[English] 日本語
Yorodumi
- PDB-4cce: STRUCTURE OF MOUSE GALACTOCEREBROSIDASE WITH GALACTOSE: ENZYME- P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cce
TitleSTRUCTURE OF MOUSE GALACTOCEREBROSIDASE WITH GALACTOSE: ENZYME- PRODUCT COMPLEX
ComponentsGALACTOCEREBROSIDASEGalactosylceramidase
KeywordsHYDROLASE / KRABBE DISEASE / GLYCOSYL HYDROLASE / LYSOSOMAL STORAGE DISEASE / ENZYME-PRODUCT COMPLEX
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
beta-D-galactopyranose / Galactocerebrosidase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsHill, C.H. / Graham, S.C. / Read, R.J. / Deane, J.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural Snapshots Illustrate the Catalytic Cycle of Beta-Galactocerebrosidase, the Defective Enzyme in Krabbe Disease
Authors: Hill, C.H. / Graham, S.C. / Read, R.J. / Deane, J.E.
History
DepositionOct 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_validate_close_contact / 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.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.ptnr2_label_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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.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
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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GALACTOCEREBROSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3117
Polymers74,5971
Non-polymers1,7156
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)248.754, 248.754, 77.632
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

-
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 / BETA-GALACTOCEREBROSIDASE / GALC


Mass: 74596.750 Da / Num. of mol.: 1 / Fragment: RESIDUES 41-684
Source method: isolated from a genetically manipulated source
Details: FRAGMENT CORRESPONDS TO RESIDUES 25-668 BASED ON NUMBERING STARTING AT SECOND UNIPROT INITIATION SITE.
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PSECTAG2B / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P54818, galactosylceramidase

-
Sugars , 3 types, 5 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
#3: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / 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
#4: 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

-
Non-polymers , 2 types, 207 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsBETA-D-GALACTOSE (GAL): A RESTRAINT FILE FOR REFINEMENT WAS GENERATED USING ELBOW WITH A SMILES ...BETA-D-GALACTOSE (GAL): A RESTRAINT FILE FOR REFINEMENT WAS GENERATED USING ELBOW WITH A SMILES STRING. AFTER REFINEMENT, LIGAND ATOMS WERE RENUMBERED TO BE CONSISTENT WITH OTHER STRUCTURES DEPOSITED FOR THIS PUBLICATION. N-ACETYL-D-GLUCOSAMINE (NAG): N-LINKED GLYCOSYLATION SITES
Sequence detailsFRAGMENT CORRESPONDS TO RESIDUES 25-668 BASED ON NUMBERING STARTING AT SECOND UNIPROT INITIATION SITE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.5 % / Description: NONE
Crystal growpH: 6.8
Details: 34% PEG 8000, 200 MM SODIUM ACETATE, 100 MM SODIUM CACODYLATE PH 6.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 3, 2012
Details: SI (111) DOUBLE CRYSTAL MONOCHROMATOR. KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.06→47.01 Å / Num. obs: 56396 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 29.77 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.9
Reflection shellResolution: 2.06→2.12 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 2.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZR5 (WITH SOLVENT REMOVED)

3zr5


Resolution: 2.06→44.251 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 19.97 / Stereochemistry target values: ML / Details: RESIDUES 416-419 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.206 2857 5.1 %
Rwork0.1715 --
obs0.1732 56378 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→44.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5119 0 111 206 5436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075400
X-RAY DIFFRACTIONf_angle_d1.0667371
X-RAY DIFFRACTIONf_dihedral_angle_d15.8951878
X-RAY DIFFRACTIONf_chiral_restr0.072792
X-RAY DIFFRACTIONf_plane_restr0.004921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0601-2.09570.27961330.26122673X-RAY DIFFRACTION100
2.0957-2.13380.29711350.25592656X-RAY DIFFRACTION100
2.1338-2.17480.27351230.23952685X-RAY DIFFRACTION100
2.1748-2.21920.2871310.23272685X-RAY DIFFRACTION100
2.2192-2.26740.27961580.22862648X-RAY DIFFRACTION100
2.2674-2.32020.25091360.23762646X-RAY DIFFRACTION100
2.3202-2.37820.27361500.21142655X-RAY DIFFRACTION100
2.3782-2.44250.25461730.19932647X-RAY DIFFRACTION100
2.4425-2.51440.24461500.18172670X-RAY DIFFRACTION100
2.5144-2.59550.19041420.18142680X-RAY DIFFRACTION100
2.5955-2.68830.18971520.16442656X-RAY DIFFRACTION100
2.6883-2.79590.22221500.17252660X-RAY DIFFRACTION100
2.7959-2.92310.21241390.17682681X-RAY DIFFRACTION100
2.9231-3.07720.19631260.17422677X-RAY DIFFRACTION100
3.0772-3.26990.23411490.18392677X-RAY DIFFRACTION100
3.2699-3.52230.21951350.16992703X-RAY DIFFRACTION100
3.5223-3.87660.18341460.15022674X-RAY DIFFRACTION100
3.8766-4.43710.1521430.12982701X-RAY DIFFRACTION100
4.4371-5.58850.1481360.12742713X-RAY DIFFRACTION100
5.5885-44.26110.18491500.16062734X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2007-0.10710.34691.1929-0.34380.70730.0475-0.1539-0.04950.27270.0253-0.1760.05970.4694-0.07650.2715-0.0653-0.0940.5912-0.01270.266982.677177.425343.6481
20.54350.2889-0.0960.1483-0.05790.29820.0230.05650.1068-0.00550.0122-0.1539-0.05440.11260.01340.3575-0.3617-0.00860.70230.01510.565698.1035104.664827.1743
30.6347-0.03090.03290.48910.01850.59320.05150.05530.027-0.0368-0.0272-0.0717-0.44680.40630.00650.3093-0.2739-0.0060.4796-0.00110.260574.536699.018222.3282
41.13030.1186-0.17770.70870.17960.67320.06830.25430.2842-0.2391-0.0557-0.3237-0.24390.3393-0.00380.7023-0.64860.25260.90810.21920.45489.8792109.8021.4846
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))

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more