[English] 日本語
Yorodumi
- PDB-2x8t: Crystal Structure of the Abn2 H318A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x8t
TitleCrystal Structure of the Abn2 H318A mutant
ComponentsENDO-ALPHA-1,5-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 ...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
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: 1.79 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 1.3Sep 25, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / reflns
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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 "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-ARABINANASE
B: ENDO-ALPHA-1,5-ARABINANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,26312
Polymers105,5722
Non-polymers69110
Water8,809489
1
A: ENDO-ALPHA-1,5-ARABINANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0725
Polymers52,7861
Non-polymers2864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDO-ALPHA-1,5-ARABINANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1917
Polymers52,7861
Non-polymers4056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.800, 57.370, 85.480
Angle α, β, γ (deg.)82.10, 88.21, 63.61
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 52786.117 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

-
Non-polymers , 7 types, 499 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 318 TO ALA ENGINEERED RESIDUE IN CHAIN B, HIS 318 TO ALA

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.36 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / Details: 65% MPD 100 mM Tris pH 8.5

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.79→46.5 Å / Num. obs: 76283 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 13.42 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.7
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.3 / % possible all: 72.2

-
Processing

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

2x8f


Resolution: 1.79→31.79 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 18.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 3664 5.1 %
Rwork0.158 --
obs0.16 72418 92.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.18 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0122 Å20.6967 Å2-2.2925 Å2
2---2.497 Å2-3.5842 Å2
3---3.5092 Å2
Refinement stepCycle: LAST / Resolution: 1.79→31.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6999 0 39 489 7527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017404
X-RAY DIFFRACTIONf_angle_d1.18510059
X-RAY DIFFRACTIONf_dihedral_angle_d17.8652652
X-RAY DIFFRACTIONf_chiral_restr0.0891034
X-RAY DIFFRACTIONf_plane_restr0.0051311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7933-1.81370.29681470.24692402X-RAY DIFFRACTION47
1.8137-1.8350.23221810.21133448X-RAY DIFFRACTION67
1.835-1.85740.25851850.21243878X-RAY DIFFRACTION73
1.8574-1.88090.25152080.21434168X-RAY DIFFRACTION82
1.8809-1.90560.25572730.20864866X-RAY DIFFRACTION94
1.9056-1.93180.26152340.18744989X-RAY DIFFRACTION95
1.9318-1.95930.22362380.18674847X-RAY DIFFRACTION94
1.9593-1.98860.22092660.18315070X-RAY DIFFRACTION95
1.9886-2.01970.21642460.174799X-RAY DIFFRACTION96
2.0197-2.05280.21742310.16465059X-RAY DIFFRACTION96
2.0528-2.08820.19332940.16624876X-RAY DIFFRACTION95
2.0882-2.12610.20052530.1584983X-RAY DIFFRACTION96
2.1261-2.1670.20512760.15284940X-RAY DIFFRACTION96
2.167-2.21120.19612830.15265001X-RAY DIFFRACTION97
2.2112-2.25930.18133190.15814860X-RAY DIFFRACTION96
2.2593-2.31180.21652250.15865051X-RAY DIFFRACTION96
2.3118-2.36960.18262540.14785002X-RAY DIFFRACTION97
2.3696-2.43370.18182700.15914999X-RAY DIFFRACTION97
2.4337-2.50530.20342840.16055008X-RAY DIFFRACTION97
2.5053-2.58610.20392730.16535046X-RAY DIFFRACTION97
2.5861-2.67850.21832460.16224956X-RAY DIFFRACTION97
2.6785-2.78570.19292380.16265015X-RAY DIFFRACTION97
2.7857-2.91230.2022810.15955088X-RAY DIFFRACTION97
2.9123-3.06580.18212490.15215061X-RAY DIFFRACTION97
3.0658-3.25770.15222540.14725017X-RAY DIFFRACTION97
3.2577-3.50890.16082620.12915024X-RAY DIFFRACTION97
3.5089-3.86150.12843190.12155032X-RAY DIFFRACTION97
3.8615-4.4190.13793190.12315008X-RAY DIFFRACTION97
4.419-5.56260.162570.13734997X-RAY DIFFRACTION97
5.5626-31.79710.18862740.17864988X-RAY DIFFRACTION96
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)
10.1745-0.0975-0.05850.3979-0.15390.2029-0.0182-0.03020.0098-0.0094-0.0165-0.0948-0.0040.01430.04760.0326-0.0039-0.00570.0426-0.00280.04720.041210.593730.3744
20.10320.0303-0.10650.11970.00670.1887-0.06120.0460.0034-0.01960.02380.07420.0831-0.04830.0033-0.01530.0140.0035-0.0105-0.0086-0.0302-24.4813-1.015965.8662
30.1310.1322-0.1010.1957-0.06170.1760.04020.00420.0912-0.07820.02270.1316-0.0377-0.0722-0.03620.01440.0402-0.02670.00420.01780.0532-17.661528.893918.8654
40.1909-0.1323-0.01990.19530.08240.1251-0.0072-0.01060.07380.02590.0365-0.07680.00790.024-0.02970.0206-0.00050.00160.0172-0.0110.0311-4.309816.062174.6292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 30:350)
2X-RAY DIFFRACTION2CHAIN B AND (RESID 30:350)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 351:469)
4X-RAY DIFFRACTION4CHAIN B AND (RESID 351:469)

+
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