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- PDB-6lcm: Crystal structure of chloroplast resolvase ZmMOC1 with the magic ... -

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Basic information

Entry
Database: PDB / ID: 6lcm
TitleCrystal structure of chloroplast resolvase ZmMOC1 with the magic triangle I3C
ComponentsZmMoc1
KeywordsHYDROLASE / chloroplast / resolvase / Holliday junction / PLANT PROTEIN
Function / homologyHolliday junction resolvase MOC1-like / crossover junction DNA endonuclease activity / metal ion binding / Chem-I3C / Holliday junction resolvase MOC1, chloroplastic
Function and homology information
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SAD / 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
DepositionNov 19, 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
C: ZmMoc1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7594
Polymers19,0831
Non-polymers1,6773
Water95553
1
C: ZmMoc1
hetero molecules

C: ZmMoc1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5198
Polymers38,1662
Non-polymers3,3536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2710 Å2
ΔGint-18 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.136, 49.136, 141.831
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11C-324-

HOH

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Components

#1: Protein ZmMoc1


Mass: 19082.768 Da / Num. of mol.: 1 / Mutation: E158Q,I211V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100192759, ZEAMMB73_Zm00001d040409 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B4FCI7
#2: Chemical ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H4I3NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Ammonium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Sep 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→45 Å / Num. obs: 6571 / % possible obs: 100 % / Redundancy: 33.8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 70.8
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.302 / Num. unique obs: 670

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Processing

Software
NameVersionClassification
PHENIXv1.5refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→45 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2799 343 5.26 %
Rwork0.2227 --
obs0.2256 6519 99.7 %
Displacement parametersBiso mean: 29.72 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 48 53 1365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571345
X-RAY DIFFRACTIONf_angle_d0.68411832
X-RAY DIFFRACTIONf_chiral_restr0.0553195
X-RAY DIFFRACTIONf_plane_restr0.0033230
X-RAY DIFFRACTIONf_dihedral_angle_d14.5754768

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