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- PDB-4ayl: Molecular structure of a metal-independent bacterial glycosyltran... -

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Basic information

Entry
Database: PDB / ID: 4ayl
TitleMolecular structure of a metal-independent bacterial glycosyltransferase that catalyzes the synthesis of histo-blood group A antigen
ComponentsBOGT-METAL-INDEPENDENT GLYCOSYLTRANSFERASE
KeywordsTRANSFERASE / HISTO-BLOOD GROUP ENZYME
Function / homology
Function and homology information


hexosyltransferase activity / carbohydrate metabolic process / nucleotide binding / membrane / metal ion binding
Similarity search - Function
: / Glycosyl transferase, family 6 / Glycosyltransferase family 6 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Glycosyltransferase family 6
Similarity search - Component
Biological speciesBACTEROIDES OVATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.919 Å
AuthorsThiyagarajan, N. / Pham, T.T.K. / Stinsonb, B. / Sundriyala, A. / Tumbale, P. / Lizotte-Waniewskib, M. / Brewb, K. / Acharya, K.R.
CitationJournal: Sci.Rep. / Year: 2012
Title: Structure of a Metal-Independent Bacterial Glycosyltransferase that Catalyzes the Synthesis of Histo-Blood Group a Antigen
Authors: Thiyagarajan, N. / Pham, T.T.K. / Stinson, B. / Sundriyal, A. / Tumbale, P. / Lizotte-Waniewski, M. / Brew, K. / Acharya, K.R.
History
DepositionJun 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Jan 29, 2014Group: Database references
Revision 1.4Feb 25, 2015Group: Database references
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: BOGT-METAL-INDEPENDENT GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3524
Polymers29,0381
Non-polymers3143
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.227, 41.227, 282.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-2081-

HOH

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Components

#1: Protein BOGT-METAL-INDEPENDENT GLYCOSYLTRANSFERASE


Mass: 29038.057 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES OVATUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A7LVT2, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 200 / 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: 45 % / Description: NONE
Crystal growpH: 7.5
Details: 15 % (W/V) PEG 4000, CONTAINING 0.1 M TRIS, PH 7.5, 0.2 M CALCIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 20120 / % possible obs: 77.7 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.1
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 4.5 / % possible all: 22.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
MrBUMPphasing
CHAINSAWphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VS4

2vs4


Resolution: 1.919→35.368 Å / SU ML: 0.5 / σ(F): 1.37 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 775 5 %
Rwork0.1787 --
obs0.1811 15587 77.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.815 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.4947 Å20 Å20 Å2
2--14.4947 Å20 Å2
3---7.0638 Å2
Refinement stepCycle: LAST / Resolution: 1.919→35.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 17 200 1971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081851
X-RAY DIFFRACTIONf_angle_d1.1142517
X-RAY DIFFRACTIONf_dihedral_angle_d13.268684
X-RAY DIFFRACTIONf_chiral_restr0.076258
X-RAY DIFFRACTIONf_plane_restr0.006316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9188-2.0390.2809480.1912898X-RAY DIFFRACTION29
2.039-2.19640.25411020.16951916X-RAY DIFFRACTION62
2.1964-2.41740.24251490.17812827X-RAY DIFFRACTION91
2.4174-2.76710.24961730.19382989X-RAY DIFFRACTION96
2.7671-3.48570.24771550.17993034X-RAY DIFFRACTION95
3.4857-35.3740.18591480.17313148X-RAY DIFFRACTION91

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