[English] 日本語
Yorodumi
- PDB-2bs9: Native crystal structure of a GH39 beta-xylosidase XynB1 from Geo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bs9
TitleNative crystal structure of a GH39 beta-xylosidase XynB1 from Geobacillus stearothermophilus
ComponentsBETA-XYLOSIDASEXylan 1,4-b-xylosidase
KeywordsHYDROLASE / BETA-XYLOSIDASE / COMPLEX OF THE COVALENT INTERMEDIATE / ENZYME-SUBSTRATE COMPLEX / FAMILY GH39 / THERMOPHILIC ENZYME
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / xylan catabolic process
Similarity search - Function
Glycosyl hydrolase domain; family 39 / : / : / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Glycosyl hydrolase domain; family 39 / : / : / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCzjzek, M. / Bravman, T. / Henrissat, B. / Shoham, Y.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Enzyme-Substrate Complex Structures of a Gh39 Beta-Xylosidase from Geobacillus Stearothermophilus.
Authors: Czjzek, M. / David, A.B. / Bravman, T. / Shoham, G. / Henrissat, B. / Shoham, Y.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and Preliminary X-Ray Analysis of Family 39 Beta-D-Xylosidase from Geobacillus Stearothermophilus T-6
Authors: Czjzek, M. / Bravman, T. / Henrissat, B. / Shoham, Y.
History
DepositionMay 19, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2005Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB BB CB" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB BB CB" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 8-STRANDED BARRELS REPRESENTED BY 9-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DB EB FB GB HB" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 7-STRANDED BARRELS REPRESENTED BY 8-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-XYLOSIDASE
B: BETA-XYLOSIDASE
C: BETA-XYLOSIDASE
D: BETA-XYLOSIDASE
E: BETA-XYLOSIDASE
F: BETA-XYLOSIDASE
G: BETA-XYLOSIDASE
H: BETA-XYLOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,75115
Polymers464,4718
Non-polymers2817
Water24,6271367
1
A: BETA-XYLOSIDASE
B: BETA-XYLOSIDASE
C: BETA-XYLOSIDASE
D: BETA-XYLOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,3567
Polymers232,2354
Non-polymers1203
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: BETA-XYLOSIDASE
F: BETA-XYLOSIDASE
G: BETA-XYLOSIDASE
H: BETA-XYLOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,3968
Polymers232,2354
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.668, 165.744, 311.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 2 - 502 / Label seq-ID: 2 - 502

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH

NCS oper:
IDCodeMatrixVector
1given(-0.99979, -0.00021, -0.02034), (0.00017, -1, 0.00185), (-0.02034, 0.00185, 0.99979)48.04726, 28.51126, 0.3604
2given(0.96939, -0.24517, 0.01295), (-0.24518, -0.96948, -0.00149), (0.01292, -0.00173, -0.99992)3.03464, 33.95127, 176.02698
3given(-0.96971, 0.24426, 0.00265), (0.24425, 0.96971, -0.00333), (-0.00338, -0.00258, -0.99999)41.8203, -4.84954, 176.43852
4given(-0.98772, -0.07849, -0.13511), (0.07645, -0.99687, 0.02026), (-0.13628, 0.00968, 0.99062)56.99773, 10.8186, -74.61298
5given(0.99105, 0.07803, -0.10835), (-0.07691, 0.99693, 0.0145), (0.10915, -0.00603, 0.99401)6.61221, -13.69988, -80.36541
6given(-0.94094, 0.32056, 0.109), (0.32129, 0.94691, -0.01124), (-0.10681, 0.02444, -0.99398)28.67579, -19.8563, 99.67416
7given(0.93855, -0.31865, 0.13263), (-0.31842, -0.94766, -0.02346), (0.13317, -0.02021, -0.99089)-7.78493, 23.0294, 94.50587

-
Components

#1: Protein
BETA-XYLOSIDASE / Xylan 1,4-b-xylosidase / 1 / 4-BETA-D-XYLAN XYLOHYDROLASE / XYLAN 1 / 4-BETA-XYLOSIDASE


Mass: 58058.824 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS STEAROTHERMOPHILUS (bacteria) / Strain: T-6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZFM2, xylan 1,4-beta-xylosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1367 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52 %
Crystal growpH: 7.5
Details: 100 MM HEPES PH 7.5, 50 MM NACL, 20% (W/V) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→24.9 Å / Num. obs: 273112 / % possible obs: 98.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 8
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.4 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PX8

1px8


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.875 / SU B: 5.067 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 11944 5 %RANDOM
Rwork0.209 ---
obs0.211 225867 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2---1.02 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32725 0 7 1367 34099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02133645
X-RAY DIFFRACTIONr_bond_other_d0.0030.0230017
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.93445676
X-RAY DIFFRACTIONr_angle_other_deg0.858369689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91354000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.24856
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0237436
X-RAY DIFFRACTIONr_gen_planes_other0.0080.027376
X-RAY DIFFRACTIONr_nbd_refined0.2030.27153
X-RAY DIFFRACTIONr_nbd_other0.2330.236088
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.218688
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.21408
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5141.519968
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.965232423
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.549313677
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5534.513253
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2941medium positional0.210.5
2B2941medium positional0.190.5
3C2941medium positional0.220.5
4D2941medium positional0.180.5
5E2941medium positional0.190.5
6F2941medium positional0.180.5
7G2941medium positional0.160.5
8H2941medium positional0.190.5
1A4890loose positional0.515
2B4890loose positional0.525
3C4890loose positional0.535
4D4890loose positional0.565
5E4890loose positional0.515
6F4890loose positional0.535
7G4890loose positional0.475
8H4890loose positional0.535
1A2941medium thermal0.482
2B2941medium thermal0.682
3C2941medium thermal0.512
4D2941medium thermal0.82
5E2941medium thermal0.572
6F2941medium thermal0.632
7G2941medium thermal0.472
8H2941medium thermal0.642
1A4890loose thermal1.3210
2B4890loose thermal1.4210
3C4890loose thermal1.3310
4D4890loose thermal1.6410
5E4890loose thermal1.3710
6F4890loose thermal1.4110
7G4890loose thermal1.2910
8H4890loose thermal1.4610
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 867
Rwork0.305 16515

+
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