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- PDB-4kxo: Crystal Structure of BBBB at pH 10.0 with MPD as the cryoprotectant -

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Basic information

Entry
Database: PDB / ID: 4kxo
TitleCrystal Structure of BBBB at pH 10.0 with MPD as the cryoprotectant
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE / MANGANESE / ABO ROSSMANN FOLD / RETAINING GLYCOSYLTRANSFERASE / BLOOD GROUP ANTIGEN / METAL-BINDING / GLYCOPROTEIN
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
Histo-blood group ABO system transferase / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJohal, A.R. / Blackler, R.J. / Alfaro, J.A. / 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
DepositionMay 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histo-blood group ABO system transferase


Theoretical massNumber of molelcules
Total (without water)34,0091
Polymers34,0091
Non-polymers00
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histo-blood group ABO system transferase

A: Histo-blood group ABO system transferase


Theoretical massNumber of molelcules
Total (without water)68,0192
Polymers68,0192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3520 Å2
ΔGint-28 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.330, 150.539, 79.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-498-

HOH

21A-512-

HOH

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Components

#1: Protein Histo-blood group ABO system transferase


Mass: 34009.273 Da / Num. of mol.: 1 / Fragment: UNP residues 64-354
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10
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 10.0, 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 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 6, 2012 / Details: OSMIC BLUE MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 20494 / % possible obs: 94.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.074.60.37198.8
2.07-2.154.60.312199
2.15-2.2540.222191.3
2.25-2.374.10.212195.1
2.37-2.524.60.162199.3
2.52-2.714.60.126199.5
2.71-2.994.60.093199.5
2.99-3.424.60.065199.7
3.42-4.33.80.05167.2
4.3-204.40.032199.4

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Processing

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

3sxg


Resolution: 2→19.89 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.888 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.872 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29046 1027 5.1 %RANDOM
Rwork0.23695 ---
obs0.2397 19263 93.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.715 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 0 202 2375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022260
X-RAY DIFFRACTIONr_bond_other_d0.0010.022175
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.9473068
X-RAY DIFFRACTIONr_angle_other_deg0.9033.0024943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.525266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.81122.661109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.38115384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7231519
X-RAY DIFFRACTIONr_chiral_restr0.1040.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212510
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02559
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 69 -
Rwork0.218 1350 -
obs--97.19 %

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