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

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Basic information

Entry
Database: PDB / ID: 7zdy
TitleCrystal structure of beta-xylosidase from Thermotoga maritima in complex with methyl-beta-D-xylopyranoside
ComponentsBeta-xylosidase
KeywordsHYDROLASE / Complex methyl-beta-D-xylopyranoside 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 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-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 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-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
methyl beta-D-xylopyranoside / beta-glucosidase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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 30, 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
W: Beta-xylosidase
Y: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,2538
Polymers179,4522
Non-polymers8016
Water14,646813
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-61 kcal/mol
Surface area47860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.620, 97.680, 100.690
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
11W
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
1WA
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: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Sugar ChemComp-6MJ / methyl beta-D-xylopyranoside / methyl beta-D-xyloside / methyl D-xyloside / methyl xyloside


Type: D-saccharide / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylp[1Me]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-b-D-xylopyranoseCOMMON NAMEGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 813 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
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: 1.46→51.25 Å / Num. obs: 302573 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 1 / Net I/σ(I): 64.2
Reflection shellResolution: 1.46→1.49 Å / Num. unique obs: 14737 / CC1/2: 0.331

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Processing

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

5jp0

5z9s

5yot

3u4a

5xxl


Resolution: 1.46→51.25 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.164 / SU B: 1.839 / SU ML: 0.062 / Average fsc free: 0.8205 / Average fsc work: 0.8253 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.06 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1909 15107 4.994 %
Rwork0.1717 287395 -
all0.173 --
obs-302502 99.549 %
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: 28.782 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å2-0 Å2
2--2.139 Å20 Å2
3----0.359 Å2
Refinement stepCycle: LAST / Resolution: 1.46→51.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11856 0 54 813 12723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01212295
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.6416629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58851550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70921.714630
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.989152212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1421595
X-RAY DIFFRACTIONr_chiral_restr0.120.21571
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029207
X-RAY DIFFRACTIONr_nbd_refined0.2030.25810
X-RAY DIFFRACTIONr_nbtor_refined0.3190.28497
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2847
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.231
X-RAY DIFFRACTIONr_mcbond_it2.0682.6536167
X-RAY DIFFRACTIONr_mcangle_it2.6573.9657728
X-RAY DIFFRACTIONr_scbond_it3.7822.9676128
X-RAY DIFFRACTIONr_scangle_it5.2624.2968901
X-RAY DIFFRACTIONr_lrange_it5.48737.40518908
X-RAY DIFFRACTIONr_ncsr_local_group_10.0590.0525782
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11WX-RAY DIFFRACTIONLocal ncs0.05870.0501
12YX-RAY DIFFRACTIONLocal ncs0.05870.0501
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
1.46-1.4980.35410960.355207520.355222630.440.43998.13590.355
1.498-1.5390.32510610.326204570.326217300.470.47399.02440.317
1.539-1.5830.3159850.296199770.296211350.5510.58299.18150.278
1.583-1.6320.26310520.267193530.267205460.7510.74499.31370.241
1.632-1.6860.2729880.248188020.249199200.8020.80999.34740.216
1.686-1.7450.2539200.23182920.231192940.8460.85299.5750.196
1.745-1.8110.2379100.202176010.203185850.8930.90199.60180.168
1.811-1.8840.2229040.185169800.187179350.9190.92899.71560.155
1.884-1.9680.28750.173163040.174172110.9350.94499.81410.146
1.968-2.0640.1997840.163156520.165164550.9430.95399.88450.142
2.064-2.1750.1957790.165149040.167156930.9480.95699.93630.148
2.175-2.3070.1938200.161140440.162148670.9530.96199.97980.145
2.307-2.4660.1826960.159133000.16139970.960.96499.99290.146
2.466-2.6630.1846690.162123690.163130400.9590.96499.98470.151
2.663-2.9160.1925620.161114820.162120440.9560.9651000.154
2.916-3.2590.1745770.162103670.162109440.9610.9661000.161
3.259-3.7610.1755260.14991480.1596750.9660.9799.98970.156
3.761-4.60.1384290.1378260.1382570.9790.9899.97580.147
4.6-6.480.172930.15661880.15664810.970.9731000.181
6.48-51.250.1921810.18735980.18837910.9750.97499.68350.221

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