5GLQ

Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compostmicrobial metagenome in complex with l-arabinose and xylotriose, calcium-free form

> Summary

Summary for 5GLQ

Related5GLK 5GLL 5GLM 5GLN 5GLO 5GLP 5GLR
DescriptorGlycoside hydrolase family 43
Functional Keywordsglycoside hydrolase family 43, hydrolase
Biological sourceuncultured bacterium
Total number of polymer chains2
Total molecular weight78201.91
Authors
Matsuzawa, T.,Kishine, N.,Fujimoto, Z.,Yaoi, K. (deposition date: 2016-07-12, release date: 2017-03-15)
Primary citation
Matsuzawa, T.,Kaneko, S.,Kishine, N.,Fujimoto, Z.,Yaoi, K.
Crystal structure of metagenomic beta-xylosidase/ alpha-l-arabinofuranosidase activated by calcium.
J. Biochem., 2017
PubMed: 28204531
DOI: 10.1093/jb/mvx012
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.7 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.184000.9%4.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5glq
no rotation
Molmil generated image of 5glq
rotated about x axis by 90°
Molmil generated image of 5glq
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5glq
no rotation
Molmil generated image of 5glq
rotated about x axis by 90°
Molmil generated image of 5glq
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5glq.pdb1.gz [62.53 KB])
Coordinate files for Biological unit (5glq.pdb2.gz [60.54 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BGlycoside hydrolase family 43polymer34438529.52
UniProt (A0A0H5BL38)
Pfam (PF04616)
uncultured bacteriumbeta-xylosidase / alpha-arabinofuranosidase
SODIUM IONnon-polymer23.04
beta-L-arabinofuranosenon-polymer150.12
BETA-D-XYLOPYRANOSEnon-polymer150.15
waterwater18.0597

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight77059.0
Non-Polymers*Number of molecules11
Total molecular weight1142.9
All*Total molecular weight78201.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.7 Å)

Cell axes74.80161.48979.047
Cell angles90.0095.7290.00
SpacegroupP 1 21 1
Resolution limits78.65 - 1.70
the highest resolution shell value1.744 - 1.700
R-factor0.15009
R-work0.14876
the highest resolution shell value0.226
R-free0.17527
the highest resolution shell value0.239
RMSD bond length0.008
RMSD bond angle1.394

Data Collection Statistics

Resolution limits100.00 - 1.70
the highest resolution shell value -
Number of reflections77216
Rmerge_l_obs0.074
the highest resolution shell value0.519
Completeness98.1
Redundancy7.2
the highest resolution shell value5.5

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP5293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC17binding site for residue NA A 401
ChainResidue
AALA270
ATRP271
AHIS319
AHOH564
AHOH615
AHOH705
AHOH775

AC26binding site for residue NA A 402
ChainResidue
ATHR363
AHOH602
AHOH771
BHOH538
BHOH622
BHOH746

AC311binding site for residue FUB A 403
ChainResidue
AASP57
AMET90
ATRP125
AALA126
AASP177
AGLU268
ATHR317
AHIS319
AARG346
AXYP404
AHOH678

AC47binding site for residue NA B 401
ChainResidue
BALA270
BTRP271
BHIS319
BHOH514
BHOH616
BHOH675
BHOH697

AC55binding site for residue NA B 402
ChainResidue
AHOH575
AHOH668
BTHR363
BHOH595
BHOH693

AC611binding site for residue FUB B 403
ChainResidue
BASP57
BMET90
BTRP125
BALA126
BASP177
BGLU268
BTHR317
BHIS319
BARG346
BXYP404
BHOH656

AC714binding site for Poly-Saccharide residues XYP A 404 through XYP A 405
ChainResidue
AGLU81
AASP83
AHIS87
APHE88
ATRP125
ATRP196
AGLY197
AGLY198
AGLU268
ATRP316
AFUB403
AHOH510
AHOH556
AHOH759

AC818binding site for Poly-Saccharide residues XYP B 404 through XYP B 406
ChainResidue
BGLU81
BASP83
BHIS87
BPHE88
BTRP125
BTRP196
BGLY197
BGLY198
BGLU268
BASP287
BTRP316
BTHR317
BFUB403
BHOH501
BHOH513
BHOH531
BHOH550
BHOH602

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
FUB_5glq_A_40315beta-L-arabinofuranose binding site
ChainResidueligand
AALA56-ASP57FUB: beta-L-arabinofuranose
ASER72FUB: beta-L-arabinofuranose
APHE88FUB: beta-L-arabinofuranose
AMET90FUB: beta-L-arabinofuranose
ATRP125-ALA126FUB: beta-L-arabinofuranose
AILE176-ASP177FUB: beta-L-arabinofuranose
AGLU268-ALA269FUB: beta-L-arabinofuranose
ATHR317FUB: beta-L-arabinofuranose
AHIS319FUB: beta-L-arabinofuranose
AHIS334FUB: beta-L-arabinofuranose
AARG346FUB: beta-L-arabinofuranose

XYP_5glq_A_40510BETA-D-XYLOPYRANOSE binding site
ChainResidueligand
AGLU81-GLY85XYP: BETA-D-XYLOPYRANOSE
AHIS87-PHE88XYP: BETA-D-XYLOPYRANOSE
ATRP196XYP: BETA-D-XYLOPYRANOSE
ATRP316XYP: BETA-D-XYLOPYRANOSE
ATHR343XYP: BETA-D-XYLOPYRANOSE

XYP_5glq_A_40415BETA-D-XYLOPYRANOSE binding site
ChainResidueligand
AASP83-GLY85XYP: BETA-D-XYLOPYRANOSE
AHIS87-PHE88XYP: BETA-D-XYLOPYRANOSE
ATRP125XYP: BETA-D-XYLOPYRANOSE
AILE176XYP: BETA-D-XYLOPYRANOSE
AILE195-GLY198XYP: BETA-D-XYLOPYRANOSE
APHE267-GLU268XYP: BETA-D-XYLOPYRANOSE
ATRP316-THR317XYP: BETA-D-XYLOPYRANOSE

FUB_5glq_B_40315beta-L-arabinofuranose binding site
ChainResidueligand
BALA56-ASP57FUB: beta-L-arabinofuranose
BSER72FUB: beta-L-arabinofuranose
BPHE88FUB: beta-L-arabinofuranose
BMET90FUB: beta-L-arabinofuranose
BTRP125-ALA126FUB: beta-L-arabinofuranose
BILE176-ASP177FUB: beta-L-arabinofuranose
BGLU268-ALA269FUB: beta-L-arabinofuranose
BTHR317FUB: beta-L-arabinofuranose
BHIS319FUB: beta-L-arabinofuranose
BHIS334FUB: beta-L-arabinofuranose
BARG346FUB: beta-L-arabinofuranose

XYP_5glq_B_40511BETA-D-XYLOPYRANOSE binding site
ChainResidueligand
BGLU81-GLY85XYP: BETA-D-XYLOPYRANOSE
BHIS87-PHE88XYP: BETA-D-XYLOPYRANOSE
BTRP196XYP: BETA-D-XYLOPYRANOSE
BPHE267XYP: BETA-D-XYLOPYRANOSE
BTRP316XYP: BETA-D-XYLOPYRANOSE
BTHR343XYP: BETA-D-XYLOPYRANOSE

XYP_5glq_B_40416BETA-D-XYLOPYRANOSE binding site
ChainResidueligand
BASN82-GLY85XYP: BETA-D-XYLOPYRANOSE
BHIS87-PHE88XYP: BETA-D-XYLOPYRANOSE
BTRP125XYP: BETA-D-XYLOPYRANOSE
BILE176XYP: BETA-D-XYLOPYRANOSE
BILE195-GLY198XYP: BETA-D-XYLOPYRANOSE
BPHE267-GLU268XYP: BETA-D-XYLOPYRANOSE
BTRP316-THR317XYP: BETA-D-XYLOPYRANOSE

XYP_5glq_B_4065BETA-D-XYLOPYRANOSE binding site
ChainResidueligand
BASP83XYP: BETA-D-XYLOPYRANOSE
BTRP196XYP: BETA-D-XYLOPYRANOSE
BASP287XYP: BETA-D-XYLOPYRANOSE
BHIS289XYP: BETA-D-XYLOPYRANOSE
BTRP316XYP: BETA-D-XYLOPYRANOSE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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