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- PDB-3v0l: Crystal structure of the Fucosylgalactoside alpha N-acetylgalacto... -

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Basic information

Entry
Database: PDB / ID: 3v0l
TitleCrystal structure of the Fucosylgalactoside alpha N-acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with a novel UDP-Gal derived inhibitor (2GW)
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / GTA / ABO / CISAB MUTANT / ROSSMANN FOLD / "Semi-closed" CONFORMATION / GLYCOSYLTRANSFERASE / GLYCOPROTEIN / BLOOD GROUP ANTIGEN / UDP-GalNAc / METAL-BINDING / MANGANESE / Glycosylation / TRANSMEMBRANE / GOLGI APPARATUS / SECRETED / SIGNAL-ANCHOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / : / Golgi cisterna membrane / : / antigen binding / manganese ion binding ...fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / : / Golgi cisterna membrane / : / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region
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
Chem-2GW / : / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsPalcic, M.M. / Jorgensen, R.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Base-modified Donor Analogues Reveal Novel Dynamic Features of a Glycosyltransferase.
Authors: Jrgensen, R. / Pesnot, T. / Lee, H.J. / Palcic, M.M. / Wagner, G.K.
History
DepositionDec 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Nov 8, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.5Sep 13, 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 / pdbx_struct_conn_angle / 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 / _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_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: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4474
Polymers34,6541
Non-polymers7933
Water3,693205
1
A: Histo-blood group ABO system transferase
hetero molecules

A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8958
Polymers69,3082
Non-polymers1,5876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5180 Å2
ΔGint-57 kcal/mol
Surface area22380 Å2
MethodPISA
2
A: Histo-blood group ABO system transferase
hetero molecules

A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8958
Polymers69,3082
Non-polymers1,5876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2190 Å2
ΔGint-48 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.430, 148.580, 78.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Histo-blood group ABO system transferase / Fucosylglycoprotein 3-alpha-galactosyltransferase / Fucosylglycoprotein alpha-N- ...Fucosylglycoprotein 3-alpha-galactosyltransferase / Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-galactosyltransferase / Histo-blood group A transferase / A transferase / Histo-blood group B transferase / B transferase / NAGAT / Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase soluble form


Mass: 34654.008 Da / Num. of mol.: 1 / Fragment: Extracellular catalytic domain / Mutation: L266G, G268A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AB0, ABO / Plasmid: PCW DELTA 1AC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-2GW / 5-phenyl-uridine-5'-alpha-d-galactosyl-diphosphate


Mass: 642.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N2O17P2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM MOPS pH 7, 50-200 mM AMMONIUM SULFATE, 50 mM MnCl2, AND 6-9% PEG-3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.90772 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 29, 2009
Details: Multilayer mirror, curved to focus in the vertical (R = 400 m)
RadiationMonochromator: Bent silicon crystal, horizontally focusing (R = 12 m). Will be planar diamond monochromator.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90772 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 31515 / Num. obs: 31474 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 25.46 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.09
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.75-1.857.40.653.27349624740473799.9
1.85-27.40.385.544061455055505100
2-2.257.40.2029.94596362316231100
2.25-2.57.40.13514.09294303979397799.9
2.5-37.40.09119.583368245674567100
3-3.57.30.05629.271721323512351100
3.5-47.20.04735.62962913331333100
4-57.20.04138.8295181325132499.9
5-67.10.04436.784260600600100
6-106.80.04137.68461867767699.9
10-205.10.03938.45106520717383.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.7 Å
Translation2.5 Å19.7 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER1.3.3phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RIT

2rit


Resolution: 1.75→19.7 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.907 / SU ML: 0.29 / Isotropic thermal model: Isotropic+tls / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 15.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1777 945 3 %Random
Rwork0.1471 ---
obs0.1481 31450 99.97 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.713 Å2 / ksol: 0.408 e/Å3
Displacement parametersBiso max: 100.62 Å2 / Biso mean: 21.896 Å2 / Biso min: 5.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.0291 Å2-0 Å20 Å2
2--0.0185 Å20 Å2
3---0.0105 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 48 205 2529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0212428
X-RAY DIFFRACTIONf_angle_d1.8843317
X-RAY DIFFRACTIONf_chiral_restr0.151364
X-RAY DIFFRACTIONf_plane_restr0.011416
X-RAY DIFFRACTIONf_dihedral_angle_d13.784897
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
1.75-1.84220.26991320.2043425643884388
1.8422-1.95760.17121340.1574433644704470
1.9576-2.10850.17261330.1331430744404440
2.1085-2.32040.1611350.1314434144764476
2.3204-2.65550.19811340.1379433344674467
2.6555-3.3430.18591360.1521438445204520
3.343-19.70120.15911410.1455454846894689
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)
13.6066-0.73171.14322.3077-1.10372.26210.12530.0783-0.12160.2019-0.2053-0.1096-0.09710.4690.05010.1084-0.0493-0.01690.17820.0250.129110.527-13.860533.7708
22.28680.0809-4.46760.0044-0.14688.8026-0.1697-0.206-0.13710.11180.08310.2364-0.3195-0.05510.01890.27010.01520.09510.2141-0.02310.20593.6923-2.258523.1827
32.32740.30760.08981.25220.1121.18640.0044-0.10910.1202-0.0257-0.0028-0.0892-0.1395-0.03670.00970.09430.00220.0060.0904-0.01130.11681.5928-10.470215.033
42.5588-1.7714-0.23295.5436-0.63081.0837-0.2201-0.32180.18020.26410.2472-0.2078-0.06880.0195-0.03490.092-0.0067-0.00070.14770.0010.112213.3699-19.74724.4954
51.77440.4056-1.61271.9817-0.76364.84660.11270.04550.01420.15530.06830.02350.1234-0.2504-0.18590.07260.0204-0.01890.07220.00690.087916.0943-28.392110.0116
61.78390.1572-0.26121.48690.27472.8520.02320.0469-0.0481-0.01680.0075-0.19680.15690.2352-0.03620.07690.02060.01150.0844-0.00240.114624.2406-21.04382.1037
71.481-0.4363-0.22651.33451.31485.52880.1716-0.02990.01030.01580.0679-0.15360.4154-0.0239-0.17080.086-0.0028-0.01980.0695-0.01240.091120.4936-29.81886.7717
82.3042-0.5488-1.34093.10292.8943.00970.0268-0.29480.03980.2460.2396-0.2160.18430.33520.0130.08990.06040.0210.1227-0.01930.090130.4185-28.5515-0.7929
90.91230.33910.24450.69360.60372.31540.02950.169-0.2004-0.18130.01380.04060.32290.1097-0.13050.1410.0124-0.02160.1257-0.03940.079723.2929-32.0783.1551
101.0416-0.87450.60653.8884-3.02265.02810.0080.3586-0.2489-0.41540.0509-0.04660.3919-0.3285-0.06030.2533-0.0198-0.00180.2894-0.06270.387810.2979-33.3816-1.8686
110.8681-0.1666-0.04560.52760.06521.98710.01620.03410.1397-0.07620.0141-0.047-0.12320.1287-0.02310.08040.02290.00920.06840.00240.095816.4008-20.72576.1395
121.0559-0.02050.34850.57960.16450.4210.02310.08150.1107-0.0182-0.05210.066-0.08430.03570.0190.0988-0.00420.01660.0879-0.00210.09496.1498-14.42177.8667
132.74011.30081.35213.0990.96893.8426-0.02820.0738-0.0582-0.3339-0.04150.1789-0.4466-0.42370.01540.1520.0402-0.0250.17240.03740.1485-4.9632-13.4856-7.1414
140.61240.53560.52291.09780.97362.82350.08180.10310.0091-0.2202-0.10890.3044-0.2271-0.5434-0.03960.1360.0352-0.0440.20480.00210.1401-8.9167-17.2883-4.9122
151.1595-0.49010.03721.1845-0.33090.80340.04240.0784-0.02780.034-0.0275-0.0684-0.03340.0443-0.01920.07560.00130.00430.07540.0140.0845.4038-19.8134.5416
165.27120.04540.71026.68060.5024.16230.2483-0.4017-0.82220.5905-0.04580.24740.6956-0.3952-0.04660.1612-0.0294-0.02840.15770.0340.16582.6057-32.21847.8506
173.0686-0.04933.25162.03040.60037.98510.16340.2185-0.1482-0.2950.0284-0.01870.3825-0.1137-0.28610.1568-0.0113-0.0020.1185-0.02640.13130.0177-30.9906-6.4532
180.89760.01530.50991.28970.34853.27430.00290.14930.0286-0.19330.0195-0.0258-0.0465-0.0398-0.01590.0810.00310.00470.11840.00750.0963-0.681-21.3062-1.8138
190.51490.57350.22392.5139-1.02070.95680.0183-0.08830.10320.0262-0.00540.0328-0.18350.0622-0.0150.13560.00190.01430.08850.01190.111913.297-6.42684.8795
201.99910.30340.03040.31610.45812.9630.0848-0.070.2438-0.1748-0.0782-0.1132-0.32440.2801-0.19650.1374-0.01590.05850.10920.01860.119216.9962-9.06516.8156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 65:76 )A65 - 76
2X-RAY DIFFRACTION2( CHAIN A AND RESID 77:82 )A77 - 82
3X-RAY DIFFRACTION3( CHAIN A AND RESID 83:98 )A83 - 98
4X-RAY DIFFRACTION4( CHAIN A AND RESID 99:111 )A99 - 111
5X-RAY DIFFRACTION5( CHAIN A AND RESID 112:122 )A112 - 122
6X-RAY DIFFRACTION6( CHAIN A AND RESID 123:143 )A123 - 143
7X-RAY DIFFRACTION7( CHAIN A AND RESID 144:154 )A144 - 154
8X-RAY DIFFRACTION8( CHAIN A AND RESID 155:163 )A155 - 163
9X-RAY DIFFRACTION9( CHAIN A AND RESID 164:177 )A164 - 177
10X-RAY DIFFRACTION10( CHAIN A AND RESID 181:203 )A181 - 203
11X-RAY DIFFRACTION11( CHAIN A AND RESID 204:218 )A204 - 218
12X-RAY DIFFRACTION12( CHAIN A AND RESID 219:241 )A219 - 241
13X-RAY DIFFRACTION13( CHAIN A AND RESID 242:250 )A242 - 250
14X-RAY DIFFRACTION14( CHAIN A AND RESID 251:262 )A251 - 262
15X-RAY DIFFRACTION15( CHAIN A AND RESID 263:274 )A263 - 274
16X-RAY DIFFRACTION16( CHAIN A AND RESID 275:279 )A275 - 279
17X-RAY DIFFRACTION17( CHAIN A AND RESID 280:293 )A280 - 293
18X-RAY DIFFRACTION18( CHAIN A AND RESID 294:318 )A294 - 318
19X-RAY DIFFRACTION19( CHAIN A AND RESID 319:335 )A319 - 335
20X-RAY DIFFRACTION20( CHAIN A AND RESID 336:345 )A336 - 345

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