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- PDB-6kvo: Crystal structure of chloroplast resolvase in complex with Hollid... -

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Basic information

Entry
Database: PDB / ID: 6kvo
TitleCrystal structure of chloroplast resolvase in complex with Holliday junction
Components
  • DNA (5'-D(*AP*CP*AP*AP*CP*AP*GP*AP*TP*GP*AP*TP*GP*GP*AP*GP*CP*T)-3')
  • DNA (5'-D(*GP*CP*CP*TP*TP*GP*CP*TP*TP*GP*GP*AP*CP*AP*TP*CP*TP*T)-3')
  • DNA (5'-D(P*AP*AP*GP*AP*TP*GP*TP*CP*CP*AP*TP*CP*TP*GP*TP*TP*GP*T)-3')
  • DNA (5'-D(P*AP*GP*CP*TP*CP*CP*AP*TP*CP*AP*AP*GP*CP*AP*AP*GP*GP*C)-3')
  • NtMOC1
KeywordsPLANT PROTEIN/DNA / chloroplast / resolvase / Holliday junction / PLANT PROTEIN / PLANT PROTEIN-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: 2.5 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
DepositionSep 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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


Theoretical massNumber of molelcules
Total (without water)59,51510
Polymers59,2746
Non-polymers2414
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-151 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.316, 92.155, 65.894
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,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NtMOC1


Mass: 18605.326 Da / Num. of mol.: 2 / Mutation: Q162K,E235Q,E239Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: LOC107823122 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1S4CVP6

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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*TP*GP*AP*TP*GP*GP*AP*GP*CP*T)-3')


Mass: 5573.644 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*TP*GP*GP*AP*CP*AP*TP*CP*TP*T)-3')


Mass: 5473.538 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*AP*AP*GP*CP*AP*AP*GP*GP*C)-3')


Mass: 5494.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(P*AP*AP*GP*AP*TP*GP*TP*CP*CP*AP*TP*CP*TP*GP*TP*TP*GP*T)-3')


Mass: 5521.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 51 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate trihydrate, PEG 3350, Tacsimate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→49.03 Å / Num. obs: 26297 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 70.19 Å2 / CC1/2: 0.954 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.108 / Rrim(I) all: 0.275 / Net I/σ(I): 5.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2898 / CC1/2: 0.891 / Rpim(I) all: 0.21 / Rrim(I) all: 0.549 / % possible all: 98.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX1.14rc3_3206refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→31.02 Å / SU ML: 0.3287 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.4468 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2343 1305 4.97 %
Rwork0.2019 24931 -
obs0.2035 26236 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.72 Å2
Refinement stepCycle: LAST / Resolution: 2.5→31.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 1468 0 47 4007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814197
X-RAY DIFFRACTIONf_angle_d0.94025994
X-RAY DIFFRACTIONf_chiral_restr0.0568661
X-RAY DIFFRACTIONf_plane_restr0.0067510
X-RAY DIFFRACTIONf_dihedral_angle_d24.10662210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.34381490.27182695X-RAY DIFFRACTION98.89
2.6-2.720.31091410.26822744X-RAY DIFFRACTION100
2.72-2.860.31311170.26252749X-RAY DIFFRACTION99.97
2.86-3.040.27071570.25242714X-RAY DIFFRACTION100
3.04-3.270.26881430.23832743X-RAY DIFFRACTION99.9
3.27-3.60.2091330.20262786X-RAY DIFFRACTION100
3.6-4.120.24431670.20132773X-RAY DIFFRACTION100
4.12-5.190.21821420.17112815X-RAY DIFFRACTION99.97
5.19-31.020.20651560.18622912X-RAY DIFFRACTION99.1
Refinement TLS params.Method: refined / Origin x: 27.0730554385 Å / Origin y: 16.7948053602 Å / Origin z: 18.1283811642 Å
111213212223313233
T0.346189180636 Å20.0132301365013 Å20.0328047822879 Å2-0.371642825595 Å2-0.00754458434689 Å2--0.383659106659 Å2
L2.12867476048 °20.565187388032 °20.498563673245 °2-3.32755729251 °2-0.190038942948 °2--2.54839233146 °2
S-0.0419655307852 Å °0.162093317283 Å °0.0848241919618 Å °0.138576099535 Å °0.199046432792 Å °-0.0287261905544 Å °0.0603765312001 Å °-0.0617971024292 Å °-0.112662973069 Å °
Refinement TLS groupSelection details: all

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