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- PDB-4ufh: Mouse Galactocerebrosidase complexed with iso-galacto-fagomine IGF -

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Basic information

Entry
Database: PDB / ID: 4ufh
TitleMouse Galactocerebrosidase complexed with iso-galacto-fagomine IGF
ComponentsGALACTOCEREBROSIDASEGalactosylceramidase
KeywordsHYDROLASE / GLYCOSYL HYDROLASE / COMPLEX / LYSOSOME
Function / homology
Function and homology information


Glycosphingolipid catabolism / galactosylceramide catabolic process / galactosylceramidase / galactosylceramidase activity / myelination / lysosome / mitochondrion
Similarity search - Function
Glycosyl hydrolase family 59, central domain / : / : / Glycosyl hydrolase family 59 central domain / Galactocerebrosidase, C-terminal lectin domain / Glycoside hydrolase, family 59 / Glycosyl hydrolase family 59 / Exo-inulinase; domain 1 / Glycosidases / Aldolase class I ...Glycosyl hydrolase family 59, central domain / : / : / Glycosyl hydrolase family 59 central domain / Galactocerebrosidase, C-terminal lectin domain / Glycoside hydrolase, family 59 / Glycosyl hydrolase family 59 / Exo-inulinase; domain 1 / Glycosidases / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
D-galacto-isofagomine / NICKEL (II) ION / Galactocerebrosidase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsHill, C.H. / Viuff, A.H. / Spratley, S.J. / Salamone, S. / Christensen, S.H. / Read, R.J. / Moriarty, N.W. / Jensen, H.H. / Deane, J.E.
CitationJournal: Chem.Sci. / Year: 2015
Title: Azasugar Inhibitors as Pharmacological Chaperones for Krabbe Disease.
Authors: Hill, C.H. / Viuff, A.H. / Spratley, S.J. / Salamone, S. / Christensen, S.H. / Read, R.J. / Moriarty, N.W. / Jensen, H.H. / Deane, J.E.
History
DepositionMar 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Atomic model / Database references ...Atomic model / Database references / Other / Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GALACTOCEREBROSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,59010
Polymers74,5971
Non-polymers1,9939
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)247.215, 247.215, 77.252
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1004-

NI

21A-2058-

HOH

31A-2104-

HOH

41A-2116-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GALACTOCEREBROSIDASE / Galactosylceramidase / GALCERASE / GALACTOCEREBROSIDE BETA-GALACTOSIDASE / GALACTOSYLCERAMIDASE / GALACTOSYLCERAMIDE BETA- ...GALCERASE / GALACTOCEREBROSIDE BETA-GALACTOSIDASE / GALACTOSYLCERAMIDASE / GALACTOSYLCERAMIDE BETA-GALACTOSIDASE


Mass: 74596.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH IGF / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P54818, galactosylceramidase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 219 molecules

#3: Chemical ChemComp-GIF / D-galacto-isofagomine


Mass: 147.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO3
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsNUMBERING IS FROM SECOND START SITE AS USED IN THE LITERATURE AND IN PDB ENTRIES 3ZR5, 3ZR6, 4CCC, 4CCD, 4CCE.

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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: 3.05 Å3/Da / Density % sol: 59.61 % / Description: NONE
Crystal growpH: 6.8
Details: 0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE (PH 6.8), 34% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.16→47.1 Å / Num. obs: 47992 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 15.1 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 12.3
Reflection shellResolution: 2.16→2.23 Å / Redundancy: 14.6 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZR5
Resolution: 2.16→47.079 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2155 2466 5.1 %
Rwork0.1904 --
obs0.1917 47992 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→47.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5142 0 124 214 5480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045535
X-RAY DIFFRACTIONf_angle_d0.7747559
X-RAY DIFFRACTIONf_dihedral_angle_d13.1311936
X-RAY DIFFRACTIONf_chiral_restr0.032804
X-RAY DIFFRACTIONf_plane_restr0.003957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.20160.32371280.29782533X-RAY DIFFRACTION100
2.2016-2.24650.33721400.29062487X-RAY DIFFRACTION100
2.2465-2.29540.29311400.28472547X-RAY DIFFRACTION100
2.2954-2.34880.29351450.26842517X-RAY DIFFRACTION100
2.3488-2.40750.28521440.25752522X-RAY DIFFRACTION100
2.4075-2.47260.26911590.23632496X-RAY DIFFRACTION100
2.4726-2.54530.25881350.23612513X-RAY DIFFRACTION100
2.5453-2.62750.28041360.22652543X-RAY DIFFRACTION100
2.6275-2.72140.24381430.2212468X-RAY DIFFRACTION98
2.7214-2.83030.25181380.21372486X-RAY DIFFRACTION99
2.8303-2.95910.22141320.21022548X-RAY DIFFRACTION100
2.9591-3.11510.21481150.20832543X-RAY DIFFRACTION100
3.1151-3.31020.23911400.19262542X-RAY DIFFRACTION100
3.3102-3.56570.1711160.17452556X-RAY DIFFRACTION100
3.5657-3.92440.18741520.15652537X-RAY DIFFRACTION100
3.9244-4.49190.15111300.1412497X-RAY DIFFRACTION98
4.4919-5.65780.15461310.14242579X-RAY DIFFRACTION100
5.6578-47.08990.21251420.17012612X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.0808-0.12531.46162.463-0.49661.30950.0667-0.0763-0.0370.33770.0126-0.19610.11330.6701-0.07190.3447-0.0558-0.08530.6839-0.01130.265482.235976.892143.7951
20.47880.5317-0.16590.5762-0.20020.1652-0.0584-0.01470.15690.0961-0.0654-0.3547-0.07840.2050.14940.5252-0.5233-0.0471.0599-0.03840.628197.6094104.12126.984
31.03210.11540.12270.80940.15830.5996-0.02010.03320.10180.00650.0291-0.114-0.48590.4967-0.01170.3854-0.2956-0.02310.54980.01110.28973.840398.390922.2879
41.72890.2544-0.41840.57020.15320.50480.10550.32070.4484-0.4005-0.0649-0.5213-0.35720.6094-0.01790.771-0.86360.25611.10360.28430.518689.4076109.38931.2744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND ((RESSEQ 472:668))
2X-RAY DIFFRACTION2CHAIN 'A' AND ((RESSEQ 453:471))
3X-RAY DIFFRACTION3CHAIN 'A' AND ((RESSEQ 41:337))
4X-RAY DIFFRACTION4CHAIN 'A' AND ((RESSEQ 25:40) OR (RESSEQ 338:452))

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