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- PDB-3u0x: Crystal structure of the B-specific-1,3-galactosyltransferase (GT... -

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Basic information

Entry
Database: PDB / ID: 3u0x
TitleCrystal structure of the B-specific-1,3-galactosyltransferase (GTB) in complex with compound 382
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ROSSMANN FOLD / OPEN CONFORMATION / GLYCOSYLTRANSFERASE / TRANSFERASE GTB / ABO / BLOOD GROUP ANTIGEN / GLYCOPROTEIN / METAL-BINDING / MANGANESE / UDP-GAL / H-ANTIGEN ACCEPTOR / MEMBRANE / 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 / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / 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 / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / 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
1-(3-phenyl-1,2,4-thiadiazol-5-yl)piperazine / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsPalcic, M.M. / Jorgensen, R.
CitationJournal: To be Published
Title: A novel compound from a molecular fragment library screen inhibits glycosyltransferases by displacing the metal ion and interfering with substrate binding
Authors: Jorgensen, R. / Grimm, L.L. / Sindhuwinata, N. / Peters, T. / Palcic, M.M.
History
DepositionSep 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Sep 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 / 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: Histo-blood group ABO system transferase
B: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,30519
Polymers69,5162
Non-polymers1,78917
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-137 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.150, 151.790, 72.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11B-399-

HOH

21B-470-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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: 34758.180 Da / Num. of mol.: 2 / Fragment: unp residues 64-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Human / Gene: ABO / Plasmid: PCW DELTA 1AC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21
References: UniProt: P16442, fucosylgalactoside 3-alpha-galactosyltransferase

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Non-polymers , 5 types, 387 molecules

#2: Chemical ChemComp-GTI / 1-(3-phenyl-1,2,4-thiadiazol-5-yl)piperazine


Mass: 246.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14N4S
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE OF THIS PROTEIN CORRESPONDS TO WILD TYPE HISTO -BLOOD GROUP B TRANSFERASE. THE ...THE SEQUENCE OF THIS PROTEIN CORRESPONDS TO WILD TYPE HISTO -BLOOD GROUP B TRANSFERASE. THE SEQUENCE DIFFERENCES WITH UNP ENTRY P16442 CORRESPOND TO THE VARIENTS BETWEEN P16442 AND GROUP B TRANSFERASE, AS INDICATED IN THE DESCRIPTION OF P16442.

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 23% PEG-3350, 300 mM Ammonium Sulfate, 50 mM MOPS, 50 mM MnCl2, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2010 / Details: Torodial focusing mirror
RadiationMonochromator: Channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 57693 / Num. obs: 57641 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 25.296 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.85-1.926.50.6872.89389886015601199.9
1.92-2.066.50.4224.596327297029701100
2.06-2.226.50.2627.35425783328331100
2.22-2.436.50.17710.465111678837880100
2.43-2.726.50.12214.44735172787277100
2.72-3.146.50.07820.994123463746372100
3.14-3.846.30.04832.29342475390538799.9
3.84-5.416.20.03343.11263344234422899.9
5.41-406.10.02744.66152792485245498.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.68 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.46 Å
Translation2.5 Å29.46 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2RIT

2rit


Resolution: 1.85→29.442 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.9054 / SU ML: 0.19 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 16.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1899 1730 3 %Random
Rwork0.1541 ---
obs0.1551 57637 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.603 Å2 / ksol: 0.422 e/Å3
Displacement parametersBiso max: 100.13 Å2 / Biso mean: 21.7192 Å2 / Biso min: 6 Å2
Baniso -1Baniso -2Baniso -3
1--0.0012 Å20 Å20 Å2
2---0.0144 Å2-0 Å2
3---0.0156 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 107 370 5141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074988
X-RAY DIFFRACTIONf_angle_d1.1116787
X-RAY DIFFRACTIONf_chiral_restr0.08733
X-RAY DIFFRACTIONf_plane_restr0.005855
X-RAY DIFFRACTIONf_dihedral_angle_d14.9671832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
1.85-1.90450.24181430.1914462547684768
1.9045-1.96590.22091420.1853457047124712
1.9659-2.03620.21321430.157462747704770
2.0362-2.11770.19191430.1501461747604760
2.1177-2.2140.17571430.1376463147744774
2.214-2.33070.15811430.1371463147744774
2.3307-2.47660.19741430.1443462247654765
2.4766-2.66780.18311430.1455463847814781
2.6678-2.9360.20291450.1448466548104810
2.936-3.36030.16561450.1358469148364836
3.3603-4.23160.16371460.1366471748634863
4.2316-29.44590.19451510.1834487350245024
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)
10.07240.0280.47961.18950.13460.35930.06440.0085-0.03370.0124-0.08160.2958-0.0486-0.01210.02210.10420.01120.02650.1099-0.00070.1309-18.0571-49.6621-9.3438
20.3453-0.0690.25690.4728-0.13270.7397-0.05130.0490.0134-0.09490.0111-0.01670.08330.02820.01360.06880.0070.00630.07690.00050.0661-14.5505-52.171-0.601
31.3979-0.0227-0.37770.33460.22160.4054-0.0477-0.28130.17860.03030.0805-0.0861-0.05170.0802-0.03260.1049-0.0014-0.0050.1331-0.04590.1247-6.1737-36.855815.9922
40.73030.19980.30310.72730.45211.0562-0.0172-0.09080.183-0.0520.0584-0.1899-0.23560.0592-0.04150.1008-0.0011-0.01040.1134-0.03340.1282-7.4925-33.046313.6407
52.63170.62760.58221.9302-0.15960.44810.0634-0.40380.06810.31340.00140.1091-0.1082-0.116-0.04810.14480.0180.01620.141-0.02910.1065-16.826-35.634420.1189
60.6618-0.4497-0.50910.81760.45791.20180.03280.0010.1316-0.01180.0842-0.0834-0.0218-0.014-0.04890.08170.0045-0.00430.0965-0.00070.0747-3.5489-44.28312.8309
70.3798-0.0853-0.0910.3240.21120.9369-0.0395-0.0805-0.01160.07490.02660.02730.12280.03830.02910.08450.01060.01070.09150.00880.0624-15.8576-57.790818.4038
80.703-0.2337-0.98682.1357-1.06722.62160.0059-0.13210.07890.32270.11180.3793-0.5079-0.4579-0.05970.10310.01660.02430.137-0.01670.1162-24.9727-45.724422.2809
90.69680.1808-0.72050.0791-0.38180.8936-0.0004-0.15330.03640.0740.03510.0222-0.02970.152-0.0250.12840.01460.01560.1006-0.00450.0873-19.1306-54.092323.6645
100.81510.3454-0.0930.79530.09820.07470.0451-0.2769-0.01040.0324-0.0983-0.11740.0146-0.09220.03590.08350.0098-0.01960.1375-0.00650.09581.2317-51.454512.5221
112.18960.13210.23260.05830.3251.4611-0.0372-0.17940.39050.03030.0730.0347-0.0061-0.0907-0.05590.1707-0.00560.01370.0819-0.0080.1943-24.2918-61.943110.7404
121.15970.36780.38450.5634-0.38990.5840.0482-0.1423-0.15850.0075-0.0577-0.03250.09450.03330.01130.128-0.00250.00180.07960.00670.1014-23.7813-62.46130.0143
131.3408-1.2081-0.20521.5415-0.05750.19020.0602-0.0876-0.21280.1147-0.06720.38440.1184-0.243-0.00050.0956-0.0528-0.03110.1295-0.0190.1286-45.2548-63.5303-9.5149
140.3922-0.2323-0.68421.0383-0.36552.3075-0.0905-0.0294-0.32150.07190.04420.35940.0019-0.45730.01730.136-0.0707-0.02310.1745-0.02740.2358-48.6328-63.5744-7.4123
150.54460.25910.52510.94790.31871.0106-0.12420.1343-0.0494-0.15030.09490.2097-0.0283-0.29140.01440.0839-0.0228-0.00080.2156-0.02220.2089-47.9381-55.2749-12.2079
160.53740.1084-0.18892.34380.7170.62290.03720.0528-0.0964-0.0648-0.09880.39130.0378-0.240.0810.1138-0.0193-0.01080.1405-0.03080.1222-42.5055-57.4505-8.2971
170.6686-0.21310.14780.3970.04110.74940.02690.0674-0.0347-0.0984-0.02250.01140.13310.036-0.01020.0840.0095-0.0090.0501-0.00820.0658-25.7826-55.6284-16.8477
180.2039-0.11040.39171.1754-1.58044.18640.1917-0.09240.10370.10030.33890.4601-0.4806-0.5805-0.09970.01890.03560.00510.0609-0.01450.0673-36.9613-44.8632-13.4422
190.2307-0.1205-0.3050.1957-0.07740.32780.05050.0292-0.0092-0.0836-0.04590.09-0.0525-0.09280.04350.11180.0058-0.02810.0897-0.00650.0735-31.4627-47.4074-23.6972
200.4403-0.08610.13390.3168-0.09810.20980.1210.058-0.0778-0.1162-0.14870.11370.1133-0.0572-0.0340.1534-0.001-0.03190.0917-0.02940.1024-28.6514-67.9672-12.2884
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 58:81)A58 - 81
2X-RAY DIFFRACTION2(chain A and resid 82:111)A82 - 111
3X-RAY DIFFRACTION3(chain A and resid 112:138)A112 - 138
4X-RAY DIFFRACTION4(chain A and resid 139:162)A139 - 162
5X-RAY DIFFRACTION5(chain A and resid 163:208)A163 - 208
6X-RAY DIFFRACTION6(chain A and resid 209:219)A209 - 219
7X-RAY DIFFRACTION7(chain A and resid 220:274)A220 - 274
8X-RAY DIFFRACTION8(chain A and resid 275:288)A275 - 288
9X-RAY DIFFRACTION9(chain A and resid 289:321)A289 - 321
10X-RAY DIFFRACTION10(chain A and resid 322:351)A322 - 351
11X-RAY DIFFRACTION11(chain B and resid 58:81)B58 - 81
12X-RAY DIFFRACTION12(chain B and resid 82:109)B82 - 109
13X-RAY DIFFRACTION13(chain B and resid 110:137)B110 - 137
14X-RAY DIFFRACTION14(chain B and resid 138:162)B138 - 162
15X-RAY DIFFRACTION15(chain B and resid 163:195)B163 - 195
16X-RAY DIFFRACTION16(chain B and resid 196:217)B196 - 217
17X-RAY DIFFRACTION17(chain B and resid 218:273)B218 - 273
18X-RAY DIFFRACTION18(chain B and resid 274:288)B274 - 288
19X-RAY DIFFRACTION19(chain B and resid 289:312)B289 - 312
20X-RAY DIFFRACTION20(chain B and resid 313:345)B313 - 345

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