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- PDB-5ig9: Crystal structure of macrocyclase MdnC bound with precursor pepti... -

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Basic information

Entry
Database: PDB / ID: 5ig9
TitleCrystal structure of macrocyclase MdnC bound with precursor peptide MdnA from Microcystis aeruginosa MRC
Components
  • ATP grasp ligase
  • Microviridin
KeywordsLIGASE / RiPP / Macrocyclase / Precursor Peptide
Function / homologyATP-grasp ribosomal peptide maturase, MvdD family / Protease inhibitor I10, marinostatin / Serine endopeptidase inhibitors / ligase activity / Microviridin / ATP grasp ligase
Function and homology information
Biological speciesMicrocystis aeruginosa MRC (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.665 Å
AuthorsLi, K. / Condurso, H.L. / Bruner, S.D.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural basis for precursor protein-directed ribosomal peptide macrocyclization.
Authors: Li, K. / Condurso, H.L. / Li, G. / Ding, Y. / Bruner, S.D.
History
DepositionFeb 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP grasp ligase
B: ATP grasp ligase
C: ATP grasp ligase
D: ATP grasp ligase
E: ATP grasp ligase
F: ATP grasp ligase
G: ATP grasp ligase
H: ATP grasp ligase
P: Microviridin
I: Microviridin
J: Microviridin
K: Microviridin
L: Microviridin
M: Microviridin
N: Microviridin
O: Microviridin


Theoretical massNumber of molelcules
Total (without water)349,62216
Polymers349,62216
Non-polymers00
Water0
1
A: ATP grasp ligase
B: ATP grasp ligase
I: Microviridin
J: Microviridin


Theoretical massNumber of molelcules
Total (without water)87,4064
Polymers87,4064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-59 kcal/mol
Surface area29370 Å2
MethodPISA
2
C: ATP grasp ligase
D: ATP grasp ligase
K: Microviridin
L: Microviridin


Theoretical massNumber of molelcules
Total (without water)87,4064
Polymers87,4064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-55 kcal/mol
Surface area28430 Å2
MethodPISA
3
E: ATP grasp ligase
H: ATP grasp ligase
P: Microviridin
M: Microviridin


Theoretical massNumber of molelcules
Total (without water)87,4064
Polymers87,4064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-56 kcal/mol
Surface area29020 Å2
MethodPISA
4
F: ATP grasp ligase
G: ATP grasp ligase
N: Microviridin
O: Microviridin


Theoretical massNumber of molelcules
Total (without water)87,4064
Polymers87,4064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9190 Å2
ΔGint-55 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.560, 132.560, 198.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
ATP grasp ligase


Mass: 37977.500 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microcystis aeruginosa MRC (bacteria) / Gene: mdnC / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / References: UniProt: B2G3D0
#2: Protein/peptide
Microviridin


Mass: 5725.292 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Microcystis aeruginosa MRC (bacteria) / References: UniProt: B2G3C8

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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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 250 mM ammonium sulfate, 28% PEG 3,350, 8% dioxane and 100mM bis-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 24, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.665→132.56 Å / Num. obs: 96926 / % possible obs: 99.9 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 17.1
Reflection shellResolution: 2.66→2.71 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.8 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.665→39.68 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.32
RfactorNum. reflection% reflection
Rfree0.2605 4861 5.02 %
Rwork0.2192 --
obs0.2292 96906 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.665→39.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20621 0 0 0 20621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321117
X-RAY DIFFRACTIONf_angle_d0.59728558
X-RAY DIFFRACTIONf_dihedral_angle_d14.73412748
X-RAY DIFFRACTIONf_chiral_restr0.0423188
X-RAY DIFFRACTIONf_plane_restr0.0043666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6665-2.71250.39682450.34044427X-RAY DIFFRACTION90
2.7125-2.76180.3452020.32024627X-RAY DIFFRACTION96
2.7618-2.81490.35152730.30514553X-RAY DIFFRACTION94
2.8149-2.87230.4192050.30084651X-RAY DIFFRACTION96
2.8723-2.93480.29752360.28354590X-RAY DIFFRACTION95
2.9348-3.0030.32882130.2874621X-RAY DIFFRACTION96
3.003-3.07810.32092360.26754591X-RAY DIFFRACTION95
3.0781-3.16120.32812340.26024599X-RAY DIFFRACTION95
3.1612-3.25420.27762830.2414567X-RAY DIFFRACTION94
3.2542-3.35910.26032440.24284623X-RAY DIFFRACTION95
3.3591-3.47910.25742290.23594620X-RAY DIFFRACTION95
3.4791-3.61830.27362430.23264585X-RAY DIFFRACTION95
3.6183-3.78280.27062340.22994622X-RAY DIFFRACTION95
3.7828-3.9820.27092950.2244567X-RAY DIFFRACTION94
3.982-4.23110.23522400.21454591X-RAY DIFFRACTION95
4.2311-4.55710.2312330.19654647X-RAY DIFFRACTION95
4.5571-5.01460.20242840.1824563X-RAY DIFFRACTION94
5.0146-5.73750.23372300.19274644X-RAY DIFFRACTION95
5.7375-7.21860.24152550.20884637X-RAY DIFFRACTION95
7.2186-35.39640.23652460.18984684X-RAY DIFFRACTION95

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