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- PDB-8c7f: Crystal structure of beta-xylosidase mutant (D281N, E517Q) from T... -

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Basic information

Entry
Database: PDB / ID: 8c7f
TitleCrystal structure of beta-xylosidase mutant (D281N, E517Q) from Thermotoga maritima in complex with xylopentaose
ComponentsXylosidase
KeywordsHYDROLASE / Complex Xylopentose Glycosyl hydrolase
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase / beta-glucosidase activity
Similarity search - Function
Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / : / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal ...Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / : / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
4beta-beta-xylotriose / beta-glucosidase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsGloster, T.M. / Foltanyi, F.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To be published
Title: Structural and functional characterisation of a glycoside hydrolase family 3 beta-xylosidase from Thermotoga maritima
Authors: Gloster, T.M. / Foltanyi, F.
History
DepositionJan 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xylosidase
B: Xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,4096
Polymers174,2122
Non-polymers1,1974
Water23,8161322
1
A: Xylosidase
B: Xylosidase
hetero molecules

A: Xylosidase
B: Xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,81812
Polymers348,4244
Non-polymers2,3948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area24420 Å2
ΔGint-100 kcal/mol
Surface area89730 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-47 kcal/mol
Surface area47800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.350, 100.890, 179.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 778 / Label seq-ID: 1 - 778

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Xylosidase


Mass: 87106.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: ATCC 43589 / Gene: TM_0076 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WXT1
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 414.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylotriose
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a212h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 546.474 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a212h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 3% polyethylene glycol 8000, 48% 2-methyl-2,4-pentanediol, 0.1 M sodium cacodylate pH 5.9

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Data collection

DiffractionMean temperature: 175 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.52→50.445 Å / Num. obs: 272231 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.06 / Rrim(I) all: 0.114 / Net I/σ(I): 9.6
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.03 / Num. unique obs: 13322 / CC1/2: 0.999 / Rpim(I) all: 0.019 / Rrim(I) all: 0.036

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→50.445 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.67 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.066 / Details: Hydrogens have not been used.
RfactorNum. reflection% reflection
Rfree0.1885 13593 4.994 %
Rwork0.1643 258572 -
all0.166 --
obs-272165 99.807 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.402 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å2-0 Å2-0 Å2
2--0.083 Å2-0 Å2
3----1.163 Å2
Refinement stepCycle: LAST / Resolution: 1.52→50.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11751 0 81 1322 13154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01212259
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611912
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.6516607
X-RAY DIFFRACTIONr_angle_other_deg0.5261.56927498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88951549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.781588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.562102187
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.39110530
X-RAY DIFFRACTIONr_chiral_restr0.0830.21874
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214291
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022673
X-RAY DIFFRACTIONr_nbd_refined0.2170.22263
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.211412
X-RAY DIFFRACTIONr_nbtor_refined0.1780.26010
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.26555
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.21039
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2750.223
X-RAY DIFFRACTIONr_nbd_other0.1970.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1270.274
X-RAY DIFFRACTIONr_mcbond_it1.6932.0126145
X-RAY DIFFRACTIONr_mcbond_other1.6912.0126145
X-RAY DIFFRACTIONr_mcangle_it2.2153.617711
X-RAY DIFFRACTIONr_mcangle_other2.2153.617712
X-RAY DIFFRACTIONr_scbond_it3.1562.326114
X-RAY DIFFRACTIONr_scbond_other3.1562.326115
X-RAY DIFFRACTIONr_scangle_it4.6694.1128896
X-RAY DIFFRACTIONr_scangle_other4.6684.1128897
X-RAY DIFFRACTIONr_lrange_it5.70121.66713857
X-RAY DIFFRACTIONr_lrange_other5.70121.66713858
X-RAY DIFFRACTIONr_ncsr_local_group_10.0610.0525136
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.060510.0501
12AX-RAY DIFFRACTIONLocal ncs0.060510.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.52-1.5590.29110140.298189000.298200240.9260.92499.45070.293
1.559-1.6020.298930.283184760.283194520.9330.93799.57330.273
1.602-1.6490.2789030.261179660.262189330.9420.94799.6620.247
1.649-1.6990.2618970.239175240.24184730.9490.95799.71850.22
1.699-1.7550.2379670.221168340.222178440.960.96699.7590.199
1.755-1.8160.2198470.199163900.2172660.9680.97399.8320.176
1.816-1.8850.2118170.185158870.186167220.9720.97799.89240.161
1.885-1.9620.2078220.17152390.172160810.9730.98199.87560.149
1.962-2.0490.1817470.155147110.156154670.9790.98599.94180.136
2.049-2.1490.1856750.151140890.153147700.9790.98699.95940.134
2.149-2.2650.1717090.146133230.147140470.9820.98799.89320.131
2.265-2.4020.1756740.142126890.143133740.9810.98899.91780.128
2.402-2.5670.1796400.137119040.139125470.9810.98999.97610.125
2.567-2.7720.1815570.139111260.141116860.980.98899.97430.129
2.772-3.0360.1815670.143102420.145108110.980.98899.98150.137
3.036-3.3930.1755420.14592730.14798160.9820.98899.98980.143
3.393-3.9150.1614670.14382450.14487130.9840.98899.98850.147
3.915-4.7870.1533700.1370330.13174060.9850.9999.95950.142
4.787-6.740.1733200.17955100.17958310.9850.98499.98280.194
6.74-50.4450.2031650.19432120.19434170.9780.9898.82940.214

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