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- PDB-3zr5: STRUCTURE OF GALACTOCEREBROSIDASE FROM MOUSE -

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Basic information

Entry
Database: PDB / ID: 3zr5
TitleSTRUCTURE OF GALACTOCEREBROSIDASE FROM MOUSE
ComponentsGALACTOCEREBROSIDASEGalactosylceramidase
KeywordsHYDROLASE / GALC / GLYCOSYL HYDROLASE / KRABBE DISEASE / TIM BARREL / LECTIN DOMAIN
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 / Golgi alpha-mannosidase II / Glycosidases ...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 / Golgi alpha-mannosidase II / Glycosidases / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Galactocerebrosidase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.1 Å
AuthorsDeane, J.E. / Graham, S.C. / Kim, N.N. / Stein, P.E. / Mcnair, R. / Cachon-Gonzalez, M.B. / Cox, T.M. / Read, R.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Insights Into Krabbe Disease from Structures of Galactocerebrosidase.
Authors: Deane, J.E. / Graham, S.C. / Kim, N.N. / Stein, P.E. / Mcnair, R. / Cachon-Gonzalez, M.B. / Cox, T.M. / Read, R.J.
History
DepositionJun 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 650 HELIX DETERMINATION METHOD: DSSP OUTPUT MODIFIED BY AUTHOR
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)76,2826
Polymers74,7481
Non-polymers1,5345
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)249.904, 249.904, 77.826
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-832-

HOH

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Components

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


Mass: 74747.906 Da / Num. of mol.: 1 / Fragment: RESIDUES 40-684
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): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P54818, galactosylceramidase
#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-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsN-ACETYL-D-GLUCOSAMINE (NAG): THE LAST 3 NUMBERS MATCH THE ASN RESIDUE THEY ARE LINKED TO. THE ...N-ACETYL-D-GLUCOSAMINE (NAG): THE LAST 3 NUMBERS MATCH THE ASN RESIDUE THEY ARE LINKED TO. THE GLYCANS ARE THEN NUMBERED ACCORDING TO THEIR POSITION DISTANT FROM THE ATTACHED ASN.
Sequence detailsTWO DIFFERENT START SITES ARE PRESENT IN MOUSE GALC, WE HAVE USED THE SECOND START SITE (TO MATCH ...TWO DIFFERENT START SITES ARE PRESENT IN MOUSE GALC, WE HAVE USED THE SECOND START SITE (TO MATCH THE LITERATURE) WHICH IS M17 IN THE UNIPROT ENTRY. THE FULL CONSTRUCT CONTAINS A SECRETION TAG (THAT IS CLEAVED) A HIS TAG AND A FACTOR XA SITE WHICH ARE NOT.

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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: 3.04 Å3/Da / Density % sol: 59.52 % / Description: NONE
Crystal growpH: 6.8
Details: 0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.8, 34% (W/V) POLYETHYLENE GLYCOL 8000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→73.23 Å / Num. obs: 53657 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 27.18 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.1→63.182 Å / SU ML: 0.61 / σ(F): 0.88 / Phase error: 20.44 / Stereochemistry target values: ML
Details: THE NUMBERS OF REFLECTIONS IN THE TWO TABLES ABOVE (FIT TO DATA USED IN REFINEMENT AND FIT TO DATA USED IN REFINEMENT (IN BINS)) ARE FOR THE DATA BEFORE MERGING OF ANOMALOUS PAIRS.
RfactorNum. reflection% reflection
Rfree0.2142 5056 5.1 %
Rwork0.1812 --
obs0.1828 53619 99.45 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.577 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 33.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.9165 Å20 Å20 Å2
2--0.9165 Å20 Å2
3----1.8329 Å2
Refinement stepCycle: LAST / Resolution: 2.1→63.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 99 258 5489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015435
X-RAY DIFFRACTIONf_angle_d1.2457423
X-RAY DIFFRACTIONf_dihedral_angle_d16.8131920
X-RAY DIFFRACTIONf_chiral_restr0.08793
X-RAY DIFFRACTIONf_plane_restr0.006934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.33091840.30112983X-RAY DIFFRACTION90
2.1239-2.14890.30341400.29663064X-RAY DIFFRACTION91
2.1489-2.17510.30031300.27143071X-RAY DIFFRACTION92
2.1751-2.20260.26081330.26933075X-RAY DIFFRACTION92
2.2026-2.23160.28881640.27623140X-RAY DIFFRACTION92
2.2316-2.26220.31211940.26933019X-RAY DIFFRACTION92
2.2622-2.29450.29011650.25623115X-RAY DIFFRACTION92
2.2945-2.32880.26961640.25623068X-RAY DIFFRACTION93
2.3288-2.36510.28721870.25193162X-RAY DIFFRACTION93
2.3651-2.40390.28311780.24443071X-RAY DIFFRACTION93
2.4039-2.44540.27141960.22793089X-RAY DIFFRACTION93
2.4454-2.48980.28151730.22353096X-RAY DIFFRACTION93
2.4898-2.53770.24531770.21963131X-RAY DIFFRACTION94
2.5377-2.58950.26151720.20513153X-RAY DIFFRACTION94
2.5895-2.64580.21671580.19753135X-RAY DIFFRACTION94
2.6458-2.70740.1961850.18483180X-RAY DIFFRACTION95
2.7074-2.77510.22141820.18583179X-RAY DIFFRACTION95
2.7751-2.85010.24951810.18393140X-RAY DIFFRACTION95
2.8501-2.9340.18961510.17223223X-RAY DIFFRACTION95
2.934-3.02870.20161650.17123208X-RAY DIFFRACTION96
3.0287-3.13690.19641490.18563275X-RAY DIFFRACTION96
3.1369-3.26250.22781700.18263207X-RAY DIFFRACTION96
3.2625-3.4110.20071920.17553251X-RAY DIFFRACTION97
3.411-3.59080.2081330.17333249X-RAY DIFFRACTION97
3.5908-3.81580.211790.16373218X-RAY DIFFRACTION96
3.8158-4.11040.19472090.13483217X-RAY DIFFRACTION97
4.1104-4.52390.15171470.12533222X-RAY DIFFRACTION96
4.5239-5.17830.13511670.11573200X-RAY DIFFRACTION96
5.1783-6.5230.16131670.15013134X-RAY DIFFRACTION93
6.523-63.21080.17671640.14543310X-RAY DIFFRACTION98
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)
10.8845-0.0738-0.22840.14390.08740.3140.02920.1410.1817-0.1451-0.0641-0.2201-0.11140.1290.02690.3967-0.19150.08870.41820.07350.287790.3702110.22971.4877
20.42440.02890.05270.3259-0.0230.30480.01630.01690.0323-0.0152-0.0076-0.0521-0.1430.1813-0.00370.1625-0.10710.0090.21910.00680.119174.655999.433922.4809
30.50110.1702-0.04890.09920.06360.16050.00210.05160.05720.0195-0.0588-0.1974-0.08610.1130.08760.2858-0.20110.00560.45710.04710.33998.4339105.155327.2285
41.1741-0.13530.44031.3959-0.29780.90630.0198-0.1171-0.00870.1833-0.0091-0.1591-0.00640.2286-0.0170.1369-0.0311-0.03680.2726-0.0050.113682.760577.835943.6245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 25:40 OR RESSEQ 338:452)
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 41:337
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 453:471
4X-RAY DIFFRACTION4CHAIN A AND RESSEQ 472:668

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