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- PDB-8kfv: Crystal structure of ZmMOC1 K229A in complex with a nicked Hollid... -

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Basic information

Entry
Database: PDB / ID: 8kfv
TitleCrystal structure of ZmMOC1 K229A in complex with a nicked Holliday junction soaked in Mn2+ for 180 seconds
Components
  • DNA (25-MER)
  • DNA (33-MER)
  • DNA (8-MER)
  • 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: 2.19 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

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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 (8-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,81413
Polymers55,3465
Non-polymers4688
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12020 Å2
ΔGint-90 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.852, 78.044, 87.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Holliday junction resolvase MOC1, chloroplastic


Mass: 17558.018 Da / Num. of mol.: 2 / Mutation: K229A
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 (8-MER)


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, 124 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#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.: 116 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 0.1 M MES pH 6.0, 35% Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.5 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 28137 / % possible obs: 99.9 % / Redundancy: 8.2 % / CC1/2: 0.983 / Rmerge(I) obs: 0.182 / Net I/σ(I): 16.28
Reflection shellResolution: 2.19→2.26 Å / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2778 / CC1/2: 0.635

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Processing

Software
NameVersionClassification
PHENIX1.21RC1_4958refinement
PHENIXmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JRG

6jrg


Resolution: 2.19→32.41 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 1382 4.93 %
Rwork0.207 26640 -
obs0.209 28022 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.33 Å2 / Biso mean: 34.4392 Å2 / Biso min: 12.94 Å2
Refinement stepCycle: final / Resolution: 2.19→32.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 1246 20 116 3862
Biso mean--35.99 33.9 -
Num. residues----387
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 (%)
2.19-2.260.28511410.28592460260193
2.26-2.360.33211540.252826312785100
2.36-2.460.29071350.231726182753100
2.46-2.590.25821580.220626362794100
2.59-2.750.27081260.22626742800100
2.75-2.970.30131330.226726452778100
2.97-3.270.25631200.223827192839100
3.27-3.740.22061520.185726672819100
3.74-4.710.19881290.172927432872100
4.71-32.410.20141340.1982847298199

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