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- PDB-4c1o: Geobacillus thermoglucosidasius GH family 52 xylosidase -

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Basic information

Entry
Database: PDB / ID: 4c1o
TitleGeobacillus thermoglucosidasius GH family 52 xylosidase
ComponentsBETA-XYLOSIDASEXylan 1,4-b-xylosidase
KeywordsHYDROLASE / GH52
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / organic substance catabolic process / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 52 / Glycosyl hydrolase family 52 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Beta-xylosidase
Similarity search - Component
Biological speciesGeobacillus thermoglucosidasius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsEspina, G. / Eley, K. / Schneider, T.R. / Crennell, S.J. / Danson, M.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: A Novel Beta-Xylosidase Structure from Geobacillus Thermoglucosidasius: The First Crystal Structure of a Glycoside Hydrolase Family Gh52 Enzyme Reveals Unpredicted Similarity to Other Glycoside Hydrolase Folds
Authors: Espina, G. / Eley, K. / Pompidor, G. / Schneider, T.R. / Crennell, S.J. / Danson, M.J.
History
DepositionAug 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Data collection
Revision 1.3Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _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_atom_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_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-XYLOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,16434
Polymers82,2001
Non-polymers2,96433
Water11,476637
1
A: BETA-XYLOSIDASE
hetero molecules

A: BETA-XYLOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,32768
Polymers164,3992
Non-polymers5,92866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area18590 Å2
ΔGint-91.9 kcal/mol
Surface area46310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.557, 105.143, 195.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2326-

HOH

21A-2535-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BETA-XYLOSIDASE / Xylan 1,4-b-xylosidase


Mass: 82199.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermoglucosidasius (bacteria)
Strain: TM242 / Description: TMO RENEWABLES / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A067XG64*PLUS, xylan 1,4-beta-xylosidase

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Non-polymers , 7 types, 670 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsGLYCEROL (GOL): CRYOPROTECTANT
Sequence detailsTM242 IS A PROPRIETARY STRAIN BELONGING TO TMO RENEWABLES. OTHER G. THERMOGLUCOSIDASIUS XYLOSIDASE ...TM242 IS A PROPRIETARY STRAIN BELONGING TO TMO RENEWABLES. OTHER G. THERMOGLUCOSIDASIUS XYLOSIDASE SEQUENCES IN THE DATABASES WILL BE SIMILAR

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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: 2.37 Å3/Da / Density % sol: 48.15 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 10MG/ML BETA-XYLOSIDASE IN 50MM TRIS-HCL PH8, 150MM NACL, MIXED EQUIVOLUME WITH 0.1M MES PH6, 0.4M AMMONIUM SULPHATE AND 25% PEG3350. CRYSTALS WERE GROWN BY THE HANGING DROP VAPOUR DIFFUSION METHOD., pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→195 Å / Num. obs: 83431 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 21.18 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.6
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.7→97.782 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 17.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.173 4165 5 %
Rwork0.1404 --
obs0.142 83366 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.42 Å2
Refinement stepCycle: LAST / Resolution: 1.7→97.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5604 0 188 637 6429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016211
X-RAY DIFFRACTIONf_angle_d1.2618423
X-RAY DIFFRACTIONf_dihedral_angle_d13.9162302
X-RAY DIFFRACTIONf_chiral_restr0.078855
X-RAY DIFFRACTIONf_plane_restr0.0071095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.22591190.222612X-RAY DIFFRACTION100
1.7193-1.73960.2431300.20982625X-RAY DIFFRACTION100
1.7396-1.76080.24251490.19862591X-RAY DIFFRACTION100
1.7608-1.78310.1921400.18962650X-RAY DIFFRACTION100
1.7831-1.80650.24571450.18492555X-RAY DIFFRACTION100
1.8065-1.83130.22041200.18272682X-RAY DIFFRACTION100
1.8313-1.85750.18841400.17542556X-RAY DIFFRACTION100
1.8575-1.88520.20651240.16492711X-RAY DIFFRACTION100
1.8852-1.91460.21661420.16122560X-RAY DIFFRACTION100
1.9146-1.9460.17961260.15662671X-RAY DIFFRACTION100
1.946-1.97960.19711230.15942600X-RAY DIFFRACTION100
1.9796-2.01560.20041310.15612640X-RAY DIFFRACTION100
2.0156-2.05440.20641220.1542649X-RAY DIFFRACTION100
2.0544-2.09630.19151460.14562606X-RAY DIFFRACTION100
2.0963-2.14190.18421490.14572642X-RAY DIFFRACTION100
2.1419-2.19170.161350.14692622X-RAY DIFFRACTION100
2.1917-2.24650.1851160.14092641X-RAY DIFFRACTION100
2.2465-2.30730.17611320.13762659X-RAY DIFFRACTION100
2.3073-2.37520.17911480.13352624X-RAY DIFFRACTION100
2.3752-2.45180.16911490.13172626X-RAY DIFFRACTION100
2.4518-2.53950.19691390.13332641X-RAY DIFFRACTION100
2.5395-2.64120.18581390.13472616X-RAY DIFFRACTION100
2.6412-2.76140.17411580.1372628X-RAY DIFFRACTION100
2.7614-2.9070.17511290.12862683X-RAY DIFFRACTION100
2.907-3.08910.13991430.13092641X-RAY DIFFRACTION100
3.0891-3.32760.17281520.12822647X-RAY DIFFRACTION100
3.3276-3.66250.13061490.1222659X-RAY DIFFRACTION100
3.6625-4.19250.14051610.11052666X-RAY DIFFRACTION100
4.1925-5.28210.1381580.1182707X-RAY DIFFRACTION100
5.2821-97.94460.21671510.17682791X-RAY DIFFRACTION99

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