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- PDB-7zb3: Crystal structure of beta-xylosidase from Thermotoga maritima in ... -

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Basic information

Entry
Database: PDB / ID: 7zb3
TitleCrystal structure of beta-xylosidase from Thermotoga maritima in complex with xylohexaose hydrolysed to xylobiose
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 / 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 ...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
D-Xylose, 4-O-beta-D-xylopyranosyl- / beta-glucosidase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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
DepositionMar 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 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
A: Beta-xylosidase
B: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,2536
Polymers179,4522
Non-polymers8014
Water18,4291023
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-42 kcal/mol
Surface area47720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.530, 98.720, 100.700
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
11A
21B

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 seq-ID: 1 - 778 / Label seq-ID: 1 - 778

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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: 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
#3: Sugar ChemComp-IVG / D-Xylose, 4-O-beta-D-xylopyranosyl- / Xylobiose


Type: saccharide / Mass: 282.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18O9 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1023 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
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: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.51→87.71 Å / Num. obs: 259769 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 1 / Net I/σ(I): 56.5
Reflection shellResolution: 1.51→1.54 Å / Num. unique obs: 8289 / CC1/2: 0.323

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292121589

Resolution: 1.51→87.709 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.971 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.069
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.19 12762 4.915 %
Rwork0.1671 246906 -
all0.168 --
obs-259668 93.495 %
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: 23.351 Å2
Baniso -1Baniso -2Baniso -3
1--1.224 Å20 Å2-0 Å2
2--2.552 Å2-0 Å2
3----1.328 Å2
Refinement stepCycle: LAST / Resolution: 1.51→87.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11867 0 54 1023 12944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01312352
X-RAY DIFFRACTIONr_bond_other_d0.0010.01512027
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.64516723
X-RAY DIFFRACTIONr_angle_other_deg1.4721.58127760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01651570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30621.743637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53152222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8761596
X-RAY DIFFRACTIONr_chiral_restr0.0860.21589
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022713
X-RAY DIFFRACTIONr_nbd_refined0.2110.22304
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.211784
X-RAY DIFFRACTIONr_nbtor_refined0.1690.26029
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.25790
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2875
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.040.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1380.218
X-RAY DIFFRACTIONr_nbd_other0.1390.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1050.229
X-RAY DIFFRACTIONr_mcbond_it1.6672.2576181
X-RAY DIFFRACTIONr_mcbond_other1.6672.2576180
X-RAY DIFFRACTIONr_mcangle_it2.23.387745
X-RAY DIFFRACTIONr_mcangle_other2.23.387746
X-RAY DIFFRACTIONr_scbond_it3.032.5566169
X-RAY DIFFRACTIONr_scbond_other3.0292.5566170
X-RAY DIFFRACTIONr_scangle_it4.4413.7038965
X-RAY DIFFRACTIONr_scangle_other4.4413.7038966
X-RAY DIFFRACTIONr_lrange_it5.08327.33413771
X-RAY DIFFRACTIONr_lrange_other5.01626.96813546
X-RAY DIFFRACTIONr_ncsr_local_group_10.0520.0525763
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.052320.0501
12BX-RAY DIFFRACTIONLocal ncs0.052320.0501
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
1.51-1.5490.3425800.357120440.356204130.2210.2261.84290.36
1.549-1.5920.3366530.329137360.329198420.4950.49272.51790.322
1.592-1.6380.3237440.3151670.301193210.4890.5182.35080.284
1.638-1.6880.2778490.268165310.268187400.7190.71292.74280.247
1.688-1.7440.2648720.234172860.235182050.8080.82699.74180.21
1.744-1.8050.2469140.208167440.21176590.8760.88399.99430.18
1.805-1.8730.2258800.187161280.189170090.910.9299.99410.16
1.873-1.9490.1978380.177155250.178163630.9310.9361000.151
1.949-2.0360.187340.162149970.163157310.950.9521000.139
2.036-2.1350.1897980.154142910.155150890.9510.9591000.134
2.135-2.2510.1846960.148136530.149143490.9550.9631000.13
2.251-2.3870.166390.14129280.141135670.9640.9691000.125
2.387-2.5520.1786350.14121370.142127720.9610.971000.127
2.552-2.7560.1785980.143113390.145119370.9610.9691000.131
2.756-3.0190.1925240.148104600.15109840.9550.9661000.139
3.019-3.3740.1854990.16295220.163100210.9620.9661000.157
3.374-3.8960.1824600.15683790.15888390.9660.9721000.156
3.896-4.7690.1373810.12371600.12375410.980.9831000.129
4.769-6.7340.1672920.16756330.16759250.9720.9751000.175
6.734-87.7090.1751760.18532450.18434240.9720.95699.91240.196

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