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- PDB-2xvg: crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus -

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Basic information

Entry
Database: PDB / ID: 2xvg
Titlecrystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus
ComponentsALPHA XYLOSIDASE
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. / PA14 / PA14 domain ...: / Jelly Rolls - #380 / : / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / glycosyl hydrolase (family 31) / PA14/GLEYA domain / PA14 domain profile. / PA14 / PA14 domain / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like 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
NICKEL (II) ION / Alpha-xylosidase, putative, xyl31A
Similarity search - Component
Biological speciesCELLVIBRIO JAPONICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: ALPHA XYLOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,74511
Polymers115,2041
Non-polymers54110
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.193, 156.193, 227.759
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ALPHA XYLOSIDASE


Mass: 115203.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) CELLVIBRIO JAPONICUS (bacteria)
References: UniProt: B3PBD9, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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Non-polymers , 5 types, 113 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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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: 3.59 Å3/Da / Density % sol: 65.72 % / 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 CCD / Detector: CCD / Date: Sep 26, 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: 2.6→49.9 Å / Num. obs: 50969 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

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

2g3m


Resolution: 2.6→49.885 Å / SU ML: 0.4 / σ(F): 1.36 / Phase error: 25.87 / Stereochemistry target values: ML
Details: DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY AND HAVE ZERO OCCUPANCIES.
RfactorNum. reflection% reflection
Rfree0.259 2587 5.1 %
Rwork0.2038 --
obs0.2065 50969 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.012 Å2 / ksol: 0.288 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7577 0 23 103 7703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097798
X-RAY DIFFRACTIONf_angle_d1.15610585
X-RAY DIFFRACTIONf_dihedral_angle_d17.6812773
X-RAY DIFFRACTIONf_chiral_restr0.0781095
X-RAY DIFFRACTIONf_plane_restr0.0051387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6930.36782430.30054746X-RAY DIFFRACTION100
2.693-2.80080.33492580.27944738X-RAY DIFFRACTION100
2.8008-2.92820.34432750.27854739X-RAY DIFFRACTION100
2.9282-3.08260.3082610.27434786X-RAY DIFFRACTION100
3.0826-3.27570.31882730.25614760X-RAY DIFFRACTION100
3.2757-3.52850.27472600.21894793X-RAY DIFFRACTION100
3.5285-3.88350.24662550.19754831X-RAY DIFFRACTION100
3.8835-4.44520.20352430.14924888X-RAY DIFFRACTION100
4.4452-5.59920.2072590.13774920X-RAY DIFFRACTION100
5.5992-49.89390.23952600.19355181X-RAY DIFFRACTION99
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)
11.0135-1.3518-0.50311.94860.22221.4952-0.1336-0.11010.4163-0.03450.1179-0.55940.17660.6906-0.03760.1560.2432-0.05161.249-0.05940.393263.066275.495524.1358
20.1535-0.26790.2221.3770.55440.74950.0083-0.22330.63690.05530.1445-0.3635-0.20280.36-0.18430.1337-0.17980.01270.8391-0.28190.711151.4626108.129233.7622
30.9906-0.5490.03970.9207-0.03150.5227-0.1413-0.53090.09010.35960.269-0.12290.01190.3483-0.11950.19010.1719-0.05920.6561-0.1170.059632.300986.569542.1281
41.4354-1.20850.17671.3971-0.10710.489-0.0314-0.02470.25220.02290.0557-0.21860.02630.3481-0.03440.17340.0214-0.00960.4379-0.00310.113928.789291.802323.6678
51.083-0.74990.53832.79870.51520.60880.23850.3598-0.0103-0.6059-0.18010.4904-0.2441-0.06960.04760.36370.2342-0.06280.649-0.07290.178713.535784.08142.6507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 45:169)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 170:384)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 385:584)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 585:950)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 951:989)

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