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- PDB-4irq: Crystal structure of catalytic domain of human beta1,4galactosylt... -

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Basic information

Entry
Database: PDB / ID: 4irq
TitleCrystal structure of catalytic domain of human beta1,4galactosyltransferase 7 in closed conformation in complex with manganese and UDP
ComponentsBeta-1,4-galactosyltransferase 7
KeywordsTRANSFERASE / GT-A fold / closed 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
: / URIDINE-5'-DIPHOSPHATE / Beta-1,4-galactosyltransferase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.1Feb 25, 2015Group: 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 1.3Oct 30, 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
C: Beta-1,4-galactosyltransferase 7
D: Beta-1,4-galactosyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,19016
Polymers116,8654
Non-polymers2,32512
Water5,206289
1
A: Beta-1,4-galactosyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7984
Polymers29,2161
Non-polymers5813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-1,4-galactosyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7984
Polymers29,2161
Non-polymers5813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-1,4-galactosyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7984
Polymers29,2161
Non-polymers5813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-1,4-galactosyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7984
Polymers29,2161
Non-polymers5813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Beta-1,4-galactosyltransferase 7
D: Beta-1,4-galactosyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5958
Polymers58,4332
Non-polymers1,1626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-36 kcal/mol
Surface area20540 Å2
MethodPISA
6
B: Beta-1,4-galactosyltransferase 7
hetero molecules

C: Beta-1,4-galactosyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5958
Polymers58,4332
Non-polymers1,1626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area4350 Å2
ΔGint-34 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.122, 121.532, 97.137
Angle α, β, γ (deg.)90.00, 95.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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.: 4
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
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tri.HCl, pH 8.5, 8% PEG 8000 as precipitating 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 27, 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: 2.3→50 Å / Num. all: 66815 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rsym value: 0.091 / Net I/σ(I): 13.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 5725 / Rsym value: 0.523 / % possible all: 83.3

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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: 2.3→37.847 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 3400 5.11 %Random
Rwork0.1846 ---
obs0.1873 66540 96.6 %-
all-66815 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→37.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8059 0 136 289 8484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088504
X-RAY DIFFRACTIONf_angle_d1.2311534
X-RAY DIFFRACTIONf_dihedral_angle_d15.4043158
X-RAY DIFFRACTIONf_chiral_restr0.0831175
X-RAY DIFFRACTIONf_plane_restr0.0041480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33290.35851380.28232180X-RAY DIFFRACTION81
2.3329-2.36770.2921390.27212300X-RAY DIFFRACTION85
2.3677-2.40470.31731440.25712327X-RAY DIFFRACTION86
2.4047-2.44410.31021370.24982388X-RAY DIFFRACTION90
2.4441-2.48620.24891370.24082500X-RAY DIFFRACTION92
2.4862-2.53140.31641330.24742521X-RAY DIFFRACTION94
2.5314-2.58010.3331210.23792662X-RAY DIFFRACTION96
2.5801-2.63270.31411420.23652661X-RAY DIFFRACTION98
2.6327-2.690.27921460.23072701X-RAY DIFFRACTION99
2.69-2.75250.31821610.21932665X-RAY DIFFRACTION100
2.7525-2.82140.2821490.21972724X-RAY DIFFRACTION100
2.8214-2.89760.31731290.22282733X-RAY DIFFRACTION100
2.8976-2.98280.29291480.22282707X-RAY DIFFRACTION100
2.9828-3.07910.31081330.21282732X-RAY DIFFRACTION100
3.0791-3.18910.26721510.2082719X-RAY DIFFRACTION100
3.1891-3.31670.20911480.19872713X-RAY DIFFRACTION100
3.3167-3.46750.22961470.19382713X-RAY DIFFRACTION100
3.4675-3.65020.21831390.18142711X-RAY DIFFRACTION100
3.6502-3.87870.22381390.16232739X-RAY DIFFRACTION100
3.8787-4.17780.20641400.15982725X-RAY DIFFRACTION100
4.1778-4.59760.1841500.13322730X-RAY DIFFRACTION100
4.5976-5.26140.1871420.13892745X-RAY DIFFRACTION100
5.2614-6.6230.21161410.16452758X-RAY DIFFRACTION100
6.623-37.85160.17411460.14482786X-RAY DIFFRACTION100

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