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

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Basic information

Entry
Database: PDB / ID: 2iuy
TitleCrystal structure of AviGT4, a glycosyltransferase involved in Avilamycin A biosynthesis
ComponentsGLYCOSYLTRANSFERASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / ANTIBIOTICS / FAMILY GT-4 / AVILAMYCIN A
Function / homologyGlycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / Glycogen Phosphorylase B; / nucleotide binding / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Putative glycosyltransferase
Function and homology information
Biological speciesSTREPTOMYCES VIRIDOCHROMOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOSYLTRANSFERASE
B: GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2406
Polymers72,6572
Non-polymers5834
Water7,927440
1
A: GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5242
Polymers36,3291
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7164
Polymers36,3291
Non-polymers3873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.521, 73.829, 92.173
Angle α, β, γ (deg.)90.00, 90.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GLYCOSYLTRANSFERASE / AVIGT4


Mass: 36328.508 Da / Num. of mol.: 2
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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growDetails: 18% PEG3350, 0.2M LI2SO4, 0.1M MES PH 6.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9777
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 16, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2→73.92 Å / Num. obs: 42291 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.5 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→19.98 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 4.621 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1902 5.1 %RANDOM
Rwork0.17 ---
obs0.173 35293 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.02 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5042 0 34 440 5516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225214
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.9637136
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7535676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6822.249209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72615716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8691547
X-RAY DIFFRACTIONr_chiral_restr0.1120.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024067
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.22467
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.23454
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2396
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3630.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0711.53457
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56625394
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.75732027
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2184.51742
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
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 130
Rwork0.176 2504

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