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- PDB-5a8n: Crystal structure of the native form of beta-glucanase SdGluc5_26... -

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Basic information

Entry
Database: PDB / ID: 5a8n
TitleCrystal structure of the native form of beta-glucanase SdGluc5_26A from Saccharophagus degradans
ComponentsPUTATIVE RETAINING B-GLYCOSIDASE
KeywordsHYDROLASE / CAZYME / GLYCOSIDE HYDROLASE / SACCHAROPHAGUS DEGRADANS / BETA- GLUCANASE / GH5_26
Function / homology
Function and homology information


glucan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Putative retaining b-glycosidase
Similarity search - Component
Biological speciesSACCHAROPHAGUS DEGRADANS 2-40 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSulzenbacher, G. / Lafond, M. / Freyd, T. / Henrissat, B. / Coutinho, R.M. / Berrin, J.G. / Garron, M.L.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Quaternary Structure of a Glycoside Hydrolase Dictates Specificity Towards Beta-Glucans
Authors: Lafond, M. / Sulzenbacher, G. / Freyd, T. / Henrissat, B. / Berrin, J.G. / Garron, M.L.
History
DepositionJul 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Jan 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" 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: PUTATIVE RETAINING B-GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,22312
Polymers42,0971
Non-polymers1,12611
Water5,495305
1
A: PUTATIVE RETAINING B-GLYCOSIDASE
hetero molecules

A: PUTATIVE RETAINING B-GLYCOSIDASE
hetero molecules

A: PUTATIVE RETAINING B-GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,66936
Polymers126,2903
Non-polymers3,37933
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
MethodPISA
Unit cell
Length a, b, c (Å)143.341, 143.341, 143.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-2074-

HOH

21A-2076-

HOH

31A-2302-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PUTATIVE RETAINING B-GLYCOSIDASE / SDGLUC5_26A


Mass: 42096.664 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROPHAGUS DEGRADANS 2-40 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q21KE5, licheninase

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Non-polymers , 6 types, 316 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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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: 3.13 Å3/Da / Density % sol: 60.7 % / Description: NONE
Crystal growpH: 6
Details: 0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM CACODYLATE BUFFER PH 6.0, 25% (W/V) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9537
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.05→32.8 Å / Num. obs: 32184 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 29.48 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.4
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WWPDB ENTRY 5A8M

5a8m


Resolution: 2.05→32.91 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.454 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.17997 1628 5.1 %RANDOM
Rwork0.15113 ---
obs0.15259 30488 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.695 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→32.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 40 305 3120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022921
X-RAY DIFFRACTIONr_bond_other_d0.0030.022698
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9343973
X-RAY DIFFRACTIONr_angle_other_deg0.75536223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0145341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90924.155142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94115469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8491513
X-RAY DIFFRACTIONr_chiral_restr0.0780.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02707
X-RAY DIFFRACTIONr_nbd_refined0.2480.2893
X-RAY DIFFRACTIONr_nbd_other0.1730.22519
X-RAY DIFFRACTIONr_nbtor_refined0.190.21432
X-RAY DIFFRACTIONr_nbtor_other0.0840.21450
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.237
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1460.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 111 -
Rwork0.237 2203 -
obs--100 %
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)
11.75143.03153.00838.28278.41398.5570.1265-0.06620.03140.4699-0.13860.01450.4847-0.13270.01210.034-0.00260.00350.0301-0.00810.011951.271326.287189.2606
20.25930.0642-0.20980.29880.03360.2484-0.03830.0731-0.0321-0.02890.00760.01190.0125-0.05920.03070.0115-0.00620.00030.0315-0.01730.010724.841418.67288.2625
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 47
2X-RAY DIFFRACTION2A48 - 364

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