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

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Basic information

Entry
Database: PDB / ID: 8kfw
TitleCrystal structure of ZmMOC1 K229A in complex with a nicked Holliday junction soaked in Mn2+ for 600 seconds
Components
  • DNA (26-MER)
  • DNA (33-MER)
  • DNA (5'-D(P*CP*AP*CP*GP*AP*TP*TP*G)-3')
  • Holliday junction resolvase MOC1, chloroplastic
KeywordsDNA BINDING PROTEIN / 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 (26-MER)
E: DNA (5'-D(P*CP*AP*CP*GP*AP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,04817
Polymers55,3465
Non-polymers70212
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12340 Å2
ΔGint-96 kcal/mol
Surface area21320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.644, 78.142, 63.621
Angle α, β, γ (deg.)90.00, 97.72, 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: 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 (26-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, 36 molecules

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


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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
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: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.5497 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: 1.5497 Å / Relative weight: 1
ReflectionResolution: 2.3→49.07 Å / Num. obs: 23234 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.123 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.997 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2266 / CC1/2: 0.782 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_4958refinement
PHENIXmodel building
HKL-2000data scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JRG

6jrg


Resolution: 2.3→49.07 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 1105 4.76 %
Rwork0.2058 --
obs0.2075 23209 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 1266 30 24 3800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083981
X-RAY DIFFRACTIONf_angle_d0.9125656
X-RAY DIFFRACTIONf_dihedral_angle_d23.5041514
X-RAY DIFFRACTIONf_chiral_restr0.054632
X-RAY DIFFRACTIONf_plane_restr0.008501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.33961460.30292739X-RAY DIFFRACTION100
2.4-2.530.28631310.25352760X-RAY DIFFRACTION100
2.53-2.690.27691360.24052775X-RAY DIFFRACTION100
2.69-2.90.31181400.24982732X-RAY DIFFRACTION100
2.9-3.190.24821480.22842749X-RAY DIFFRACTION100
3.19-3.650.23281200.21492771X-RAY DIFFRACTION100
3.65-4.60.2511390.17762775X-RAY DIFFRACTION100
4.6-49.070.19261450.1782803X-RAY DIFFRACTION99

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