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- PDB-5fjs: Bacterial beta-glucosidase reveals the structural and functional ... -

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Basic information

Entry
Database: PDB / ID: 5fjs
TitleBacterial beta-glucosidase reveals the structural and functional basis of genetic defects in human glucocerebrosidase 2 (GBA2)
ComponentsGLUCOSYLCERAMIDASE
KeywordsHYDROLASE / BILE ACID BETA-GLUCOSIDASE / GLUCOSYLCERAMIDASE / GBA2 / HEREDITARY ATAXIA
Function / homology
Function and homology information


glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / carbohydrate metabolic process / membrane / metal ion binding
Similarity search - Function
Glycosyl-hydrolase family 116, catalytic region / Beta-glucosidase GBA2-type / Glycosyl-hydrolase family 116, N-terminal / : / Glycosyl-hydrolase family 116, catalytic region / beta-glucosidase 2, glycosyl-hydrolase family 116 N-term / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological speciesTHERMOANAEROBACTERIUM XYLANOLYTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCharoenwattanasatien, R. / Pengthaisong, S. / Breen, I. / Mutoha, R. / Sansenya, S. / Hua, Y. / Tankrathok, A. / Wu, L. / Songsiriritthigul, C. / Tanaka, H. ...Charoenwattanasatien, R. / Pengthaisong, S. / Breen, I. / Mutoha, R. / Sansenya, S. / Hua, Y. / Tankrathok, A. / Wu, L. / Songsiriritthigul, C. / Tanaka, H. / Williams, S.J. / Davies, G.J. / Kurisu, G. / Ketudat Cairns, J.R.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Bacterial Beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (Gba2)
Authors: Charoenwattanasatien, R. / Pengthaisong, S. / Breen, I. / Mutoha, R. / Sansenya, S. / Hua, Y. / Tankrathok, A. / Wu, L. / Songsiriritthigul, C. / Tanaka, H. / Williams, S.J. / Davies, G.J. / ...Authors: Charoenwattanasatien, R. / Pengthaisong, S. / Breen, I. / Mutoha, R. / Sansenya, S. / Hua, Y. / Tankrathok, A. / Wu, L. / Songsiriritthigul, C. / Tanaka, H. / Williams, S.J. / Davies, G.J. / Kurisu, G. / Ketudat Cairns, J.R.
History
DepositionOct 12, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOSYLCERAMIDASE
B: GLUCOSYLCERAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,8134
Polymers180,7332
Non-polymers802
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.974, 187.974, 99.075
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein GLUCOSYLCERAMIDASE / BETA-GLUCOSIDASE


Mass: 90366.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOANAEROBACTERIUM XYLANOLYTICUM (bacteria)
Strain: LX-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F6BL85, beta-glucosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN TERMINAL SIGNAL SEQUENCE NOT INCLUDED IN CONSTRUCT

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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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PROPANE, PH 8, 15 % W/V PEG 6000.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Apr 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.6→45.1 Å / Num. obs: 61406 / % possible obs: 100 % / Observed criterion σ(I): 1.7 / Redundancy: 10.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.9
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.32 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5BVU

5bvu


Resolution: 2.6→162.61 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.877 / SU B: 10.974 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.491 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 21-34, 114-125, 804-806 DISORDERED FOR BOTH CHAINS A AND B. IN CHAIN A RESIDUES 134, 201-205, 223- - ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 21-34, 114-125, 804-806 DISORDERED FOR BOTH CHAINS A AND B. IN CHAIN A RESIDUES 134, 201-205, 223- -227, 240-242, 254, 297-302, 329, 428-431 ARE DISORDERED. IN CHAIN B RESIDUES 132-135, 166-169, 201-209, 222-228, 234-242, 248-249, 257-260, 275-279, 286-287, 294, 300-302, , 309, 314, 429-432 ARE DISORDERED. THERE IS UNMODELLED DENSITY BETWEEN RESIDUES 114-125, 200-206, 234-240 FOR CHAINS A AND B, BETWEEN RESIDUES 299-302 IN CHAIN A AND BETWEEN RESIDUES 132-135, 166-169 IN CHAIN B.
RfactorNum. reflection% reflectionSelection details
Rfree0.26649 3081 5 %RANDOM
Rwork0.20559 ---
obs0.20862 58306 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.022 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.27 Å20 Å2
2---0.54 Å20 Å2
3---1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.6→162.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11055 0 2 78 11135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211389
X-RAY DIFFRACTIONr_bond_other_d0.0020.029892
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.92615483
X-RAY DIFFRACTIONr_angle_other_deg1.021322658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05451414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92924.716511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.838151655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.161522
X-RAY DIFFRACTIONr_chiral_restr0.0920.21594
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213164
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022752
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4766.1215715
X-RAY DIFFRACTIONr_mcbond_other4.4756.1215714
X-RAY DIFFRACTIONr_mcangle_it6.5949.1627099
X-RAY DIFFRACTIONr_mcangle_other6.5939.1637100
X-RAY DIFFRACTIONr_scbond_it4.2086.0435674
X-RAY DIFFRACTIONr_scbond_other4.2086.0445675
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2359.0128382
X-RAY DIFFRACTIONr_long_range_B_refined8.3648.2713275
X-RAY DIFFRACTIONr_long_range_B_other8.35448.27613272
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 211 -
Rwork0.289 4284 -
obs--99.93 %

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