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- PDB-7lv6: The structure of MalL mutant enzyme S536R from Bacillus subtilis -

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Basic information

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


oligo-1,6-glucosidase / oligo-1,6-glucosidase activity / oligosaccharide catabolic process / alpha-amylase activity / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

#1: Protein Oligo-1,6-glucosidase 1 / Sucrase-isomaltase / 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 / Tris


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 / Glycerol


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 / Water


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

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Experimental details

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Experiment

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

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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

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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

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Phasing

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

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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

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