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- PDB-4irp: Crystal structure of catalytic domain of human beta1,4-galactosyl... -

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Basic information

Entry
Database: PDB / ID: 4irp
TitleCrystal structure of catalytic domain of human beta1,4-galactosyltransferase-7 in open conformation with manganses and UDP
ComponentsBeta-1,4-galactosyltransferase 7
KeywordsTRANSFERASE / GT-A fold / open conformation / manganese and UDP complex / glycosyltransferase / Golgi
Function / homology
Function and homology information


xylosylprotein 4-beta-galactosyltransferase / xylosylprotein 4-beta-galactosyltransferase activity / galactosyltransferase activity / Defective B4GALT7 causes EDS, progeroid type / : / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity / Glycosaminoglycan-protein linkage region biosynthesis / glycosaminoglycan biosynthetic process / proteoglycan biosynthetic process / glycosaminoglycan metabolic process ...xylosylprotein 4-beta-galactosyltransferase / xylosylprotein 4-beta-galactosyltransferase activity / galactosyltransferase activity / Defective B4GALT7 causes EDS, progeroid type / : / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity / Glycosaminoglycan-protein linkage region biosynthesis / glycosaminoglycan biosynthetic process / proteoglycan biosynthetic process / glycosaminoglycan metabolic process / proteoglycan metabolic process / protein N-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / negative regulation of fibroblast proliferation / supramolecular fiber organization / protein modification process / manganese ion binding / carbohydrate metabolic process / Golgi membrane / Golgi apparatus / membrane
Similarity search - Function
Beta-1,4-galactosyltransferase / Galactosyltransferase, N-terminal / N-terminal region of glycosyl transferase group 7 / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / 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
ACETATE ION / IMIDAZOLE / : / URIDINE-5'-DIPHOSPHATE / Beta-1,4-galactosyltransferase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTsutsui, Y. / Ramakrishnan, B. / Qasba, P.K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal Structures of beta-1,4-Galactosyltransferase 7 Enzyme Reveal Conformational Changes and Substrate Binding.
Authors: Tsutsui, Y. / Ramakrishnan, B. / Qasba, P.K.
History
DepositionJan 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Sep 20, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,4-galactosyltransferase 7
B: Beta-1,4-galactosyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,77413
Polymers58,4332
Non-polymers1,34211
Water5,296294
1
A: Beta-1,4-galactosyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9818
Polymers29,2161
Non-polymers7647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-1,4-galactosyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7935
Polymers29,2161
Non-polymers5774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-12 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.186, 125.186, 87.326
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-1,4-galactosyltransferase 7 / Beta-1 / 4-GalTase 7 / Beta4Gal-T7 / b4Gal-T7 / UDP-Gal:beta-GlcNAc beta-1 / 4- ...Beta-1 / 4-GalTase 7 / Beta4Gal-T7 / b4Gal-T7 / UDP-Gal:beta-GlcNAc beta-1 / 4-galactosyltransferase 7 / UDP-galactose:beta-N-acetylglucosamine beta-1 / 4-galactosyltransferase 7 / Xylosylprotein 4-beta-galactosyltransferase / Proteoglycan UDP-galactose:beta-xylose beta1 / 4-galactosyltransferase I / UDP-galactose:beta-xylose beta-1 / 4-galactosyltransferase / XGPT / XGalT-1 / Xylosylprotein beta-1 / 4-galactosyltransferase


Mass: 29216.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: human galectin 1 as fusion protein / Source: (gene. exp.) Homo sapiens (human)
Gene: 4galactosyltransferase, B4GALT7, beta1, UNQ748/PRO1478, XGALT1
Plasmid: PET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9UBV7, Transferases; Glycosyltransferases; Hexosyltransferases, xylosylprotein 4-beta-galactosyltransferase

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Non-polymers , 5 types, 305 molecules

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


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.7 to 1.0 M Sodium accetate, 100 mM imidazole.HCL pH 6.5 as precipating agent, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 17, 2012 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 44450 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 13.1 % / Rsym value: 0.063 / Net I/σ(I): 36.5
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.493 / % possible all: 93.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LW6

3lw6


Resolution: 2.1→44.26 Å / SU ML: 0.24 / σ(F): 0.55 / Phase error: 31.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2746 2081 5.11 %
Rwork0.2182 --
obs0.2209 40726 99.25 %
all-44450 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3755 0 81 294 4130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0224144
X-RAY DIFFRACTIONf_angle_d1.935647
X-RAY DIFFRACTIONf_dihedral_angle_d15.3881541
X-RAY DIFFRACTIONf_chiral_restr0.139577
X-RAY DIFFRACTIONf_plane_restr0.01730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14890.30531620.23832505X-RAY DIFFRACTION99
2.1489-2.20260.2811450.232526X-RAY DIFFRACTION99
2.2026-2.26220.28141370.21032539X-RAY DIFFRACTION99
2.2622-2.32870.30761450.21022532X-RAY DIFFRACTION99
2.3287-2.40390.28421280.20872556X-RAY DIFFRACTION99
2.4039-2.48980.26741320.2082550X-RAY DIFFRACTION100
2.4898-2.58950.331430.21752566X-RAY DIFFRACTION100
2.5895-2.70730.27061250.22012562X-RAY DIFFRACTION100
2.7073-2.850.26371330.21112579X-RAY DIFFRACTION99
2.85-3.02860.27731610.22322538X-RAY DIFFRACTION100
3.0286-3.26230.25981230.21622596X-RAY DIFFRACTION99
3.2623-3.59050.2581410.20272592X-RAY DIFFRACTION99
3.5905-4.10970.23041420.1942598X-RAY DIFFRACTION99
4.1097-5.17660.2631390.19812645X-RAY DIFFRACTION99
5.1766-44.26970.33581250.28252761X-RAY DIFFRACTION98

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