[English] 日本語
Yorodumi
- PDB-7lv6: The structure of MalL mutant enzyme S536R from Bacillus subtilis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lv6
TitleThe structure of MalL mutant enzyme S536R from Bacillus subtilis
ComponentsOligo-1,6-glucosidase 1
KeywordsHYDROLASE / TIM barrel / glycoside hydrolase / enzyme design / Rosetta
Function / homology
Function and homology information


oligo-1,6-glucosidase / oligo-1,6-glucosidase activity / alpha-amylase activity / oligosaccharide catabolic process / metal ion binding / cytoplasm
Similarity search - Function
Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Oligo-1,6-glucosidase 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsHamill, C.J. / Prentice, E.J. / Bahl, C.D. / Truebridge, I.S. / Arcus, V.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden Fund16-UOW-027 New Zealand
CitationJournal: To Be Published
Title: Urea binding to guide rational design of mutations that influence enzyme dynamics
Authors: Hamill, C.J. / Arcus, V.L. / Prentice, E.J. / Bahl, C. / Truebridge, I.
History
DepositionFeb 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Oligo-1,6-glucosidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5604
Polymers69,3061
Non-polymers2543
Water14,142785
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-8 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.749, 100.999, 61.749
Angle α, β, γ (deg.)90.000, 113.060, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Oligo-1,6-glucosidase 1 / Dextrin 6-alpha-D-glucanohydrolase / Oligosaccharide alpha-1 / 6-glucosidase 1 / Sucrase-isomaltase ...Dextrin 6-alpha-D-glucanohydrolase / Oligosaccharide alpha-1 / 6-glucosidase 1 / Sucrase-isomaltase 1 / Isomaltase 1


Mass: 69305.555 Da / Num. of mol.: 1 / Mutation: S536R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: malL, yvdL, BSU34560 / Plasmid: pPROEX-Htb / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: O06994, oligo-1,6-glucosidase
#2: 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 785 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris, pH 8.0, 0.2 M ammonium acetate, 18% w/v PEG10000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953735 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953735 Å / Relative weight: 1
ReflectionResolution: 1.1→44.85 Å / Num. obs: 208774 / % possible obs: 94.2 % / Redundancy: 10.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.031 / Rrim(I) all: 0.112 / Net I/σ(I): 12.7 / Num. measured all: 2270037 / Scaling rejects: 1914
Reflection shell

Diffraction-ID: 1 / Resolution: 1.1→1.12 Å

Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
6.90.54895090.8840.2210.59287.1
12.50.07813720.9970.0240.08198.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.36
Highest resolutionLowest resolution
Rotation23.06 Å2 Å

-
Processing

Software
NameVersionClassification
XDSVERSION Nov 1, 2016 BUILT=20161205data reduction
Aimless0.7.4data scaling
MOLREP11.6.04phasing
REFMAC5.8.0238refinement
PHENIX1.18.2refinement
Coot0.8.9.2model building
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4M56

4m56


Resolution: 1.1→33.54 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1451 10435 5 %
Rwork0.1255 198289 -
obs0.1265 208724 94.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.07 Å2 / Biso mean: 16.1338 Å2 / Biso min: 7.2 Å2
Refinement stepCycle: final / Resolution: 1.1→33.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4611 0 30 785 5426
Biso mean--10.96 29.24 -
Num. residues----559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.1-1.110.2412970.2059602786
1.11-1.130.17783200.1697627690
1.13-1.140.18493210.1618637991
1.14-1.150.17073380.1504634691
1.15-1.170.16333190.1455644391
1.17-1.190.15393700.1406639491
1.19-1.20.14683270.1322643092
1.2-1.220.16333200.1334654592
1.22-1.240.16273340.1294640392
1.24-1.260.15733440.128649192
1.26-1.280.14933140.1277656493
1.28-1.30.1513460.1212654393
1.3-1.330.15223700.1212647593
1.33-1.360.14413400.1188660394
1.36-1.390.15563660.1191657694
1.39-1.420.15723300.118659294
1.42-1.450.14233310.1128665095
1.45-1.490.1274020.1091661695
1.49-1.540.1293810.1076667295
1.54-1.590.13073550.108668295
1.59-1.640.13723580.107669296
1.64-1.710.13714060.1106670496
1.71-1.790.13883590.1151677096
1.79-1.880.12843560.1201684497
1.88-20.1433730.1255679497
2-2.150.13593320.1225689897
2.15-2.370.13243590.1215688998
2.37-2.710.14543850.1295688798
2.71-3.420.1593560.1346698599
3.42-33.540.14263260.1271711999

+
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