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- PDB-6vqp: Structure of CalU17 from the Calicheamicin Biosynthesis Pathway o... -

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Basic information

Entry
Database: PDB / ID: 6vqp
TitleStructure of CalU17 from the Calicheamicin Biosynthesis Pathway of Micromonospora echinospora
Components
  • CalU17
  • CalU17 His-Tagged protein
KeywordsUNKNOWN FUNCTION / Enediyne biosynthetic pathway / Calicheamicin Biosynthesis
Function / homologyformylglycine-generating oxidase activity / : / Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1-like domain / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold / metal ion binding / CalU17
Function and homology information
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKosgei, A.J. / Miller, M.D. / Xu, W. / Van Lanen, S.G. / Thorson, J.S. / Phillips Jr., G.N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM115261 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA217255 United States
National Science Foundation (NSF, United States)STC-1231306 United States
CitationJournal: To Be Published
Title: Structure of DynF from the Dynemicin Biosynthesis Pathway of Micromonospora chersina
Authors: Kosgei, A.J. / Miller, M.D. / Xu, W. / Van Lanen, S.G. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionFeb 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Assembly

Deposited unit
A: CalU17
Q: CalU17 His-Tagged protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5196
Polymers39,2862
Non-polymers2334
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size Exclusion Chromatography shows that it is a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-29 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.951, 53.951, 218.923
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-811-

HOH

21A-819-

HOH

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Components

#1: Protein CalU17


Mass: 37235.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calU17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KND1
#2: Protein/peptide CalU17 His-Tagged protein


Mass: 2051.233 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chain Q, is the N-terminus tag from a neighboring chain. Due to the disorderd gap from residue -3 to 16, it is not clear which of two possible crystallographic symmetry transformations would ...Details: Chain Q, is the N-terminus tag from a neighboring chain. Due to the disorderd gap from residue -3 to 16, it is not clear which of two possible crystallographic symmetry transformations would transform chain Q to the position of the N-terminus of chain A. It is likely either Y+1/2, -X+1/2, Z+1/4 or -Y, -X+1, -Z+1/2
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calU17 / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 39.33 %
Description: It took a month fro the crystals to grow. The size of the crystals were about 70 microns length, width and height.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Bis-Tris pH 6.5 20% w/v PEG 1500
Temp details: Set the crystallization trays at room temperature then incubated at 4 degrees

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2018
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→48.39 Å / Num. obs: 23026 / % possible obs: 99.8 % / Redundancy: 12.622 % / Biso Wilson estimate: 38.227 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.111 / Χ2: 1.06 / Net I/σ(I): 16.03 / Num. measured all: 290624
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.1212.2070.8692.4343785362635870.8170.90798.9
2.12-2.2613.1190.6263.8344814341634160.9090.651100
2.26-2.4412.5960.4175.8840409320832080.9550.435100
2.44-2.6812.7590.2748.8937626294929490.9830.285100
2.68-2.9913.3290.16614.8136216271727170.9940.173100
2.99-3.4512.470.09723.8229966240324030.9980.101100
3.45-4.2212.3930.05838.5925753207820780.9980.06100
4.22-5.9512.6450.04745.1520903165516530.9990.04999.9
5.95-48.3910.9870.03549.1511152101710150.9990.03799.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
XDSVERSION Mar 15, 2019data reduction
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1y1e

1y1e


Resolution: 2→48.39 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 1166 5.06 %
Rwork0.1552 21856 -
obs0.1588 23022 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.11 Å2 / Biso mean: 42.2929 Å2 / Biso min: 22.66 Å2
Refinement stepCycle: final / Resolution: 2→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 30 326 2719
Biso mean--60.28 45.38 -
Num. residues----300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.090.24311500.18842606275699
2.09-2.20.23511430.17626592802100
2.2-2.330.24951330.164626922825100
2.33-2.510.21651460.165326862832100
2.51-2.770.22691360.157627152851100
2.77-3.170.22231500.157127632913100
3.17-3.990.22441480.14327662914100
3.99-48.390.22271600.151329693129100

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