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- PDB-8kfr: Crystal structure of ZmMOC1/nicked Holliday junction/Ca2+ complex -

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Basic information

Entry
Database: PDB / ID: 8kfr
TitleCrystal structure of ZmMOC1/nicked Holliday junction/Ca2+ complex
Components
  • DNA (25-MER)
  • DNA (33-MER)
  • DNA (5'-D(P*CP*AP*CP*GP*AP*TP*TP*G)-3')
  • Holliday junction resolvase MOC1, chloroplastic
KeywordsHYDROLASE / MOC1 / Holliday Junction / Time-resolved crystallography
Function / homologyHolliday junction resolvase MOC1-like / crossover junction DNA endonuclease activity / metal ion binding / DNA / DNA (> 10) / Holliday junction resolvase MOC1, chloroplastic
Function and homology information
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, D. / Luo, Z. / Lin, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971222 China
CitationJournal: Nat Commun / Year: 2024
Title: MOC1 cleaves Holliday junctions through a cooperative nick and counter-nick mechanism mediated by metal ions.
Authors: Zhang, D. / Xu, S. / Luo, Z. / Lin, Z.
History
DepositionAug 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Holliday junction resolvase MOC1, chloroplastic
B: Holliday junction resolvase MOC1, chloroplastic
C: DNA (33-MER)
D: DNA (25-MER)
E: DNA (5'-D(P*CP*AP*CP*GP*AP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,79111
Polymers55,4625
Non-polymers3286
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11630 Å2
ΔGint-81 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.980, 77.600, 63.280
Angle α, β, γ (deg.)90.00, 98.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Holliday junction resolvase MOC1, chloroplastic


Mass: 17616.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100192759 / Production host: Escherichia coli (E. coli) / References: UniProt: B4FCI7

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DNA chain , 3 types, 3 molecules CDE

#2: DNA chain DNA (33-MER)


Mass: 10137.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize)
#3: DNA chain DNA (25-MER)


Mass: 7665.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize)
#4: DNA chain DNA (5'-D(P*CP*AP*CP*GP*AP*TP*TP*G)-3')


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize)

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Non-polymers , 3 types, 143 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.05 M Calcium chloride, HEPES 7.0, 40% Polyethylene glycol 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 24, 2020
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→62.66 Å / Num. obs: 30203 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.153 / Net I/σ(I): 10.5
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 1.053 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2212 / CC1/2: 0.995

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_4958refinement
autoPROCdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JRG

6jrg


Resolution: 2.1→43.81 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 1573 5.22 %
Rwork0.201 --
obs0.2031 30149 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 1345 18 137 3992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084076
X-RAY DIFFRACTIONf_angle_d0.9485807
X-RAY DIFFRACTIONf_dihedral_angle_d23.7051569
X-RAY DIFFRACTIONf_chiral_restr0.057648
X-RAY DIFFRACTIONf_plane_restr0.009506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.34271470.28522567X-RAY DIFFRACTION100
2.15-2.250.2681250.2592613X-RAY DIFFRACTION100
2.25-2.340.291280.23682623X-RAY DIFFRACTION100
2.34-2.440.23391490.21822584X-RAY DIFFRACTION100
2.44-2.570.25211380.22242604X-RAY DIFFRACTION100
2.57-2.730.31611490.22762570X-RAY DIFFRACTION100
2.73-2.940.2631570.22532589X-RAY DIFFRACTION100
2.94-3.240.23951470.22772597X-RAY DIFFRACTION100
3.24-3.710.24211560.19772591X-RAY DIFFRACTION100
3.71-4.670.2181410.16452601X-RAY DIFFRACTION99
4.67-43.810.18961360.16982637X-RAY DIFFRACTION98

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