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- PDB-3mgb: Teg 12 Ternary Structure Complexed with PAP and the Teicoplanin A... -

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Basic information

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


sulfotransferase activity / peptide binding
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #460 / Sulfotransferase domain / Sulfotransferase domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Teicoplanin Aglycone / ACETATE ION / 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE / Teg12
Similarity search - Component
Biological speciesUNCULTURED SOIL BACTERIUM (environmental samples)
NONOMURAEA SP. ATCC 39727 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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 1.4Nov 1, 2017Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value
Revision 2.0Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,5299
Polymers72,3614
Non-polymers1,1685
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-24 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.001, 78.344, 99.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein TEG12


Mass: 34973.391 Da / Num. of mol.: 2
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

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Non-polymers , 4 types, 345 molecules

#3: Chemical ChemComp-PAP / 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growpH: 9.1
Details: PROTEIN CONCENTRATION OF 10MG/ML. 1:1 UL PROTEIN TO CRYSTALLIZATION SOLUTION. 25 MM CHES, PH 9.1, 1 MM TEICOPLANIN AGLYCONE, 2 MM PAP, 0.2 M AMMONIUM ACETATE, 20% W/V PEG 3350, VAPOR ...Details: PROTEIN CONCENTRATION OF 10MG/ML. 1:1 UL PROTEIN TO CRYSTALLIZATION SOLUTION. 25 MM CHES, PH 9.1, 1 MM TEICOPLANIN AGLYCONE, 2 MM PAP, 0.2 M AMMONIUM ACETATE, 20% W/V PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K

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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 8, 2009
RadiationMonochromator: HORIZONTAL AND VERTICAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.039→50 Å / Num. obs: 37695 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 16.43
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.055 / Mean I/σ(I) obs: 2.62 / Rsym value: 0.055 / % possible all: 96.6

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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: 2.04→32.95 Å / SU ML: 0.25 / σ(F): 0.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 1851 5.01 %
Rwork0.171 --
obs0.174 36948 93.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.51 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.1818 Å20 Å20 Å2
2---1.7576 Å20 Å2
3----2.4242 Å2
Refinement stepCycle: LAST / Resolution: 2.04→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4417 0 63 340 4820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074595
X-RAY DIFFRACTIONf_angle_d1.1836252
X-RAY DIFFRACTIONf_dihedral_angle_d20.1881764
X-RAY DIFFRACTIONf_chiral_restr0.08641
X-RAY DIFFRACTIONf_plane_restr0.016806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.039-2.11140.27751630.20183026X-RAY DIFFRACTION82
2.1114-2.19590.2541550.18573269X-RAY DIFFRACTION88
2.1959-2.29580.25051830.18233401X-RAY DIFFRACTION91
2.2958-2.41680.24671800.17613395X-RAY DIFFRACTION92
2.4168-2.56820.24721800.17863485X-RAY DIFFRACTION93
2.5682-2.76640.27511910.183554X-RAY DIFFRACTION95
2.7664-3.04460.2481790.18733645X-RAY DIFFRACTION97
3.0446-3.48470.20972110.1773696X-RAY DIFFRACTION98
3.4847-4.38880.18522020.14763776X-RAY DIFFRACTION98
4.3888-32.95740.20562070.15873850X-RAY DIFFRACTION97
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)
11.48640.04530.38421.739-0.02791.73780.03170.01-0.0640.09150.0537-0.02930.09510.0774-0.07450.08850.0129-0.01140.1068-0.00370.0984-26.4834-49.5635-12.2684
20.883-1.13260.33071.7611-0.35490.30970.2056-0.1337-0.0895-0.1675-0.1654-0.0668-0.0257-0.08340.03190.1551-0.0434-0.02660.20590.03790.1928
31.33860.0171-0.17251.3357-0.74011.85540.07350.10460.2187-0.3273-0.0311-0.0127-0.14150.1466-0.0330.2075-0.0265-0.00230.20120.04560.1795
41.9776-0.01980.20281.95820.72150.78920.0338-0.00670.2402-0.33780.0693-0.1923-0.14240.0547-0.09630.2534-0.05710.09720.1454-0.04280.1463
50.0084-0.0549-0.11360.51660.49661.47390.10170.02060.0468-0.14950.26450.10070.0923-0.0173-0.23040.4687-0.0583-0.01860.20750.12090.3291
61.56830.7360.35022.12271.12070.7862-0.0321-0.03270.1126-0.4655-0.09920.4249-0.2173-0.1990.12380.2690.0049-0.03590.2171-0.03990.1893
71.062-0.4198-0.38950.637-0.37680.7847-0.21040.07080.3234-0.09520.3269-0.04270.0832-0.0306-0.05910.3265-0.0160.00730.27580.01130.3113
81.83050.6179-0.45730.2906-0.27351.0225-0.06070.09970.54490.04610.16560.27890.2554-0.2412-0.0760.2354-0.0134-0.00110.27890.00980.2997
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 0:90 OR RESID 132:224)
2X-RAY DIFFRACTION2CHAIN C AND (RESID 1:1)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 91:131 OR RESID 241:285)
4X-RAY DIFFRACTION4CHAIN B AND (RESID 0:90 OR RESID 136:224)
5X-RAY DIFFRACTION5CHAIN C AND (RESID 2:2)
6X-RAY DIFFRACTION6CHAIN B AND (RESID 91:129 OR RESID 240:285)
7X-RAY DIFFRACTION7CHAIN A AND (RESID -31:-22 OR RESID 231:240)
8X-RAY DIFFRACTION8CHAIN D AND (RESID 1:2)

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