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- PDB-2xvk: crystal structure of alpha-xylosidase (GH31) from Cellvibrio japo... -

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Basic information

Entry
Database: PDB / ID: 2xvk
Titlecrystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus in complex with 5-fluoro-alpha-D-xylopyranosyl fluoride
ComponentsALPHA-XYLOSIDASE, PUTATIVE, XYL31A
KeywordsHYDROLASE / GLYCOSYL HYDROLASE FAMILY 31 / (BETA/ALPHA) 8 BARREL
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Jelly Rolls - #380 / : / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / glycosyl hydrolase (family 31) / PA14/GLEYA domain / PA14 domain profile. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / PA14 ...Jelly Rolls - #380 / : / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / glycosyl hydrolase (family 31) / PA14/GLEYA domain / PA14 domain profile. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / PA14 / PA14 domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
(2R,3S,5R,6S)-2,6-DIFLUOROOXANE-3,4,5-TRIOL / NICKEL (II) ION / Alpha-xylosidase, putative, xyl31A
Similarity search - Component
Biological speciesCELLVIBRIO JAPONICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsLarsbrink, J. / Izumi, A. / Ibatullin, F. / Nakhai, A. / Gilbert, H.J. / Davies, G.J. / Brumer, H.
CitationJournal: Biochem.J. / Year: 2011
Title: Structural and Enzymatic Characterisation of a Glycoside Hydrolase Family 31 Alpha-Xylosidase from Cellvibrio Japonicus Involved in Xyloglucan Saccharification.
Authors: Larsbrink, J. / Izumi, A. / Ibatullin, F. / Nakhai, A. / Gilbert, H.J. / Davies, G.J. / Brumer, H.
History
DepositionOct 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_database_status.status_code_sf ..._chem_comp.type / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _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: ALPHA-XYLOSIDASE, PUTATIVE, XYL31A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,5757
Polymers115,2041
Non-polymers3716
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.524, 156.524, 227.762
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein ALPHA-XYLOSIDASE, PUTATIVE, XYL31A / ALPHA XYLOSIDASE


Mass: 115203.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE OD ATOM OF D582 LINKS TO THE C1 ATOM OF FFX. / Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B3PBD9, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Sugar ChemComp-FFX / (2R,3S,5R,6S)-2,6-DIFLUOROOXANE-3,4,5-TRIOL


Type: D-saccharide / Mass: 170.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8F2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details5-FLUORO-ALPHA-D-XYLOPYRANOSYL FLUORIDE (FFX): THE FLUORIDE ATOM AT C1 OF THIS LIGAND WAS REMOVED ...5-FLUORO-ALPHA-D-XYLOPYRANOSYL FLUORIDE (FFX): THE FLUORIDE ATOM AT C1 OF THIS LIGAND WAS REMOVED BECAUSE OF THE NUCLEOPHILIC ATTACK BY THE ENZYME

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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: 3.5 Å3/Da / Density % sol: 64.81 % / Description: NONE
Crystal growpH: 7
Details: 25 % PEG MONOMETHYL ETHER 550 (PEG MME 550), 0.1 M BIS-TRIS (PH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2009 / Details: MIRRORS
RadiationMonochromator: SI (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 57181 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 8 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G3M

2g3m


Resolution: 2.503→49.985 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 25.51 / Stereochemistry target values: ML
Details: DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY AND HAVE ZERO OCCUPANCIES.
RfactorNum. reflection% reflection
Rfree0.2397 2904 5.1 %
Rwork0.1949 --
obs0.1972 57181 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.99 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.7567 Å20 Å2-0 Å2
2--7.7567 Å20 Å2
3----15.5134 Å2
Refinement stepCycle: LAST / Resolution: 2.503→49.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7572 0 15 83 7670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087796
X-RAY DIFFRACTIONf_angle_d1.110591
X-RAY DIFFRACTIONf_dihedral_angle_d17.3662775
X-RAY DIFFRACTIONf_chiral_restr0.0751099
X-RAY DIFFRACTIONf_plane_restr0.0051389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5025-2.5920.3222870.28325254X-RAY DIFFRACTION99
2.592-2.69580.31982850.26975351X-RAY DIFFRACTION100
2.6958-2.81840.29262610.25145381X-RAY DIFFRACTION100
2.8184-2.9670.33252840.26725335X-RAY DIFFRACTION100
2.967-3.15290.31613180.26815359X-RAY DIFFRACTION100
3.1529-3.39630.29152820.23345405X-RAY DIFFRACTION100
3.3963-3.73790.22232800.19875432X-RAY DIFFRACTION100
3.7379-4.27860.19993090.15935429X-RAY DIFFRACTION100
4.2786-5.38950.17693100.13065513X-RAY DIFFRACTION100
5.3895-49.99540.2092880.16795818X-RAY DIFFRACTION100
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)
10.7191-0.63930.15311.04190.19450.9766-0.0659-0.10110.14730.05640.1233-0.2340.53620.5233-0.01480.25130.3154-0.08631.1894-0.07370.495762.895772.608421.8031
20.3662-0.68810.01361.69620.41860.98530.0043-0.3480.60660.18670.2361-0.5791-0.12130.5044-0.23290.0941-0.1447-0.05340.8773-0.34230.764552.9051106.242933.4572
30.7328-0.7861-0.30971.1739-0.18540.8292-0.3027-0.67880.16890.46570.412-0.17710.01670.5355-0.11030.30160.2155-0.07680.8382-0.15270.261132.348286.974442.1166
41.4738-1.1154-0.04351.11040.02261.128-0.0495-0.10220.27240.08620.1269-0.232-0.01590.3397-0.06480.21230.0219-0.01170.4366-0.02180.338428.894192.070623.9259
50.5547-0.33160.35170.70690.21260.71260.16980.4285-0.0464-0.5414-0.13150.7072-0.1546-0.38730.03660.42130.1638-0.10450.6069-0.05650.3513.548584.0622.9757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 45:141)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 142:384)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 385:578)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 579:950)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 951:988)

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