0.07060.01650.4847-0.08230.500728.7536-20.5056-2.5858
81.4157-0.60180.59244.0411-0.95982.67620.0203-0.0126-0.19020.020.39410.75060.5347-0.6015-0.09030.8297-0.1106-0.03950.4786-0.02020.430237.3764-22.910211.0292
93.8755-4.22432.57138.8218-3.67783.95320.2212-0.68540.658-0.00980.0873-0.0918-0.06080.0823-0.0680.5046-0.17390.05810.4638-0.04530.490334.3432-19.60494.5745
100.92961.083-0.38781.5560.02220.9867-0.02540.2846-0.24590.07880.0334-0.268-0.0548-0.37290.0330.3937-0.08460.0030.4625-0.03910.423632.2855-25.2337-9.7848
115.4968-0.0266-0.86784.0178-0.78730.58350.0237-0.8037-0.73360.93270.0917-0.83030.08250.22810.12280.5186-0.27740.07390.4991-0.02720.57922.1964-44.1085-1.6409
122.49850.895-0.8582.4090.64551.1604-0.9753-0.1969-0.3799-0.90720.0629-1.08730.1418-0.05670.10080.6351-0.06870.18980.4453-0.0680.704532.7281-43.7882-5.1408
132.89390.32160.08533.85872.89322.16720.6708-0.2328-0.16881.5346-0.9581.24010.5978-0.25940.03781.0249-0.28220.19390.7551-0.14070.880625.7907-22.48678.4932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 81 THROUGH 90 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 91 THROUGH 100 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 101 THROUGH 115 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 116 THROUGH 132 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 133 THROUGH 153 )A0
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 154 THROUGH 164 )A0
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 165 THROUGH 190 )A0
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 191 THROUGH 201 )A0
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 202 THROUGH 209 )A0
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 210 THROUGH 224 )A0
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 225 THROUGH 237 )A0
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 238 THROUGH 251 )A0
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 1 THROUGH 12 )B0

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