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- PDB-7zgz: Crystal structure of beta-xylosidase from Thermotoga maritima in ... -

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Basic information

Entry
Database: PDB / ID: 7zgz
TitleCrystal structure of beta-xylosidase from Thermotoga maritima in complex with methyl-beta-D-xylopyranoside hydrolysed to xylose
ComponentsBeta-xylosidase
KeywordsHYDROLASE / Complex Xylobiose Glycosyl hydrolase
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase activity / beta-glucosidase / carbohydrate metabolic process
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 / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily ...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 / Glycoside hydrolase, family 3, N-terminal domain / 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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-xylopyranose / beta-glucosidase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGloster, T.M. / Foltanyi, F.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structural and further functional characterisation of a glycoside hydrolase family 3 beta-xylosidase from Thermotoga maritima
Authors: Gloster, T.M. / Foltanyi, F. / Hobbs, E.M. / Pritchard, L.
History
DepositionApr 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Beta-xylosidase
Y: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,9886
Polymers179,4522
Non-polymers5374
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-44 kcal/mol
Surface area47360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.580, 97.210, 99.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11X
21Y

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 1 - 780 / Label seq-ID: 1 - 780

Dom-IDAuth asym-IDLabel asym-ID
1XA
2YB

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

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Components

#1: Protein Beta-xylosidase / TmGH3


Mass: 89725.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Gene: Tmari_0073 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4NX63, xylan 1,4-beta-xylosidase
#2: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
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: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→54.923 Å / Num. obs: 147912 / % possible obs: 99.6 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 67.8
Reflection shellResolution: 1.85→1.88 Å / Num. unique obs: 7190 / CC1/2: 0.433

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JP0, 5Z9S, 5YOT, 3U4A, 5XXL

5jp0

5z9s

5yot

3u4a

5xxl


Resolution: 1.85→54.923 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.186 / SU B: 5.818 / SU ML: 0.151 / Average fsc free: 0.749 / Average fsc work: 0.759 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2442 7499 5.074 %
Rwork0.2037 140282 -
all0.206 --
obs-147781 99.529 %
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: 45.489 Å2
Baniso -1Baniso -2Baniso -3
1--4.742 Å20 Å2-0 Å2
2--2.876 Å20 Å2
3---1.866 Å2
Refinement stepCycle: LAST / Resolution: 1.85→54.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11783 0 36 222 12041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01312098
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511787
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.64316349
X-RAY DIFFRACTIONr_angle_other_deg1.2711.58127190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.49151520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30821.906614
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.555152173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5711589
X-RAY DIFFRACTIONr_chiral_restr0.0670.21547
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213529
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022637
X-RAY DIFFRACTIONr_nbd_refined0.20.22154
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.211250
X-RAY DIFFRACTIONr_nbtor_refined0.1590.25862
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.25691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2413
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0410.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.212
X-RAY DIFFRACTIONr_nbd_other0.130.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.210
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0660.21
X-RAY DIFFRACTIONr_mcbond_it3.2454.6236077
X-RAY DIFFRACTIONr_mcbond_other3.2454.6236076
X-RAY DIFFRACTIONr_mcangle_it4.2056.9247598
X-RAY DIFFRACTIONr_mcangle_other4.2056.9247599
X-RAY DIFFRACTIONr_scbond_it4.025.0026020
X-RAY DIFFRACTIONr_scbond_other4.025.0036021
X-RAY DIFFRACTIONr_scangle_it5.6997.3338751
X-RAY DIFFRACTIONr_scangle_other5.6987.3348752
X-RAY DIFFRACTIONr_lrange_it6.77653.29412859
X-RAY DIFFRACTIONr_lrange_other6.77853.28512844
X-RAY DIFFRACTIONr_ncsr_local_group_10.0720.0524609
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11XX-RAY DIFFRACTIONLocal ncs0.07230.05009
12YX-RAY DIFFRACTIONLocal ncs0.07230.05009
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
1.85-1.8980.4855580.468101840.469108250.3670.37799.23330.445
1.898-1.950.4974750.47798660.478105970.2690.27397.58420.454
1.95-2.0060.3685560.34797640.348103280.4520.46499.92250.315
2.006-2.0680.3615070.33994390.3499880.5730.56799.57950.3
2.068-2.1360.3145010.29391840.29497310.7110.69899.52730.251
2.136-2.2110.2764960.24588960.24793990.8230.84199.92550.209
2.211-2.2940.3544610.32484020.32690680.6710.70297.73930.275
2.294-2.3870.2544610.20182970.20387620.9030.91499.95430.169
2.387-2.4930.2394110.19680020.19884180.9180.92999.94060.166
2.493-2.6150.2583880.19176310.19480200.9230.93899.98750.161
2.615-2.7560.2614010.19972400.20276470.9210.93899.92150.17
2.756-2.9230.2313690.19369090.19572780.9260.9371000.17
2.923-3.1240.2523260.18865370.19168630.9230.9391000.171
3.124-3.3730.2462970.19260570.19463580.9230.93999.93710.18
3.373-3.6940.2362950.1856010.18259030.9350.95399.88140.174
3.694-4.1270.2062630.1650910.16353670.9570.96599.75780.161
4.127-4.7610.1492440.13145080.13247520.9740.9781000.143
4.761-5.8210.1952030.16738650.16840690.9590.96699.97540.183
5.821-8.1860.2511860.20230110.20431970.9390.9541000.225
8.186-54.9230.2171010.19417980.19519030.9560.96299.78980.228

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