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

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Basic information

Entry
Database: PDB / ID: 2xvl
Titlecrystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus in complex with Pentaerythritol propoxylate (5 4 PO OH)
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
NICKEL (II) ION / Chem-PXN / Alpha-xylosidase, putative, xyl31A
Similarity search - Component
Biological speciesCELLVIBRIO JAPONICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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, PUTATIVE, XYL31A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,28515
Polymers115,2041
Non-polymers1,08114
Water12,863714
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.653, 157.653, 226.688
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1995-

CL

21A-2400-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 115203.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 5 types, 728 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PXN / (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol / PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH)


Mass: 368.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O8
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 714 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPENTAERYTHRITOL PROPOXYLATE (5 4 PO OH) (54P): AVERAGE MOLECULAR WEIGHT 426

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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: 3.53 Å3/Da / Density % sol: 65.15 %
Crystal growpH: 7
Details: 40 % PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), 0.1 M BIS-TRIS (PH 7.0), 5 MM NI SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2009 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111),GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.3→58.5 Å / Num. obs: 74143 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 24.33 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 16.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 7.5 / % possible all: 100

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Processing

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

2g3m


Resolution: 2.3→54.548 Å / SU ML: 0.22 / σ(F): 1.38 / Phase error: 16.07 / Stereochemistry target values: ML
Details: DISORDERED SIDE CHAINS WERE MODELED WITH ZERO-OCCUPANCY.
RfactorNum. reflection% reflection
Rfree0.1853 3736 5 %
Rwork0.145 --
obs0.147 74143 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.4 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8439 Å20 Å20 Å2
2--2.8439 Å20 Å2
3----5.6878 Å2
Refinement stepCycle: LAST / Resolution: 2.3→54.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7572 0 50 714 8336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077830
X-RAY DIFFRACTIONf_angle_d1.04310638
X-RAY DIFFRACTIONf_dihedral_angle_d17.1832793
X-RAY DIFFRACTIONf_chiral_restr0.071101
X-RAY DIFFRACTIONf_plane_restr0.0041391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.25893370.18936956X-RAY DIFFRACTION100
2.3822-2.47760.22563820.16756883X-RAY DIFFRACTION100
2.4776-2.59040.20783510.16166968X-RAY DIFFRACTION100
2.5904-2.72690.193600.15236974X-RAY DIFFRACTION100
2.7269-2.89780.22123850.15196942X-RAY DIFFRACTION100
2.8978-3.12150.18673870.15316961X-RAY DIFFRACTION100
3.1215-3.43560.19233880.14457011X-RAY DIFFRACTION100
3.4356-3.93260.17174010.13727044X-RAY DIFFRACTION100
3.9326-4.95410.13193650.10797159X-RAY DIFFRACTION100
4.9541-54.56360.17563800.1457509X-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)
10.2192-0.2783-0.05150.45010.24530.63680.01960.04370.01750.02880.1013-0.21140.20070.4304-0.12420.05530.134-0.00450.4744-0.09250.175662.829573.097621.6658
20.2451-0.064-0.07010.4870.15790.53920.0690.02040.1376-0.01910.0449-0.2023-0.13450.2907-0.10890.0948-0.0890.04590.3061-0.08520.241552.9523106.617833.5811
30.3183-0.14170.02270.38220.04610.40440.0038-0.09330.03640.0960.0672-0.0881-0.01440.1175-0.06490.0470.0365-0.00260.1548-0.0370.03932.255387.390241.9725
40.4397-0.2381-0.03490.3988-0.00760.58680.03340.03250.0907-0.01310.0185-0.1003-0.04840.1332-0.05160.03260.00740.02930.1087-0.01460.058128.892192.446323.7425
50.4442-0.1952-0.10080.3042-0.06110.07460.05790.2535-0.0799-0.1881-0.00050.07370.0466-0.1553-0.0270.12730.0576-0.02840.2108-0.03330.017313.689884.53752.775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 45:142)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 143:384)
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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