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- PDB-2iv3: Crystal structure of AviGT4, a glycosyltransferase involved in Av... -

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Basic information

Entry
Database: PDB / ID: 2iv3
TitleCrystal structure of AviGT4, a glycosyltransferase involved in Avilamycin A biosynthesis
ComponentsGLYCOSYLTRANSFERASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / ANTIBIOTICS / FAMILY GT-4 / AVILAMYCIN A
Function / homology
Function and homology information


glycosyltransferase activity / nucleotide binding
Similarity search - Function
Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Putative glycosyltransferase
Similarity search - Component
Biological speciesSTREPTOMYCES VIRIDOCHROMOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMartinez-Fleites, C. / Proctor, M. / Roberts, S. / Bolam, D.N. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Chem.Biol. / Year: 2006
Title: Insights Into the Synthesis of Lipopolysaccharide and Antibiotics Through the Structures of Two Retaining Glycosyltransferases from Family Gt4
Authors: Martinez-Fleites, C. / Proctor, M. / Roberts, S. / Bolam, D.N. / Gilbert, H.J. / Davies, G.J.
History
DepositionJun 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOSYLTRANSFERASE
B: GLYCOSYLTRANSFERASE
C: GLYCOSYLTRANSFERASE
D: GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,54912
Polymers144,5644
Non-polymers1,9858
Water7,963442
1
A: GLYCOSYLTRANSFERASE
B: GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2746
Polymers72,2822
Non-polymers9934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: GLYCOSYLTRANSFERASE
D: GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2746
Polymers72,2822
Non-polymers9934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.470, 74.370, 90.640
Angle α, β, γ (deg.)89.99, 92.70, 100.73
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 1000
2114B1 - 1000
3114C1 - 1000
4114D1 - 1000

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Components

#1: Protein
GLYCOSYLTRANSFERASE / AVIGT4


Mass: 36140.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES VIRIDOCHROMOGENES (bacteria)
Description: DSM 40721 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93KV2
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.2 Å3/Da / Density % sol: 41 %
Crystal growDetails: 18% PEG 3350, 0.2M LI2SO4, 0.1M MES PH6.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 56829 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.6 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IUY

2iuy


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.873 / SU B: 18.759 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.473 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2869 5 %RANDOM
Rwork0.207 ---
obs0.21 53958 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å2-0.19 Å2-0.04 Å2
2--0.62 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10034 0 124 442 10600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02210469
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9714331
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.52951345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08722.19420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.785151441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.371596
X-RAY DIFFRACTIONr_chiral_restr0.1130.21579
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028124
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.25364
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.26942
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2628
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2870.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.551.56856
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.825210746
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47934137
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1124.53584
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2507 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.40.5
2Bmedium positional0.440.5
3Cmedium positional0.410.5
4Dmedium positional0.410.5
1Amedium thermal0.772
2Bmedium thermal0.782
3Cmedium thermal0.742
4Dmedium thermal0.732
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.357 214
Rwork0.266 3557
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)
11.9817-0.89220.87471.7864-0.06991.92950.0521-0.03350.14020.0742-0.0289-0.17530.08310.0664-0.0232-0.1772-0.0422-0.004-0.0699-0.0095-0.052612.796610.14469.8803
21.30661.0063-0.76422.3829-0.59961.8922-0.02170.0734-0.04760.09550.0464-0.04730.14140.0554-0.0247-0.14690.01460.009-0.0747-0.0218-0.08667.478333.836931.0663
31.28760.46090.85121.63450.39371.90210.07230.0430.02410.0709-0.0025-0.04360.0408-0.0781-0.0698-0.08020.0307-0.0142-0.08420.0073-0.1053-3.7574-30.8128-15.3584
41.4874-0.5493-0.80371.04680.46411.86210.0503-0.00930.0010.108-0.01410.039-0.1375-0.0819-0.0361-0.0368-0.01260.0181-0.09710.0382-0.0966-6.5673-6.7282-36.2587
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 352
2X-RAY DIFFRACTION1A1353 - 1354
3X-RAY DIFFRACTION2B13 - 352
4X-RAY DIFFRACTION2B1353 - 1354
5X-RAY DIFFRACTION3C13 - 352
6X-RAY DIFFRACTION3C1353 - 1354
7X-RAY DIFFRACTION4D13 - 352
8X-RAY DIFFRACTION4D1353 - 1354

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