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- PDB-6lct: Crystal structure of catalytic inactive chloroplast resolvase NtM... -

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Basic information

Entry
Database: PDB / ID: 6lct
TitleCrystal structure of catalytic inactive chloroplast resolvase NtMOC1 in complex with Holliday junction
Components
  • DNA (5'-D(*AP*AP*GP*AP*TP*GP*TP*CP*CP*CP*TP*CP*TP*GP*TP*TP*GP*T)-3')
  • DNA (5'-D(*AP*CP*AP*AP*CP*AP*GP*AP*GP*GP*AP*TP*GP*GP*AP*GP*CP*T)-3')
  • DNA (5'-D(*GP*CP*CP*TP*TP*GP*CP*TP*GP*GP*GP*AP*CP*AP*TP*CP*TP*T)-3')
  • DNA (5'-D(P*AP*GP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*CP*AP*AP*GP*GP*C)-3')
  • NtMOC1
KeywordsHYDROLASE/DNA / chloroplast / resolvase / Holliday junction / PLANT PROTEIN / HYDROLASE / HYDROLASE-DNA complex
Function / homologyHolliday junction resolvase MOC1-like / crossover junction DNA endonuclease activity / metal ion binding / DNA / DNA (> 10) / Holliday junction resolvase MOC1, chloroplastic-like
Function and homology information
Biological speciesNicotiana tabacum (common tobacco)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsYan, J.J. / Hong, S.X. / Guan, Z.Y. / Yin, P.
CitationJournal: Nat Commun / Year: 2020
Title: Structural insights into sequence-dependent Holliday junction resolution by the chloroplast resolvase MOC1.
Authors: Yan, J. / Hong, S. / Guan, Z. / He, W. / Zhang, D. / Yin, P.
History
DepositionNov 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NtMOC1
B: NtMOC1
C: DNA (5'-D(*AP*CP*AP*AP*CP*AP*GP*AP*GP*GP*AP*TP*GP*GP*AP*GP*CP*T)-3')
D: DNA (5'-D(*GP*CP*CP*TP*TP*GP*CP*TP*GP*GP*GP*AP*CP*AP*TP*CP*TP*T)-3')
E: DNA (5'-D(P*AP*GP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*CP*AP*AP*GP*GP*C)-3')
F: DNA (5'-D(*AP*AP*GP*AP*TP*GP*TP*CP*CP*CP*TP*CP*TP*GP*TP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6568
Polymers58,4636
Non-polymers1922
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-125 kcal/mol
Surface area24440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.054, 89.807, 68.478
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NtMOC1


Mass: 18199.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1S4CVP6*PLUS

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DNA chain , 4 types, 4 molecules CDEF

#2: DNA chain DNA (5'-D(*AP*CP*AP*AP*CP*AP*GP*AP*GP*GP*AP*TP*GP*GP*AP*GP*CP*T)-3')


Mass: 5598.656 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*CP*TP*TP*GP*CP*TP*GP*GP*GP*AP*CP*AP*TP*CP*TP*T)-3')


Mass: 5498.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*AP*GP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*CP*AP*AP*GP*GP*C)-3')


Mass: 5470.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(*AP*AP*GP*AP*TP*GP*TP*CP*CP*CP*TP*CP*TP*GP*TP*TP*GP*T)-3')


Mass: 5497.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 11 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, Sodium acetate trihydrate, 3-Methyl-1,5-Pentane Diol, D-sorbitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.55→45.35 Å / Num. obs: 24991 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 83.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Net I/σ(I): 28.2
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2962 / CC1/2: 0.812 / Rpim(I) all: 0.418 / Rrim(I) all: 0.789

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KVO

6kvo


Resolution: 2.55→45.35 Å / SU ML: 0.3925 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9102
RfactorNum. reflection% reflection
Rfree0.2449 1223 4.91 %
Rwork0.2199 --
obs0.2211 24896 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 111.17 Å2
Refinement stepCycle: LAST / Resolution: 2.55→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2365 1465 10 9 3849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314078
X-RAY DIFFRACTIONf_angle_d0.51675844
X-RAY DIFFRACTIONf_chiral_restr0.0345651
X-RAY DIFFRACTIONf_plane_restr0.0036490
X-RAY DIFFRACTIONf_dihedral_angle_d22.35572124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.650.37521430.32412560X-RAY DIFFRACTION100
2.65-2.770.32411370.30722593X-RAY DIFFRACTION100
2.77-2.920.27861420.30872591X-RAY DIFFRACTION100
2.92-3.10.3521370.28872623X-RAY DIFFRACTION99.82
3.1-3.340.30741520.25672548X-RAY DIFFRACTION98.43
3.34-3.680.23161300.24322623X-RAY DIFFRACTION99.6
3.68-4.210.25781120.20632667X-RAY DIFFRACTION99.93
4.21-5.30.22991260.19662695X-RAY DIFFRACTION99.93
5.3-45.350.20451440.19352773X-RAY DIFFRACTION98.75
Refinement TLS params.Method: refined / Origin x: -33.647013864 Å / Origin y: 16.0341433139 Å / Origin z: -15.3068916811 Å
111213212223313233
T0.500532351905 Å20.00730019156377 Å20.0810800913265 Å2-0.520038447066 Å20.0320146729854 Å2--0.529289624265 Å2
L3.26962969232 °20.103398416172 °20.529255393096 °2-5.32656032121 °2-0.0649928312498 °2--2.80684978269 °2
S0.0746805618229 Å °0.223707476494 Å °0.24685230342 Å °0.240890050983 Å °0.227262248325 Å °0.086124688945 Å °0.0694925030414 Å °-0.101167707549 Å °-0.247758249861 Å °
Refinement TLS groupSelection details: all

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