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- PDB-3mgc: Teg12 Apo -

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Basic information

Entry
Database: PDB / ID: 3mgc
TitleTeg12 Apo
ComponentsTeg12
KeywordsTRANSFERASE / Sulfotransferase / Teicoplanin / Antibiotic / Environmental DNA / PAPS
Function / homology
Function and homology information


sulfotransferase activity / peptide binding
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / N-L-ALPHA-ASPARTYL L-PHENYLALANINE 1-METHYL ESTER / Teg12
Similarity search - Component
Biological speciesuncultured soil bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 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 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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: Teg12
B: Teg12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5867
Polymers69,9472
Non-polymers6405
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-12 kcal/mol
Surface area22890 Å2
MethodPISA
2
A: Teg12
B: Teg12
hetero molecules

A: Teg12
B: Teg12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,17314
Polymers139,8944
Non-polymers1,27910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area7150 Å2
ΔGint-46 kcal/mol
Surface area41040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.388, 126.086, 145.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

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Components

#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-PME / N-L-ALPHA-ASPARTYL L-PHENYLALANINE 1-METHYL ESTER / ASPARTAME / Aspartame


Mass: 294.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N2O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: Protein concentration of 7.5 mg/ml. 1:1 ul ratio of protein to crystallization solution. 1.0 M Sodium Citrate, 0.1 M Sodium Cacodylate, pH 6.5, Silver Bullet Reagent 29 (Hampton), VAPOR ...Details: Protein concentration of 7.5 mg/ml. 1:1 ul ratio of protein to crystallization solution. 1.0 M Sodium Citrate, 0.1 M Sodium Cacodylate, pH 6.5, Silver Bullet Reagent 29 (Hampton), VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.91→72.57 Å / Num. all: 15372 / Num. obs: 14643 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 19.1
Reflection shellResolution: 2.93→3.03 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.03 / Num. unique all: 1541 / Rsym value: 0.063 / % possible all: 98

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OV8

2ov8


Resolution: 2.91→72.57 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.849 / SU B: 31.101 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 5.584 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27193 764 5 %RANDOM
Rwork0.21672 ---
obs0.21957 14562 94.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.313 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å2-0 Å2
2---1.02 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.91→72.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3550 0 44 34 3628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213673
X-RAY DIFFRACTIONr_bond_other_d0.0010.022384
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9634991
X-RAY DIFFRACTIONr_angle_other_deg0.93535795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9115474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5423.5140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27115518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5661518
X-RAY DIFFRACTIONr_chiral_restr0.0760.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214149
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02761
X-RAY DIFFRACTIONr_mcbond_it0.5721.52386
X-RAY DIFFRACTIONr_mcbond_other0.091.5977
X-RAY DIFFRACTIONr_mcangle_it1.07123762
X-RAY DIFFRACTIONr_scbond_it1.58331287
X-RAY DIFFRACTIONr_scangle_it2.6264.51229
LS refinement shellResolution: 2.915→2.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 36 -
Rwork0.25 926 -
obs--81.87 %
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)
14.51490.9351-3.92532.78530.279711.7304-0.05070.08610.311-0.14880.031-0.0984-0.0941-0.19680.01970.01550.0177-0.01270.26960.01160.1468-43.763630.057837.8445
23.0786-0.5259-1.38821.39740.463110.86830.12-0.0409-0.1122-0.15550.0995-0.10980.3157-0.058-0.21960.08160.01310.01550.1074-0.00860.1055-4.565719.695817.9434
33.5107-0.1075-0.21432.61-0.33961.6082-0.0405-0.1267-0.2779-0.06020.0731-0.05540.0539-0.0945-0.03260.04790.0076-0.00680.1670.03340.0732-21.21625.537533.2847
44.37121.58042.61496.88375.33368.1420.08650.1473-0.0616-0.32290.2945-0.1044-0.349-0.2532-0.3810.21860.0623-0.02370.12540.04190.0558-36.2852.82575.5499
52.0868-0.74410.44332.8297-2.32763.2793-0.1242-0.1930.38790.2904-0.0968-0.3454-0.6680.14140.2210.3473-0.0293-0.02780.0676-0.08520.1916-18.810658.640120.6312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-31 - -10
2X-RAY DIFFRACTION1A1 - 287
3X-RAY DIFFRACTION2A91 - 129
4X-RAY DIFFRACTION2A251 - 285
5X-RAY DIFFRACTION3A0 - 90
6X-RAY DIFFRACTION3A136 - 203
7X-RAY DIFFRACTION3A3 - 288
8X-RAY DIFFRACTION3A1 - 289
9X-RAY DIFFRACTION3A1 - 290
10X-RAY DIFFRACTION4B91 - 128
11X-RAY DIFFRACTION4B247 - 285
12X-RAY DIFFRACTION5B1 - 90
13X-RAY DIFFRACTION5B137 - 210

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