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

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Basic information

Entry
Database: PDB / ID: 8kft
TitleCrystal structure of ZmMOC1 in complex with a nicked Holliday junction soaked in Mn2+ for 15 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: 2.43 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)55,5727
Polymers55,4625
Non-polymers1102
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10720 Å2
ΔGint-85 kcal/mol
Surface area21640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.280, 78.160, 63.310
Angle α, β, γ (deg.)90.00, 98.00, 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 , 2 types, 48 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
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: BL19U1 / 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: 2.43→50 Å / Num. obs: 19395 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.1
Reflection shellResolution: 2.43→2.49 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1425 / CC1/2: 0.698 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4958: ???)refinement
PHENIXmodel building
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JRG

6jrg


Resolution: 2.43→43.46 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 953 4.91 %
Rwork0.203 --
obs0.2055 19395 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→43.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 1345 2 46 3875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084054
X-RAY DIFFRACTIONf_angle_d0.9635786
X-RAY DIFFRACTIONf_dihedral_angle_d23.8141558
X-RAY DIFFRACTIONf_chiral_restr0.054647
X-RAY DIFFRACTIONf_plane_restr0.007504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.560.3321350.26642635X-RAY DIFFRACTION100
2.56-2.720.3781340.30982584X-RAY DIFFRACTION99
2.72-2.930.29161520.24642616X-RAY DIFFRACTION100
2.93-3.220.31721240.22692630X-RAY DIFFRACTION100
3.22-3.690.26471330.21142649X-RAY DIFFRACTION99
3.69-4.650.21511430.17182639X-RAY DIFFRACTION100
4.65-43.460.20381320.16792689X-RAY DIFFRACTION99

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