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- PDB-7ml6: Structure of CalU17 from the Calicheamicin Biosynthesis Pathway o... -

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Basic information

Entry
Database: PDB / ID: 7ml6
TitleStructure of CalU17 from the Calicheamicin Biosynthesis Pathway of Micromonospora echinospora
ComponentsCalU17
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 / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.1 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: Acta Crystallogr.,Sect.F / Year: 2022
Title: The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina.
Authors: Kosgei, A.J. / Miller, M.D. / Bhardwaj, M. / Xu, W. / Thorson, J.S. / Van Lanen, S.G. / Phillips Jr., G.N.
History
DepositionApr 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CalU17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4733
Polymers35,2891
Non-polymers1842
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.686, 53.686, 223.960
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-790-

HOH

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Components

#1: Protein CalU17


Mass: 35289.055 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Description: It took a month for the crystals to grow. The size of the crystals was about 70 microns length, width, and height
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M BICINE pH 8.5 20% w/v PEG 10,000

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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: 2.1→48.41 Å / Num. obs: 20150 / % possible obs: 100 % / Redundancy: 19.286 % / Biso Wilson estimate: 48.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.19 / Rrim(I) all: 0.195 / Net I/σ(I): 11.97 / Num. measured all: 388617 / Scaling rejects: 8
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
2.1-2.1520.0524.4890.6329155145914540.3054.60599.7
2.15-2.2120.3213.2210.9528266139113910.463.304100
2.21-2.2820.0512.7841.1327590137613760.5292.856100
2.28-2.3519.732.0251.5826833136013600.6562.079100
2.35-2.4219.041.6221.9924581129112910.7821.666100
2.42-2.5119.2441.322.4724171125612560.7871.356100
2.51-2.619.4780.9673.4424016123412330.9130.99399.9
2.6-2.7119.3280.7174.5822710117511750.9360.736100
2.71-2.8320.1830.5556.0922908113511350.9690.569100
2.83-2.9719.7540.4058.0521374108210820.9810.416100
2.97-3.1319.5610.30810.7420285103710370.9870.316100
3.13-3.3218.9640.21914.36187179879870.9940.225100
3.32-3.5517.7950.14819.61167459419410.9970.152100
3.55-3.8318.560.10426.63164078848840.9980.107100
3.83-4.218.9440.07934.15153078088080.9990.081100
4.2-4.719.6770.0737.92144827367360.9980.072100
4.7-5.4218.7820.06838.57127726806800.9990.07100
5.42-6.6417.3150.06935.8497835655650.9990.071100
6.64-9.3917.0870.05143.8280654724720.9990.053100
9.39-48.4115.5050.03749.88445028928710.03899.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
PHENIX1.17.1phasing
XSCALEdata scaling
XDSVERSION Mar 15, 2019data reduction
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6VQP

6vqp


Resolution: 2.1→48.41 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2467 957 4.76 %
Rwork0.1739 19161 -
obs0.1773 20118 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.18 Å2 / Biso mean: 54.3848 Å2 / Biso min: 31.19 Å2
Refinement stepCycle: final / Resolution: 2.1→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 27 293 2624
Biso mean--63.06 54.83 -
Num. residues----292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.210.41551180.32812636275499
2.21-2.350.31481470.261326722819100
2.35-2.530.29061200.218327012821100
2.53-2.790.26481370.196626902827100
2.79-3.190.29461430.181127302873100
3.19-4.020.19271500.148727552905100
4.02-48.410.23741420.152829773119100

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