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- PDB-8kfu: Crystal structure of ZmMOC1 in complex with a nicked Holliday jun... -

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Basic information

Entry
Database: PDB / ID: 8kfu
TitleCrystal structure of ZmMOC1 in complex with a nicked Holliday junction soaked in Mn2+ for 180 seconds
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: 2.3 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)55,80611
Polymers55,4625
Non-polymers3446
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11790 Å2
ΔGint-97 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.573, 77.838, 63.548
Angle α, β, γ (deg.)90.000, 97.981, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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, 205 molecules

#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 48.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 6% Isopropyl alcohol, 0.1 M Sodium acetate pH5.0, 35% Polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 23115 / % possible obs: 96.5 % / Redundancy: 4.4 % / CC1/2: 0.971 / Rmerge(I) obs: 0.0903 / Net I/σ(I): 3.04
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.4078 / Mean I/σ(I) obs: 3.31 / Num. unique obs: 2739 / CC1/2: 0.6 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_4958refinement
PHENIXmodel building
autoPROCdata scaling
PHASERphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→43.66 Å / SU ML: 0.2784 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2413 1146 5.14 %
Rwork0.2117 21133 -
obs0.2133 22279 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 1285 12 199 3984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00394009
X-RAY DIFFRACTIONf_angle_d0.6375706
X-RAY DIFFRACTIONf_chiral_restr0.044637
X-RAY DIFFRACTIONf_plane_restr0.0056504
X-RAY DIFFRACTIONf_dihedral_angle_d22.06211537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.33791290.25272484X-RAY DIFFRACTION91.2
2.4-2.530.27891350.25432676X-RAY DIFFRACTION97.91
2.53-2.690.28081500.2482278X-RAY DIFFRACTION84.07
2.69-2.90.26081480.24222707X-RAY DIFFRACTION99.79
2.9-3.190.26031490.23262730X-RAY DIFFRACTION99.93
3.19-3.650.21831520.20442728X-RAY DIFFRACTION99.93
3.65-4.60.21651300.17972759X-RAY DIFFRACTION99.93
4.6-43.660.21551530.18932771X-RAY DIFFRACTION98.95

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