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- PDB-3mg9: Teg 12 Binary Structure Complexed with the Teicoplanin Aglycone -

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Basic information

Entry
Database: PDB / ID: 3mg9
TitleTeg 12 Binary Structure Complexed with the Teicoplanin Aglycone
Components
  • TEG12
  • TEICOPLANIN AGLYCONE
KeywordsTRANSFERASE/ANTIBIOTIC / SULFOTRANSFERASE / GLYOPEPTIDE / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


sulfotransferase activity / peptide binding
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Teicoplanin Aglycone / FORMIC ACID / Teg12
Similarity search - Component
Biological speciesUNCULTURED SOIL BACTERIUM (environmental samples)
NONOMURAEA SP. ATCC 39727 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsBick, M.J. / Banik, J.J. / Darst, S.A. / Brady, S.F.
CitationJournal: Biochemistry / Year: 2010
Title: Crystal Structures of the Glycopeptide Sulfotransferase Teg12 in a Complex with the Teicoplanin Aglycone.
Authors: Bick, M.J. / Banik, J.J. / Darst, S.A. / Brady, S.F.
History
DepositionApr 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 2.0Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / 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 / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 22, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TEG12
B: TEICOPLANIN AGLYCONE
C: TEICOPLANIN AGLYCONE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7866
Polymers34,6023
Non-polymers1843
Water1,71195
1
A: TEG12
B: TEICOPLANIN AGLYCONE
C: TEICOPLANIN AGLYCONE
hetero molecules

A: TEG12
B: TEICOPLANIN AGLYCONE
C: TEICOPLANIN AGLYCONE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,57312
Polymers69,2056
Non-polymers3686
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455-x-1/2,y,-z1
Buried area9210 Å2
ΔGint-47.2 kcal/mol
Surface area21490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.119, 80.154, 132.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-2056-

HOH

21A-2060-

HOH

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Components

#1: Protein TEG12


Mass: 32188.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) UNCULTURED SOIL BACTERIUM (environmental samples)
Gene: TEG1, TEG12 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B7T1D7, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Protein/peptide TEICOPLANIN AGLYCONE


Type: Oligopeptide / Class: Antibiotic / Mass: 1206.984 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: TEICOPLANIN AGLYCON IS THE NONSUGAR COMPONENT OF TEICOPLANIN, CONSISTING OF THE TETRACYCLIC HEPTAPEPTIDE ONLY.
Source: (natural) NONOMURAEA SP. ATCC 39727 (bacteria) / References: Teicoplanin Aglycone
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTEICOPLANIN IS A FAMILY OF TETRACYCLIC GLYCOPEPTIDE ANTIBIOTICS. THE SCAFFOLD IS A HEPTAPEPTIDE ...TEICOPLANIN IS A FAMILY OF TETRACYCLIC GLYCOPEPTIDE ANTIBIOTICS. THE SCAFFOLD IS A HEPTAPEPTIDE FURTHER GLYCOSYLATED BY THREE MONO SACCHARIDES: MANNOSE, N-ACETYLGLUCOSAMINE AND BETA-D-GLUCOSAMINE AND ONLY DIFFER BY THE SIDE CHAIN ATTACHED TO THE LATTER. HERE, TEICOPLANIN AGLYCON IS REPRESENTED BY THE SEQUENCE (SEQRES)

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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: 50.57 %
Crystal growpH: 4.6
Details: 10MG/ML PROTEIN. 1:1 UL HANGING DROPS. 1.0M SODIUM FORMATE, 0.1 M SODIUM ACETATE, PH 4.6, 1MM TEICOPLANIN AGLYCONE, 25 MM CHES, PH 9.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2008
RadiationMonochromator: VERTICAL AND HORIZONTAL FOCUSING MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.266→50 Å / Num. obs: 16630 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.0868 / Rsym value: 0.0868 / Net I/σ(I): 15.5
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.17 / Rsym value: 0.542 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(PHENIX.REFINE: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OV8

2ov8


Resolution: 2.27→34.32 Å / SU ML: 0.26 / σ(F): 0.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 798 5.06 %
Rwork0.173 --
obs0.176 15758 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.09 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 43.03 Å2
Baniso -1Baniso -2Baniso -3
1--3.0232 Å20 Å20 Å2
2--0.9791 Å20 Å2
3---2.0441 Å2
Refinement stepCycle: LAST / Resolution: 2.27→34.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2115 0 12 95 2222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062184
X-RAY DIFFRACTIONf_angle_d1.0382983
X-RAY DIFFRACTIONf_dihedral_angle_d22.406874
X-RAY DIFFRACTIONf_chiral_restr0.074310
X-RAY DIFFRACTIONf_plane_restr0.019377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.266-2.40780.23451170.20182160X-RAY DIFFRACTION82
2.4078-2.59370.2341370.19572333X-RAY DIFFRACTION90
2.5937-2.85460.25521550.19162449X-RAY DIFFRACTION94
2.8546-3.26740.25471430.19112578X-RAY DIFFRACTION98
3.2674-4.11550.20871250.14862648X-RAY DIFFRACTION99
4.1155-34.3250.19481210.16452792X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0187-0.02980.00140.55670.38610.29470.2607-0.2286-0.0025-0.1869-0.2214-0.15820.0670.14380.00260.23890.17020.13050.66610.02760.3258-3.56570.848910.0219
20.00270.0062-0.00420.04530.0270.0496-1.06270.88160.0382-0.2371-0.231.41430.1323-1.18770.00060.8886-0.10560.3530.8005-0.18071.0637
30.526-0.37870.0950.49190.20950.3578-0.2905-0.3636-0.69330.20510.0488-0.02910.5835-0.138900.2129-0.03150.08590.2830.05850.2611
40.01040.0379-0.05580.89750.02630.36380.05540.0709-0.05920.9519-0.3189-0.7983-0.40650.0353-0.00620.4299-0.06810.11880.30680.04110.3577
50.04040.0506-0.03840.1163-0.06130.0372-0.23850.1503-1.1334-0.8433-0.05380.8226-0.1195-0.47850.00020.40390.00580.08470.54260.13350.7145
60.77010.59931.04061.7311-0.05512.41560.1389-0.0723-0.2427-0.0144-0.0747-0.05050.32630.0318-0.00010.17730.0560.03020.15630.07910.1706
71.334-0.0453-0.21290.8737-1.24631.8145-0.32510.20680.1433-0.15450.11890.1712-0.0996-0.0112-0.00010.19970.05360.00490.1894-0.0240.2031
80.25310.2062-0.04040.26060.17720.4403-0.313-0.93890.18120.32720.24570.1852-0.2779-0.12390.00020.23990.1532-0.00860.3857-0.04320.2129
91.18710.04480.3491.34560.10171.91750.03960.0735-0.2382-0.0826-0.12-0.16640.10660.19460.00010.1520.07740.0720.13450.03710.1783
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID -8:-5)
2X-RAY DIFFRACTION2(CHAIN C)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 91:109)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 205:216)
5X-RAY DIFFRACTION5(CHAIN B)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 0:90)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 247:285)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 110:129)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 135:204)

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