[English] 日本語
Yorodumi
- PDB-8dge: BoGH13ASus from Bacteroides ovatus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dge
TitleBoGH13ASus from Bacteroides ovatus
ComponentsAlpha amylase, catalytic domain proteinAlpha-amylase
KeywordsHYDROLASE / alpha-amylase / starch / GH13 / glycoside hydrolase
Function / homology
Function and homology information


carbohydrate metabolic process
Similarity search - Function
Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
IMIDAZOLE / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Alpha amylase, catalytic domain protein
Similarity search - Component
Biological speciesBacteroides ovatus ATCC 8483 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsBrown, H.A. / DeVeaux, A.L. / Koropatkin, N.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118475 United States
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)AT011278 United States
CitationJournal: Cell.Mol.Life Sci. / Year: 2023
Title: BoGH13A Sus from Bacteroides ovatus represents a novel alpha-amylase used for Bacteroides starch breakdown in the human gut.
Authors: Brown, H.A. / DeVeaux, A.L. / Juliano, B.R. / Photenhauer, A.L. / Boulinguiez, M. / Bornschein, R.E. / Wawrzak, Z. / Ruotolo, B.T. / Terrapon, N. / Koropatkin, N.M.
History
DepositionJun 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha amylase, catalytic domain protein
B: Alpha amylase, catalytic domain protein
C: Alpha amylase, catalytic domain protein
D: Alpha amylase, catalytic domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,837118
Polymers336,2234
Non-polymers7,614114
Water28,1751564
1
A: Alpha amylase, catalytic domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,35735
Polymers84,0561
Non-polymers2,30134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha amylase, catalytic domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,83528
Polymers84,0561
Non-polymers1,77927
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Alpha amylase, catalytic domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,29335
Polymers84,0561
Non-polymers2,23734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Alpha amylase, catalytic domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,35220
Polymers84,0561
Non-polymers1,29619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.387, 148.443, 112.770
Angle α, β, γ (deg.)90.000, 91.000, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Alpha amylase, catalytic domain protein / Alpha-amylase


Mass: 84055.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus ATCC 8483 (bacteria)
Strain: ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153
Gene: BACOVA_03514,Bovatus_03803 / Production host: Escherichia coli (E. coli) / References: UniProt: A7M087

-
Non-polymers , 8 types, 1678 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 91 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1564 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 11% MPD, 11% PEG1000, 11% PEG3350, 0.1 M MES/Imidazole pH 6.5, 0.12M ethylene glycol mix

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97987 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 13, 2019
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97987 Å / Relative weight: 1
ReflectionResolution: 1.89→62 Å / Num. obs: 262849 / % possible obs: 99.7 % / Redundancy: 5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.8
Reflection shellResolution: 1.89→1.96 Å / Rmerge(I) obs: 0.954 / Num. unique obs: 25868 / CC1/2: 0.688

-
Processing

Software
NameVersionClassification
xia2data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M07

3m07


Resolution: 1.89→62 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.421 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.395 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 13119 5 %RANDOM
Rwork0.2091 ---
obs0.2122 249303 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.74 Å2 / Biso mean: 29.055 Å2 / Biso min: 19 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å20.06 Å2
2---0.08 Å2-0 Å2
3----1.43 Å2
Refinement stepCycle: final / Resolution: 1.89→62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22749 0 478 1564 24791
Biso mean--40.49 35.18 -
Num. residues----2842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01323820
X-RAY DIFFRACTIONr_bond_other_d0.0020.01721217
X-RAY DIFFRACTIONr_angle_refined_deg1.291.65532201
X-RAY DIFFRACTIONr_angle_other_deg1.1831.57848860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0852843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43423.9171274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73153615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7521575
X-RAY DIFFRACTIONr_chiral_restr0.0550.23005
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0227191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025735
X-RAY DIFFRACTIONr_rigid_bond_restr0.96345037
LS refinement shellResolution: 1.89→1.938 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.356 942 -
Rwork0.261 17911 -
obs--96.97 %
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)
11.1256-0.28920.1320.3982-0.0360.33190.0001-0.0366-0.14620.01920.01360.01920.09280.0028-0.01370.04360.0115-0.00760.0090.0050.035368.036896.38076.4359
20.96720.13280.47820.31070.16520.55060.02040.0536-0.0274-0.0272-0.02420.02250.03660.00360.00380.0091-0.0005-0.00320.02390.00660.018235.589952.73827.9322
31.14790.3466-0.10920.4414-0.01160.3361-0.01490.04520.1135-0.02560.02820.013-0.0788-0.033-0.01340.0220.0043-0.00550.00660.00960.036326.684190.54749.7808
41.02670.1507-0.47160.3395-0.12310.53020.0140.03120.0323-0.0396-0.0108-0.0167-0.0213-0.0193-0.00320.01310.0059-0.00850.0038-0.00340.023924.796459.9675-28.6634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 758
2X-RAY DIFFRACTION2B45 - 758
3X-RAY DIFFRACTION3C45 - 758
4X-RAY DIFFRACTION4D44 - 757

+
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