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- PDB-6is9: Crystal Structure of ZmMOC1 -

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Basic information

Entry
Database: PDB / ID: 6is9
TitleCrystal Structure of ZmMOC1
ComponentsMonokaryotic chloroplast 1
KeywordsDNA BINDING PROTEIN / Holliday junction resolvase
Function / homologyHolliday junction resolvase MOC1-like / crossover junction DNA endonuclease activity / metal ion binding / Holliday junction resolvase MOC1, chloroplastic
Function and homology information
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.86 Å
AuthorsLin, Z. / Lin, H. / Zhang, D. / Yuan, C.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Structural basis of sequence-specific Holliday junction cleavage by MOC1.
Authors: Lin, H. / Zhang, D. / Zuo, K. / Yuan, C. / Li, J. / Huang, M. / Lin, Z.
History
DepositionNov 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Monokaryotic chloroplast 1
B: Monokaryotic chloroplast 1


Theoretical massNumber of molelcules
Total (without water)47,8562
Polymers47,8562
Non-polymers00
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-25 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.373, 74.604, 97.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Monokaryotic chloroplast 1


Mass: 23928.240 Da / Num. of mol.: 2 / Fragment: RuvC domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: Moc1 / Plasmid: Modified pET vector / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B4FCI7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 1.76 Å3/Da / Density % sol: 30.11 % / Mosaicity: 0.945 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.6
Details: 0.07 M Bis-tris propane pH 7.6, 20% PEG 3350, 0.03 M citrate acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 31645 / % possible obs: 99.5 % / Redundancy: 8.5 % / Biso Wilson estimate: 24.79 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.044 / Rrim(I) all: 0.131 / Χ2: 1.177 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.86-1.948.60.96331010.8370.3431.0240.94299.5
1.94-2.038.50.6231120.9110.2230.661.00899.5
2.03-2.138.20.42731200.9530.1560.4561.11699.6
2.13-2.2780.41831160.9570.1540.4471.6899.6
2.27-2.4490.23531710.9810.0820.2491.31799.7
2.44-2.698.80.16631450.990.0580.1761.44199.5
2.69-3.088.50.11631940.9940.0410.1241.35199.8
3.08-3.888.80.07932160.9970.0280.0841.13799.7
3.88-508.10.05233680.9980.0190.0560.87899.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 1.86→41.868 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22
RfactorNum. reflection% reflection
Rfree0.2094 1428 4.93 %
Rwork0.1745 --
obs0.1762 28948 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.68 Å2 / Biso mean: 31.3464 Å2 / Biso min: 14.44 Å2
Refinement stepCycle: final / Resolution: 1.86→41.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2640 0 0 222 2862
Biso mean---39 -
Num. residues----348
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.86-1.92650.29511520.24352675282799
1.9265-2.00360.26211300.21822712284299
2.0036-2.09480.24011490.19792691284099
2.0948-2.20520.26961550.19092728288399
2.2052-2.34340.23171270.182227242851100
2.3434-2.52430.231590.177427132872100
2.5243-2.77830.22191280.17827652893100
2.7783-3.18020.21921480.172827692917100
3.1802-4.00620.16911450.15542800294599
4.0062-41.87880.17951350.16232943307899

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