[English] 日本語
Yorodumi
- PDB-2x8s: Crystal Structure of the Abn2 D171A mutant in complex with arabin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x8s
TitleCrystal Structure of the Abn2 D171A mutant in complex with arabinotriose
ComponentsENDO-ALPHA-1,5-L-ARABINANASE
KeywordsHYDROLASE
Function / homology
Function and homology information


arabinan endo-1,5-alpha-L-arabinanase / arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process / extracellular region / metal ion binding
Similarity search - Function
Extracellular endo-alpha-(1->5)-L-arabinanase, C-terminal / C-terminal lipocalin-like domain / Lipocalin - #10 / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Lipocalin ...Extracellular endo-alpha-(1->5)-L-arabinanase, C-terminal / C-terminal lipocalin-like domain / Lipocalin - #10 / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Extracellular endo-alpha-(1->5)-L-arabinanase 2 / Extracellular endo-alpha-(1->5)-L-arabinanase 2
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsdeSanctis, D. / Inacio, J.M. / Lindley, P.F. / de Sa-Nogueira, I. / Bento, I.
CitationJournal: FEBS J. / Year: 2010
Title: New Evidence for the Role of Calcium in the Glycosidase Reaction of Gh43 Arabinanases.
Authors: De Sanctis, D. / Inacio, J.M. / Lindley, P.F. / De Sa-Nogueira, I. / Bento, I.
History
DepositionMar 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDO-ALPHA-1,5-L-ARABINANASE
B: ENDO-ALPHA-1,5-L-ARABINANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,38519
Polymers105,4762
Non-polymers1,90917
Water12,448691
1
A: ENDO-ALPHA-1,5-L-ARABINANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5867
Polymers52,7381
Non-polymers8486
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDO-ALPHA-1,5-L-ARABINANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,79912
Polymers52,7381
Non-polymers1,06111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.950, 57.985, 85.595
Angle α, β, γ (deg.)96.14, 91.77, 117.34
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.96281, -0.04159, -0.26695), (-0.0046, 0.99046, -0.13771), (0.27013, -0.13136, -0.95382)
Vector: 37.6219, -2.32137, 89.19862)

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein ENDO-ALPHA-1,5-L-ARABINANASE / ENDO-ALPHA- ARABINANASE


Mass: 52738.098 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: B3FRL6, UniProt: P42293*PLUS, arabinan endo-1,5-alpha-L-arabinanase
#2: Polysaccharide alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-5LArafa1-5LArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a211h-1a_1-4]/1-1-1/a5-b1_b5-c1WURCSPDB2Glycan 1.1.0
[][a-L-Araf]{[(5+1)][a-L-Araf]{[(5+1)][a-L-Araf]{}}}LINUCSPDB-CARE

-
Non-polymers , 8 types, 706 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 171 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 171 TO ALA

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 38.93 % / Description: NONE

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.06725
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06725 Å / Relative weight: 1
ReflectionResolution: 1.5→84.8 Å / Num. obs: 133640 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2 % / Rmerge(I) obs: 0.38 / % possible all: 92.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X8F

2x8f


Resolution: 1.5→24.595 Å / SU ML: 0.21 / σ(F): 2.01 / Phase error: 14.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1666 6372 4.96 %
Rwork0.1473 --
obs0.1482 128476 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.573 Å2 / ksol: 0.375 e/Å3
Refinement stepCycle: LAST / Resolution: 1.5→24.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6998 0 119 691 7808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0177485
X-RAY DIFFRACTIONf_angle_d1.40310165
X-RAY DIFFRACTIONf_dihedral_angle_d18.5912735
X-RAY DIFFRACTIONf_chiral_restr0.1261030
X-RAY DIFFRACTIONf_plane_restr0.0061314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.22922200.19614195X-RAY DIFFRACTION93
1.517-1.53490.20872360.194190X-RAY DIFFRACTION94
1.5349-1.55360.21181930.17894162X-RAY DIFFRACTION93
1.5536-1.57330.19552250.16894210X-RAY DIFFRACTION95
1.5733-1.5940.19142130.1644213X-RAY DIFFRACTION93
1.594-1.61580.19692220.16614235X-RAY DIFFRACTION95
1.6158-1.63890.18852030.1614184X-RAY DIFFRACTION94
1.6389-1.66330.18772090.15274286X-RAY DIFFRACTION95
1.6633-1.68930.18932440.14724188X-RAY DIFFRACTION94
1.6893-1.7170.17122200.14124231X-RAY DIFFRACTION96
1.717-1.74660.14352340.13084266X-RAY DIFFRACTION95
1.7466-1.77840.14932190.13724238X-RAY DIFFRACTION96
1.7784-1.81260.16822140.13584268X-RAY DIFFRACTION95
1.8126-1.84950.15812270.1364245X-RAY DIFFRACTION95
1.8495-1.88970.15072340.13524251X-RAY DIFFRACTION96
1.8897-1.93370.14542420.13474281X-RAY DIFFRACTION96
1.9337-1.9820.16292050.12964299X-RAY DIFFRACTION96
1.982-2.03560.1652220.13324292X-RAY DIFFRACTION97
2.0356-2.09550.15052500.13264271X-RAY DIFFRACTION97
2.0955-2.1630.15821910.13634362X-RAY DIFFRACTION97
2.163-2.24030.15572260.13534331X-RAY DIFFRACTION97
2.2403-2.32990.15142300.144273X-RAY DIFFRACTION97
2.3299-2.43590.17052470.14694312X-RAY DIFFRACTION97
2.4359-2.56420.17881990.15424360X-RAY DIFFRACTION97
2.5642-2.72470.17552340.15784391X-RAY DIFFRACTION98
2.7247-2.93470.15872140.15124356X-RAY DIFFRACTION98
2.9347-3.22950.15722540.1474364X-RAY DIFFRACTION98
3.2295-3.69540.16092340.1334385X-RAY DIFFRACTION98
3.6954-4.65070.13162370.12264384X-RAY DIFFRACTION99
4.6507-24.59840.16512050.14924417X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8195-0.21560.00760.87270.28340.8379-0.0049-0.04710.0083-0.0042-0.03250.0992-0.0121-0.051-00.0428-0.00470.00790.05230.00360.0479-2.1446-10.335831.2645
20.5156-0.0336-0.16560.7048-0.01110.41450.04410.0322-0.1519-0.1318-0.0077-0.20150.10620.1462-00.13390.03480.01350.135-0.01280.145915.7777-28.470919.7325
30.89860.3543-0.10170.6929-0.15130.6372-0.04730.046-0.0151-0.0260.028-0.0376-0.02290.007500.04230.0054-0.00320.03860.00050.036622.78551.19767.1001
40.77680.2822-0.05740.7031-0.02620.219-0.01750.0366-0.096-0.02290.06230.10790.0357-0.035300.0809-0.0031-0.00050.08450.01520.09712.3565-15.815175.6152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 28:350)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 351:470)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 28:350)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 351:470)

+
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