[English] 日本語
Yorodumi
- PDB-4aee: CRYSTAL STRUCTURE OF MALTOGENIC AMYLASE FROM S.MARINUS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aee
TitleCRYSTAL STRUCTURE OF MALTOGENIC AMYLASE FROM S.MARINUS
ComponentsALPHA AMYLASE, CATALYTIC REGIONAlpha-amylase
KeywordsHYDROLASE / HYPERTHERMOSTABLE / CYCLODEXTRIN HYDROLASE / GH13
Function / homology
Function and homology information


catalytic activity / carbohydrate metabolic process
Similarity search - Function
Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily ...Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Alpha amylase, catalytic region
Similarity search - Component
Biological speciesSTAPHYLOTHERMUS MARINUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsJung, T.Y. / Park, C.H. / Yoon, S.M. / Park, S.H. / Park, K.H. / Woo, E.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Association of Novel Domain in Active Site of Archaic Hyperthermophilic Maltogenic Amylase from Staphylothermus Marinus.
Authors: Jung, T.Y. / Li, D. / Park, J.T. / Yoon, S.M. / Tran, P.L. / Oh, B.H. / Janecek, S. / Park, S.G. / Woo, E.J. / Park, K.H.
History
DepositionJan 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALPHA AMYLASE, CATALYTIC REGION
B: ALPHA AMYLASE, CATALYTIC REGION


Theoretical massNumber of molelcules
Total (without water)165,1522
Polymers165,1522
Non-polymers00
Water5,368298
1
A: ALPHA AMYLASE, CATALYTIC REGION


Theoretical massNumber of molelcules
Total (without water)82,5761
Polymers82,5761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA AMYLASE, CATALYTIC REGION


Theoretical massNumber of molelcules
Total (without water)82,5761
Polymers82,5761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.394, 117.512, 199.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ALPHA AMYLASE, CATALYTIC REGION / Alpha-amylase


Mass: 82575.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOTHERMUS MARINUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MC1061
References: UniProt: A3DM60, glucan 1,4-alpha-maltohydrolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.32 Å3/Da / Density % sol: 46.98 % / Description: NONE
Crystal growpH: 6.5
Details: 12% PEG 4K, 2% ISO-PROPANOL, 0.1 M ADA PH 6.5, 0.1 M LITHIUM SULFATE

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→49.55 Å / Num. obs: 65614 / % possible obs: 85.6 % / Observed criterion σ(I): 2.13 / Redundancy: 8.2 % / Biso Wilson estimate: 34.35 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 37.12
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.19 / % possible all: 72.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→49.554 Å / SU ML: 0.28 / σ(F): 2.13 / Phase error: 23.23 / Stereochemistry target values: ML
Details: IN BOTH CHAIN A AND B, THE RESIDUES FROM 656-659 AND 671-678 REGIONS ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2379 3087 5.1 %
Rwork0.1847 --
obs0.1874 60614 85.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.207 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 4.54 Å2
Baniso -1Baniso -2Baniso -3
1-12.6395 Å20 Å20 Å2
2---8.0802 Å20 Å2
3----4.5593 Å2
Refinement stepCycle: LAST / Resolution: 2.28→49.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11474 0 0 298 11772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212256
X-RAY DIFFRACTIONf_angle_d1.11616085
X-RAY DIFFRACTIONf_dihedral_angle_d15.3834479
X-RAY DIFFRACTIONf_chiral_restr0.0771663
X-RAY DIFFRACTIONf_plane_restr0.0042047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.36150.29812720.22354820X-RAY DIFFRACTION73
2.3615-2.4560.30292830.20724919X-RAY DIFFRACTION74
2.456-2.56780.25232920.1934950X-RAY DIFFRACTION75
2.5678-2.70320.28952760.19735162X-RAY DIFFRACTION78
2.7032-2.87250.25852800.19385415X-RAY DIFFRACTION81
2.8725-3.09430.25962840.19675813X-RAY DIFFRACTION86
3.0943-3.40560.24263350.18916215X-RAY DIFFRACTION93
3.4056-3.89820.24343270.17766553X-RAY DIFFRACTION97
3.8982-4.91070.21023440.15616698X-RAY DIFFRACTION98
4.9107-49.56610.21233940.19466982X-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