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- PDB-4c1p: Geobacillus thermoglucosidasius GH family 52 xylosidase -

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Basic information

Entry
Database: PDB / ID: 4c1p
TitleGeobacillus thermoglucosidasius GH family 52 xylosidase
ComponentsBETA-XYLOSIDASE
KeywordsHYDROLASE / GH52 / XYLOBIOSE
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / 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
4beta-beta-xylobiose / DI(HYDROXYETHYL)ETHER / Beta-xylosidase
Similarity search - Component
Biological speciesGEOBACILLUS THERMOGLUCOSIDASIUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.634 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 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-XYLOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6114
Polymers82,2001
Non-polymers4113
Water5,513306
1
A: BETA-XYLOSIDASE
hetero molecules

A: BETA-XYLOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,2228
Polymers164,3992
Non-polymers8236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area7090 Å2
ΔGint-62.8 kcal/mol
Surface area44780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.369, 105.335, 194.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BETA-XYLOSIDASE


Mass: 82199.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CONTAINS XYLOBIOSE, ENZYME SUBSTRATE
Source: (gene. exp.) GEOBACILLUS THERMOGLUCOSIDASIUS (bacteria)
Strain: TM242 / Description: TMO RENEWABLES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A067XG64*PLUS, xylan 1,4-beta-xylosidase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 282.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylobiose
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBETA-D-XYLOBIOPYRANOSE (BXP): THIS CONTAINS THE COMPLETE BXP INCLUDING O1A
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: STRUCTURE SOLVED BY RIGID BODY REFINEMENT OF NATIVE STRUCTURE INTO THESE DATA
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 10MG/ML BETA-XYLOSIDASE IN 50MM TRIS-HCL PH8, 150MM NACL, 100MM XYLOSE WAS MIXED EQUIVOLUME WITH 0.1M MES PH6, 0.4M AMMONIUM SULPHATE, 25% 3350. CRYSTALS WERE GROWN BY THE HANGING DROP ...Details: 10MG/ML BETA-XYLOSIDASE IN 50MM TRIS-HCL PH8, 150MM NACL, 100MM XYLOSE WAS MIXED EQUIVOLUME WITH 0.1M MES PH6, 0.4M AMMONIUM SULPHATE, 25% 3350. CRYSTALS WERE GROWN BY THE HANGING DROP VAPOUR DIFFUSION METHOD., pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 22164 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 24.13 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.62
Reflection shellResolution: 2.64→2.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.73 / % possible all: 78

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE STRUCTURE

Resolution: 2.634→27.311 Å / SU ML: 0.32 / σ(F): 1.35 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 1169 5.3 %
Rwork0.1823 --
obs0.1852 22136 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.92 Å2
Refinement stepCycle: LAST / Resolution: 2.634→27.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5613 0 27 306 5946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035871
X-RAY DIFFRACTIONf_angle_d0.8057986
X-RAY DIFFRACTIONf_dihedral_angle_d14.4612147
X-RAY DIFFRACTIONf_chiral_restr0.047840
X-RAY DIFFRACTIONf_plane_restr0.0031036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6338-2.75350.3441370.25522273X-RAY DIFFRACTION87
2.7535-2.89860.29171210.22792585X-RAY DIFFRACTION96
2.8986-3.07990.30171400.21722620X-RAY DIFFRACTION98
3.0799-3.31740.24161450.19472657X-RAY DIFFRACTION100
3.3174-3.65050.22421520.18982645X-RAY DIFFRACTION99
3.6505-4.17710.22961600.1742670X-RAY DIFFRACTION100
4.1771-5.25660.2041630.13622714X-RAY DIFFRACTION100
5.2566-27.31250.19081510.15562803X-RAY DIFFRACTION99

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