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- PDB-4cce: STRUCTURE OF MOUSE GALACTOCEREBROSIDASE WITH GALACTOSE: ENZYME- P... -

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Basic information

Entry
Database: PDB / ID: 4cce
TitleSTRUCTURE OF MOUSE GALACTOCEREBROSIDASE WITH GALACTOSE: ENZYME- PRODUCT COMPLEX
ComponentsGALACTOCEREBROSIDASE
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 / membrane
Similarity search - Function
Glycosyl hydrolase family 59, central domain / Glycosyl hydrolase family 59 central domain / Glycoside hydrolase, family 59 / : / Galactocerebrosidase, C-terminal lectin domain / : / Glycosyl hydrolase family 59 / Exo-inulinase; domain 1 / Glycosidases / Aldolase class I ...Glycosyl hydrolase family 59, central domain / Glycosyl hydrolase family 59 central domain / Glycoside hydrolase, family 59 / : / Galactocerebrosidase, C-terminal lectin domain / : / 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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)76,3117
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

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GALACTOCEREBROSIDASE / 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

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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


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


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 , 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


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

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Details

Has protein modificationY
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.

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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: 3.19 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

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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

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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))

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