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- PDB-3iaa: Crystal Structure of CalG2, Calicheamicin Glycosyltransferase, TD... -

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Basic information

Entry
Database: PDB / ID: 3iaa
TitleCrystal Structure of CalG2, Calicheamicin Glycosyltransferase, TDP bound form
ComponentsCalG2
KeywordsTRANSFERASE / Glycosyltransferase / Calicheamicin / CalG2 / TDP / enediyne
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / biosynthetic process
Similarity search - Function
Glycosyltransferase family 28 C-terminal domain / UDP-glycosyltransferase, MGT-like / Erythromycin biosynthesis protein CIII-like, central / Erythromycin biosynthesis protein CIII-like, C-terminal domain / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-DIPHOSPHATE / CalG2
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.505 Å
AuthorsChang, A. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Complete set of glycosyltransferase structures in the calicheamicin biosynthetic pathway reveals the origin of regiospecificity.
Authors: Chang, A. / Singh, S. / Helmich, K.E. / Goff, R.D. / Bingman, C.A. / Thorson, J.S. / Phillips, G.N.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CalG2
B: CalG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3954
Polymers91,5912
Non-polymers8042
Water3,873215
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-27 kcal/mol
Surface area29530 Å2
MethodPISA
2
A: CalG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1982
Polymers45,7961
Non-polymers4021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: CalG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1982
Polymers45,7961
Non-polymers4021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.787, 48.539, 107.565
Angle α, β, γ (deg.)90.000, 101.790, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CalG2


Mass: 45795.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Strain: Micromonospora echinospora / Gene: calG2, Q8KNE0 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q8KNE0
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (20 mg/ml CalG4 Protein, 0.05 M NaCl, 0.015 M Tris pH 8) mixed in a 1:1 ratio with the Well Solution (0.8M Na3Citrate, 0.1M BisTris pH 6.5) Cryoprotected with 20% ethylene ...Details: Protein Solution (20 mg/ml CalG4 Protein, 0.05 M NaCl, 0.015 M Tris pH 8) mixed in a 1:1 ratio with the Well Solution (0.8M Na3Citrate, 0.1M BisTris pH 6.5) Cryoprotected with 20% ethylene glycol, 0.8M Na3Citrate, 0.1M BisTris pH 6.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97957 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 7, 2009 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 30322 / % possible obs: 96.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.162 / Χ2: 1.099 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.544.40.49312991.158181.3
2.54-2.594.70.52513071.12183.8
2.59-2.6450.54113331.116188
2.64-2.695.40.45214071.236189.3
2.69-2.755.60.4414291.205191.7
2.75-2.825.80.39114721.228193.9
2.82-2.895.90.37315121.201196.6
2.89-2.9660.34515471.144199.1
2.96-3.056.30.31515631.174199.3
3.05-3.156.40.28815401.156199.9
3.15-3.266.50.25915861.0761100
3.26-3.396.60.21515401.0911100
3.39-3.556.60.16915921.0171100
3.55-3.736.60.14815771.0561100
3.73-3.976.60.12715580.9651100
3.97-4.276.50.11415880.9871100
4.27-4.76.50.09315951.0471100
4.7-5.386.50.08815981.0561100
5.38-6.786.40.09415971.0191100
6.78-506.20.05416821.092199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.69
Highest resolutionLowest resolution
Rotation2.51 Å49.76 Å
Translation2.51 Å49.76 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVE2.13phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.505→49.761 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.833 / SU ML: 2.49 / σ(F): 0.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 1879 6.73 %
Rwork0.184 --
obs0.188 27920 88.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.387 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 93.51 Å2 / Biso mean: 26.08 Å2 / Biso min: 8.42 Å2
Baniso -1Baniso -2Baniso -3
1-11.229 Å2-0 Å2-1.707 Å2
2---6.158 Å20 Å2
3----4.027 Å2
Refinement stepCycle: LAST / Resolution: 2.505→49.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6054 0 50 215 6319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086252
X-RAY DIFFRACTIONf_angle_d0.9068550
X-RAY DIFFRACTIONf_chiral_restr0.059970
X-RAY DIFFRACTIONf_plane_restr0.0031124
X-RAY DIFFRACTIONf_dihedral_angle_d17.0392208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.505-2.5730.3281050.2371471157666
2.573-2.6490.3191220.241591171373
2.649-2.7340.3061270.2251765189278
2.734-2.8320.2731270.2111792191980
2.832-2.9450.2661380.2071907204586
2.945-3.0790.2731510.2082064221592
3.079-3.2420.261540.2032084223893
3.242-3.4450.2471530.1842164231796
3.445-3.7110.2441580.1692193235197
3.711-4.0840.1991570.1562196235398
4.084-4.6740.1911570.1372231238899
4.674-5.8880.1891610.1582262242398
5.888-49.7710.2181690.1882321249099

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