[English] 日本語
Yorodumi
- PDB-5m99: Functional Characterization and Crystal Structure of Thermostable... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m99
TitleFunctional Characterization and Crystal Structure of Thermostable Amylase from Thermotoga petrophila, reveals High Thermostability and an Archaic form of Dimerization
Components(Alpha-amylase) x 2
KeywordsHYDROLASE / Hydrolase Glycosyl hydrolase 13 family alpha amylase activity
Function / homology
Function and homology information


alpha-amylase activity => GO:0004556 / cation binding / alpha-amylase / alpha-amylase activity / carbohydrate metabolic process
Similarity search - Function
Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga petrophila RKU-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.96 Å
AuthorsHameed, U. / Price, I. / Mirza, O.A.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Functional characterization and crystal structure of thermostable amylase from Thermotoga petrophila, reveals high thermostability and an unusual form of dimerization.
Authors: Hameed, U. / Price, I. / Ke, A. / Wilson, D.B. / Mirza, O.
History
DepositionNov 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-amylase
B: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,59831
Polymers119,1402
Non-polymers1,45829
Water18,6461035
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-71 kcal/mol
Surface area35230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.237, 153.237, 143.056
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Alpha-amylase /


Mass: 59627.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga petrophila RKU-1 (bacteria) / Plasmid: a pHIS-parallel1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): codon plus / References: UniProt: A0A059TXD8, alpha-amylase
#2: Protein Alpha-amylase /


Mass: 59513.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga petrophila RKU-1 (bacteria) / Plasmid: pHIS-parallel1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059TXD8, alpha-amylase

-
Non-polymers , 6 types, 1064 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#7: 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
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1035 / 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: 4.07 Å3/Da / Density % sol: 69.78 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris, 1.2 M Na/K tartrate

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.96→50.16 Å / Num. obs: 136221 / % possible obs: 95.6 % / Redundancy: 5.3 % / Net I/σ(I): 16.8
Reflection shellResolution: 1.96→2 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.4 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.96→50.159 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.92
RfactorNum. reflection% reflection
Rfree0.184 1929 1.48 %
Rwork0.152 --
obs0.1525 130271 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→50.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8448 0 84 1035 9567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078966
X-RAY DIFFRACTIONf_angle_d0.99712181
X-RAY DIFFRACTIONf_dihedral_angle_d13.4533230
X-RAY DIFFRACTIONf_chiral_restr0.0451201
X-RAY DIFFRACTIONf_plane_restr0.0051576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9597-2.00870.25081200.23288208X-RAY DIFFRACTION86
2.0087-2.0630.24781330.21598477X-RAY DIFFRACTION89
2.063-2.12370.25771330.2088679X-RAY DIFFRACTION90
2.1237-2.19230.24341350.20198872X-RAY DIFFRACTION93
2.1923-2.27060.24921350.18329110X-RAY DIFFRACTION95
2.2706-2.36150.22321380.17139124X-RAY DIFFRACTION95
2.3615-2.4690.20921390.16999285X-RAY DIFFRACTION97
2.469-2.59920.19011380.16659279X-RAY DIFFRACTION97
2.5992-2.7620.18421460.16669378X-RAY DIFFRACTION98
2.762-2.97520.21211440.16379492X-RAY DIFFRACTION99
2.9752-3.27460.19851450.15639597X-RAY DIFFRACTION100
3.2746-3.74830.17281420.13379552X-RAY DIFFRACTION100
3.7483-4.72190.14161400.11249617X-RAY DIFFRACTION100
4.7219-50.1750.13571410.13099672X-RAY DIFFRACTION99

+
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