5H4R

the complex of Glycoside Hydrolase 5 Lichenase from Caldicellulosiruptor sp. F32 E188Q mutant and cellotetraose

> Summary

Summary for 5H4R

Related4X0V
DescriptorBeta-1,3-1,4-glucanase, beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose, GLYCEROL, ... (4 entities in total)
Functional Keywordsglycoside hydrolase 5 lichenase, hydrolase
Biological sourceCaldicellulosiruptor sp. F32
Total number of polymer chains1
Total molecular weight46640.73
Authors
Dong, S.,Zhou, H.,Liu, X.,Wang, X.,Feng, Y. (deposition date: 2016-11-02, release date: 2017-09-13)
Primary citation
Meng, D.D.,Liu, X.,Dong, S.,Wang, Y.F.,Ma, X.Q.,Zhou, H.,Wang, X.,Yao, L.S.,Feng, Y.,Li, F.L.
Structural Insights into the Substrate Specificity of a Glycoside Hydrolase Family 5 Lichenase from Caldicellulosiruptor sp. F32
Biochem. J., 2017
PubMed: 28838949 (PDB entries with the same primary citation)
DOI: 10.1042/BCJ20170328
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.70310440144 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.1711001.9%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5h4r
no rotation
Molmil generated image of 5h4r
rotated about x axis by 90°
Molmil generated image of 5h4r
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ABeta-1,3-1,4-glucanasepolymer39645882.11
UniProt (R9RX81)
Pfam (PF00150)
Caldicellulosiruptor sp. F32Glycoside hydrolase F32EG5
beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosenon-polymer666.61
GLYCEROLnon-polymer92.11
waterwater18.0443

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight45882.1
Non-Polymers*Number of molecules2
Total molecular weight758.7
All*Total molecular weight46640.7
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.70310440144 Å)

Cell axes62.58176.31595.611
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits28.40 - 1.70
the highest resolution shell value1.736 - 1.703
R-factor0.142735000316
R-work0.14126
the highest resolution shell value0.157
R-free0.16984
the highest resolution shell value0.184
RMSD bond length0.009
RMSD bond angle0.992

Data Collection Statistics

Resolution limits28.40 - 1.70
the highest resolution shell value -
Number of reflections49925
Completeness98.3
Redundancy5

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1EVAPORATION8.5291

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
AC127binding site for residue CTT A 401
ChainResidue
AASN55
ATRP76
AHIS141
AHIS142
AASN187
AGLN188
AGLY230
AVAL233
ATYR274
ALEU281
AGLU326
ATRP360
AASN362
AGLU370
AGOL402
AHOH501
AHOH514
AHOH525
AHOH530
AHOH547
AHOH556
AHOH563
AHOH564
AHOH594
AHOH650
AHOH695
AHOH803

AC26binding site for residue GOL A 402
ChainResidue
AALA273
ATYR274
AARG275
ACTT401
AHOH511
AHOH799

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

site_idNumber of ResiduesDetails
CTT_5h4r_A_40122beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose binding site
ChainResidueligand
AASN55CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
AASP58CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
AALA75-TRP76CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
AARG98CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
AHIS141-HIS142CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
AASN187-GLN188CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
ATRP198CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
AALA243CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
AHIS272-TYR274CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
ATYR277CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
ALEU281CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
AGLU326CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
ATRP360CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
AASN362CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
AGLY369-GLU370CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
APHE372CTT: beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose

GOL_5h4r_A_4028GLYCEROL binding site
ChainResidueligand
ATRP198GOL: GLYCEROL
APRO246GOL: GLYCEROL
AHIS272-ARG275GOL: GLYCEROL
ATYR277GOL: GLYCEROL
ALEU281GOL: GLYCEROL

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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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