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- PDB-6kvn: Crystal structure of chloroplast resolvase -

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Basic information

Entry
Database: PDB / ID: 6kvn
TitleCrystal structure of chloroplast resolvase
ComponentsNtMOC1
KeywordsPLANT PROTEIN / chloroplast / resolvase
Function / homologyHolliday junction resolvase MOC1-like / crossover junction DNA endonuclease activity / metal ion binding / Holliday junction resolvase MOC1, chloroplastic-like
Function and homology information
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NtMOC1


Theoretical massNumber of molelcules
Total (without water)18,6051
Polymers18,6051
Non-polymers00
Water1,09961
1
A: NtMOC1

A: NtMOC1


Theoretical massNumber of molelcules
Total (without water)37,2112
Polymers37,2112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1800 Å2
ΔGint-19 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.793, 40.335, 60.504
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,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-334-

HOH

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Components

#1: Protein NtMOC1


Mass: 18605.326 Da / Num. of mol.: 1 / 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris, PEG 3350, Lithium sulphat

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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: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.02→43.57 Å / Num. obs: 10538 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 29.46 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.09 / Rrim(I) all: 0.226 / Net I/σ(I): 6
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4218 / CC1/2: 0.778 / Rpim(I) all: 0.387 / Rrim(I) all: 0.94 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.14rc3_3206refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→43.57 Å / SU ML: 0.227 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.8629 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2367 566 5.39 %
Rwork0.1915 9942 -
obs0.1939 10508 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.33 Å2
Refinement stepCycle: LAST / Resolution: 2.02→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1154 0 0 61 1215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661185
X-RAY DIFFRACTIONf_angle_d0.77361607
X-RAY DIFFRACTIONf_chiral_restr0.0547174
X-RAY DIFFRACTIONf_plane_restr0.0065202
X-RAY DIFFRACTIONf_dihedral_angle_d20.8455427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.220.26181300.21242418X-RAY DIFFRACTION99.3
2.22-2.550.24181530.2082429X-RAY DIFFRACTION99.77
2.55-3.210.27151510.20382477X-RAY DIFFRACTION99.73
3.21-43.570.21091320.1772618X-RAY DIFFRACTION99.64
Refinement TLS params.Method: refined / Origin x: -10.2845034781 Å / Origin y: 11.2041636706 Å / Origin z: -16.4450170179 Å
111213212223313233
T0.179157027984 Å20.0131925676349 Å20.0376014572383 Å2-0.177873741396 Å2-0.0173194682698 Å2--0.164623778471 Å2
L2.64771481858 °20.134915277141 °20.268984901229 °2-3.09002879714 °2-0.573258904543 °2--1.13041601103 °2
S-0.00415579405164 Å °-0.233701243891 Å °0.175480118362 Å °0.362160308674 Å °-0.0210060302995 Å °0.371137114947 Å °-0.163065515233 Å °-0.224590602558 Å °0.022960556683 Å °
Refinement TLS groupSelection details: all

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