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- PDB-4fro: Crystal Structure of BBBB+UDP+Gal at pH 9.0 with MPD as the cryop... -

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Basic information

Entry
Database: PDB / ID: 4fro
TitleCrystal Structure of BBBB+UDP+Gal at pH 9.0 with MPD as the cryoprotectant
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE / MANGANESE / ABO ROSSMANN FOLD / RETAINING GLYCOSYLTRANSFERASE / GLYCOPROTEIN / BLOOD GROUP ANTIGEN / METAL-BINDING
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 / hexosyltransferase activity / : / Golgi cisterna membrane / : / antigen 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 / hexosyltransferase activity / : / Golgi cisterna membrane / : / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region / metal ion binding / membrane
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
beta-D-galactopyranose / GLYCINE / : / URIDINE-5'-DIPHOSPHATE / Histo-blood group ABO system transferase / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJohal, A.R. / Alfaro, J.A. / Blackler, R.J. / Schuman, B. / Borisova, S.N. / Evans, S.V.
CitationJournal: Glycobiology / Year: 2014
Title: pH-induced conformational changes in human ABO(H) blood group glycosyltransferases confirm the importance of electrostatic interactions in the formation of the semi-closed state.
Authors: Johal, A.R. / Blackler, R.J. / Alfaro, J.A. / Schuman, B. / Borisova, S. / Evans, S.V.
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)34,8535
Polymers34,1381
Non-polymers7144
Water4,179232
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)69,70510
Polymers68,2772
Non-polymers1,4298
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6490 Å2
ΔGint-49 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.164, 150.737, 79.182
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Histo-blood group ABO system transferase


Mass: 34138.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Plasmid: PCW DELTA 1AC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD
References: UniProt: H6A2X0, UniProt: P16442*PLUS, fucosylgalactoside 3-alpha-galactosyltransferase
#5: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 235 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1% PEG 4000, 5% MPD, 5 mM manganese chloride, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM glycine, 30 mM sodium acetate with 20% MPD as cryoprotectant, pH 9.0, VAPOR DIFFUSION, ...Details: 1% PEG 4000, 5% MPD, 5 mM manganese chloride, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM glycine, 30 mM sodium acetate with 20% MPD as cryoprotectant, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 26, 2012 / Details: 9 CCDs, 9 TILED FIBER-OPTIC TAPERS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 33618 / % possible obs: 96.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.057 / Χ2: 0.97 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.735.10.23816500.676196.4
1.73-1.765.10.21116680.77197.8
1.76-1.7950.18416660.816196.5
1.79-1.8350.16716580.884198.2
1.83-1.8750.1516880.925196.9
1.87-1.9150.13416501.022197.6
1.91-1.964.90.11716861.086198.5
1.96-2.0250.10816791.093196.7
2.02-2.074.90.09816881.14198.1
2.07-2.144.80.09316981.193198.4
2.14-2.224.80.08716911.224197
2.22-2.314.80.08216611.259197
2.31-2.414.80.07816751.2197.2
2.41-2.544.80.07117021.111198
2.54-2.74.70.06417090.995197.7
2.7-2.914.70.05916890.948197
2.91-3.24.60.05517090.91197.1
3.2-3.664.60.04716700.773195.2
3.66-4.614.50.04516870.665194.3
4.61-404.40.04616940.685189.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SXG

3sxg


Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.195 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 1564 5.1 %RANDOM
Rwork0.1834 ---
obs0.1854 30772 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.52 Å2 / Biso mean: 24.7674 Å2 / Biso min: 6.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2265 0 43 232 2540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022378
X-RAY DIFFRACTIONr_bond_other_d0.0020.021635
X-RAY DIFFRACTIONr_angle_refined_deg2.0431.9673231
X-RAY DIFFRACTIONr_angle_other_deg1.133.0073953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90322.679112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92515397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4261519
X-RAY DIFFRACTIONr_chiral_restr0.1250.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212567
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02524
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 109 -
Rwork0.216 1954 -
all-2063 -
obs--95.03 %

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