[English] 日本語
Yorodumi
- PDB-7zb3: Crystal structure of beta-xylosidase from Thermotoga maritima in ... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more