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- PDB-2vrq: STRUCTURE OF AN INACTIVE MUTANT OF ARABINOFURANOSIDASE FROM THERM... -

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Basic information

Entry
Database: PDB / ID: 2vrq
TitleSTRUCTURE OF AN INACTIVE MUTANT OF ARABINOFURANOSIDASE FROM THERMOBACILLUS XYLANILYTICUS IN COMPLEX WITH A PENTASACCHARIDE
ComponentsALPHA-L-ARABINOFURANOSIDASE
KeywordsHYDROLASE / GLYCOSIDASE
Function / homology
Function and homology information


L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / polysaccharide catabolic process
Similarity search - Function
Alpha-L-arabinofuranosidase, C-terminal / Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like ...Alpha-L-arabinofuranosidase, C-terminal / Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / non-reducing end alpha-L-arabinofuranosidase
Similarity search - Component
Biological speciesTHERMOBACILLUS XYLANILYTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPaes, G. / Skov, L.K. / Odonohue, M.J. / Remond, C. / Kastrup, J.S. / Gajhede, M. / Mirza, O.
CitationJournal: Biochemistry / Year: 2008
Title: The Structure of the Complex between a Branched Pentasaccharide and Thermobacillus Xylanilyticus Gh-51 Arabinofuranosidase Reveals Xylan-Binding Determinants and Induced Fit.
Authors: Paes, G. / Skov, L.K. / O'Donohue, M.J. / Remond, C. / Kastrup, J.S. / Gajhede, M. / Mirza, O.
History
DepositionApr 9, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag
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. 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. 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: ALPHA-L-ARABINOFURANOSIDASE
B: ALPHA-L-ARABINOFURANOSIDASE
C: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,2478
Polymers168,5503
Non-polymers1,6975
Water20,8971160
1
A: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8253
Polymers56,1831
Non-polymers6412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7302
Polymers56,1831
Non-polymers5461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6933
Polymers56,1831
Non-polymers5092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.800, 156.800, 378.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.2508, -0.07385, 0.9652), (0.932, -0.2509, -0.2614), (0.2615, 0.9652, 0.005886)-38.89, -93.49, 112.8
2given(0.259, 0.9319, 0.254), (-0.05744, -0.2477, 0.9671), (0.9642, -0.2651, -0.01063)67.57, -135.6, 12.97

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Components

#1: Protein ALPHA-L-ARABINOFURANOSIDASE / ARABINOFURANOSIDASE


Mass: 56183.324 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOBACILLUS XYLANILYTICUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O69262, non-reducing end alpha-L-arabinofuranosidase
#2: Polysaccharide alpha-L-arabinofuranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 546.474 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-3[DXylpb1-4]DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a212h-1b_1-5][a211h-1a_1-4]/1-1-2-1/a4-b1_b3-c1_b4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(3+1)][a-L-Araf]{}[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-arabinofuranose-(1-3)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-3DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a212h-1b_1-5][a211h-1a_1-4]/1-1-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(3+1)][a-L-Araf]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1160 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 176 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 176 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, GLU 176 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 176 TO GLN ENGINEERED RESIDUE IN CHAIN C, GLU 176 TO GLN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.25 % / Description: NONE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.078
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2→78.33 Å / Num. obs: 184568 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XIA-DPAdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→78.4 Å / SU ML: 0.22 / σ(F): 1.48 / Phase error: 16.6 / Stereochemistry target values: ML
Details: THE FIRST 3 RESIDUES WERE NOT MODELED DUE TO POOR DENSITY.
RfactorNum. reflection% reflection
Rfree0.201 1847 1 %
Rwork0.182 --
obs0.182 184417 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.04 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5965 Å20 Å20 Å2
2--1.5965 Å20 Å2
3----3.193 Å2
Refinement stepCycle: LAST / Resolution: 2→78.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11790 0 112 1160 13062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812235
X-RAY DIFFRACTIONf_angle_d1.3216626
X-RAY DIFFRACTIONf_dihedral_angle_d22.6114491
X-RAY DIFFRACTIONf_chiral_restr0.0881719
X-RAY DIFFRACTIONf_plane_restr0.0062145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.27181460.248213781X-RAY DIFFRACTION100
2.0541-2.11450.27721380.234313859X-RAY DIFFRACTION100
2.1145-2.18280.22461410.212513883X-RAY DIFFRACTION100
2.1828-2.26080.19761450.207213854X-RAY DIFFRACTION100
2.2608-2.35130.19921590.193813873X-RAY DIFFRACTION100
2.3513-2.45830.22631260.189713952X-RAY DIFFRACTION100
2.4583-2.5880.20891400.180213941X-RAY DIFFRACTION100
2.588-2.75010.19951420.174613994X-RAY DIFFRACTION100
2.7501-2.96250.16551360.16314019X-RAY DIFFRACTION100
2.9625-3.26060.17671390.158614072X-RAY DIFFRACTION100
3.2606-3.73240.16451370.152614155X-RAY DIFFRACTION100
3.7324-4.70240.16491490.146314281X-RAY DIFFRACTION100
4.7024-78.46030.23321490.20914906X-RAY DIFFRACTION100

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