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

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Basic information

Entry
Database: PDB / ID: 7msy
TitleStructure of CalU17 from the Calicheamicin Biosynthesis Pathway of Micromonospora echinospora
ComponentsCalU17
KeywordsUNKNOWN FUNCTION / Enediyne biosynthetic pathway / Calicheamicin Biosynthesis
Function / homologySulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1 / 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 / Resolution: 2.21 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
DepositionMay 12, 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

Downloads & links

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Assembly

Deposited unit
A: CalU17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,97711
Polymers35,2891
Non-polymers68810
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-44 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.465, 53.465, 223.468
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-689-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CalU17


Mass: 35289.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This is CalU17 structure with the tag cleaved and soaked in Calcium to find out if the calcium binding site is conserved.
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calU17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KND1

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Non-polymers , 5 types, 234 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Magnesium formate dihydrate 20% w/v PEG 3,350 pH 7.0;

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.5497 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2019
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5497 Å / Relative weight: 1
ReflectionResolution: 2.21→48.23 Å / Num. obs: 16890 / % possible obs: 97.8 % / Redundancy: 20.735 % / Biso Wilson estimate: 62.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.096 / Χ2: 1.049 / Net I/σ(I): 19.79 / Num. measured all: 350217
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
2.21-2.263.2212.6580.25298912389283.12775
2.26-2.337.5481.9090.658703122311532.05294.30.334
2.33-2.3912.0361.3961.3113962116311601.45999.70.641
2.39-2.4715.4561.12.0117574113711371.1371000.82
2.47-2.5520.6950.813.4523634114211420.8311000.95
2.55-2.6424.7180.5725.6726349106610660.5841000.974
2.64-2.7426.1720.4237.9927193103910390.4311000.988
2.74-2.8525.960.30310.9726349101510150.3091000.994
2.85-2.9825.1690.23414.18246919819810.2391000.995
2.98-3.1224.7110.17718.2227849229220.1811000.997
3.12-3.2924.9030.13623.47221898918910.1391000.998
3.29-3.4926.0060.10130.96220018468460.1031000.999
3.49-3.7325.8680.08437.61206177977970.0861000.999
3.73-4.0324.9560.07243.69186927497490.0741000.999
4.03-4.4124.0380.06347.69168997037030.0641000.999
4.41-4.9423.9560.06150.6152846386380.0621000.999
4.94-5.725.5030.05952.25145625715710.0611000.999
5.7-6.9824.0980.05652.15120254994990.0571000.999
6.98-9.8721.6820.04656.2787164024020.0481001
9.87-48.2319.9360.04160.650042532510.04299.20.999

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.17.1phasing
XSCALEVERSION Mar 15, 2019data scaling
XDS0.86data reduction
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7ML6

7ml6


Resolution: 2.21→48.23 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 840 4.98 %
Rwork0.1837 16043 -
obs0.1864 16883 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 197.27 Å2 / Biso mean: 73.7953 Å2 / Biso min: 48.48 Å2
Refinement stepCycle: final / Resolution: 2.21→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 84 225 2613
Biso mean--101.88 68.49 -
Num. residues----292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.350.49281090.4522318242786
2.35-2.530.41931690.358126322801100
2.53-2.780.2661450.188126702815100
2.78-3.180.30771170.208127252842100
3.18-4.010.23651330.148827662899100
4.01-48.230.18991670.162529323099100
Refinement TLS params.Method: refined / Origin x: 22.2761 Å / Origin y: 0.8286 Å / Origin z: 38.6378 Å
111213212223313233
T0.5651 Å20.0228 Å20.0243 Å2-0.6731 Å20.0468 Å2--0.6164 Å2
L1.3401 °20.1853 °2-0.1008 °2-1.5325 °2-0.5008 °2--1.298 °2
S-0.0224 Å °-0.0045 Å °-0.0583 Å °-0.0016 Å °-0.016 Å °-0.05 Å °0.1297 Å °0.0293 Å °-0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA16 - 307
2X-RAY DIFFRACTION1allB2
3X-RAY DIFFRACTION1allC401 - 408
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allS2 - 327
6X-RAY DIFFRACTION1allE1 - 2

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