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- PDB-5a8m: Crystal structure of the selenomethionine derivative of beta-gluc... -

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Basic information

Entry
Database: PDB / ID: 5a8m
TitleCrystal structure of the selenomethionine derivative of beta-glucanase SdGluc5_26A from Saccharophagus degradans
ComponentsPUTATIVE RETAINING B-GLYCOSIDASE
KeywordsHYDROLASE / CAZYME / GLYCOSIDE HYDROLASE / 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 / SAD / Resolution: 1.86 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 / Structure summary / Category: diffrn_detector / struct / Item: _diffrn_detector.type / _struct.title
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" 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. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CB" 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
B: PUTATIVE RETAINING B-GLYCOSIDASE
C: PUTATIVE RETAINING B-GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,90347
Polymers127,2753
Non-polymers4,62944
Water22,0321223
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13030 Å2
ΔGint-122.1 kcal/mol
Surface area39120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.605, 142.605, 136.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA29 - 36329 - 363
21ASNASNBB29 - 36329 - 363
12SERSERAA28 - 36428 - 364
22SERSERCC28 - 36428 - 364
13ASNASNBB29 - 36329 - 363
23ASNASNCC29 - 36329 - 363

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.01813, 0.002405, 0.9998), (-0.9998, 0.01253, -0.01816), (-0.01257, -0.9999, 0.002177)56.92, 107.3, 52.84
2given(-0.03568, -0.9985, -0.04077), (-0.008928, 0.04111, -0.9991), (0.9993, -0.03529, -0.01038)110.5, 50.72, -53.94

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein PUTATIVE RETAINING B-GLYCOSIDASE / SDGLUC5_26A


Mass: 42424.930 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-365 / 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, 1267 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical...
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1223 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.2 % / Description: NONE
Crystal growpH: 6.5
Details: 25% (W/V) PEG3350, 0.2 M MGCL2, 0.1 M BIS-TRIS BUFFER PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.86→47.53 Å / Num. obs: 116426 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.5
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.5 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.86→47.33 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.598 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.16513 5841 5 %RANDOM
Rwork0.14336 ---
obs0.14445 110515 99.17 %-
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: 18.061 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.86→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8348 0 157 1223 9728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028953
X-RAY DIFFRACTIONr_bond_other_d0.0050.028300
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.94312192
X-RAY DIFFRACTIONr_angle_other_deg1.043319191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05751072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95624.243436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.397151403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2361540
X-RAY DIFFRACTIONr_chiral_restr0.0890.21251
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110029
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022159
X-RAY DIFFRACTIONr_nbd_refined0.2640.23166
X-RAY DIFFRACTIONr_nbd_other0.1760.27627
X-RAY DIFFRACTIONr_nbtor_refined0.1870.24397
X-RAY DIFFRACTIONr_nbtor_other0.0850.24252
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2250
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.060.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3190.281
X-RAY DIFFRACTIONr_symmetry_vdw_other0.180.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2990.215
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A220040.06
12B220040.06
21A221220.07
22C221220.07
31B217990.06
32C217990.06
LS refinement shellResolution: 1.862→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 420 -
Rwork0.183 8004 -
obs--98.37 %
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)
10.21410.09840.01860.33810.08070.28210.0054-0.02340.0010.0294-0.03070.0039-0.0029-0.01370.02530.0132-0.00410.00090.0266-0.00660.003851.586346.954632.5432
20.3329-0.0665-0.08420.22030.14670.38910.0215-0.01260.0206-0.02510.0205-0.0258-0.02790.0372-0.04210.0173-0.01290.01360.0116-0.01150.01288.695455.77095.3209
30.32780.0369-0.12210.3204-0.030.2406-0.01720.0045-0.033-0.00910.02030.00260.0086-0.0105-0.00320.0161-0.00220.00410.0107-0.0020.005760.375619.6666-4.3623
44.2404-1.4366-3.91181.02451.21633.666-0.099-0.1922-0.01660.02510.0653-0.00480.12790.1670.03360.0346-0.00730.01170.0147-0.00050.009253.212420.5424.134
52.21652.6725-0.77733.5869-1.10140.5343-0.00470.0196-0.23210.0837-0.0028-0.2548-0.048-0.02660.00760.0366-0.01170.00640.0617-0.01030.052180.28154.184131.4218
60.88221.41271.72912.93743.60844.4806-0.00080.01820.00340.20120.01910.02340.25080.0689-0.01830.06280.00570.01130.0421-0.02930.046987.07527.109-1.6141
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 364
2X-RAY DIFFRACTION2B48 - 365
3X-RAY DIFFRACTION3C48 - 364
4X-RAY DIFFRACTION4A28 - 47
5X-RAY DIFFRACTION5B29 - 47
6X-RAY DIFFRACTION6C28 - 47

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