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- PDB-5wcz: Crystal Structure of Wild-Type MalL from Bacillus subtilis with T... -

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Basic information

Entry
Database: PDB / ID: 5wcz
TitleCrystal Structure of Wild-Type MalL from Bacillus subtilis with TS analogue 1-deoxynojirimycin
ComponentsOligo-1,6-glucosidase 1
KeywordsHYDROLASE / TIM barrel / glucosidase / 1-deoxynojirimycin
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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily ...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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1-DEOXYNOJIRIMYCIN / Oligo-1,6-glucosidase 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsArcus, V.L. / Prentice, E.J.
CitationJournal: Nat Commun / Year: 2018
Title: Dynamical origins of heat capacity changes in enzyme-catalysed reactions.
Authors: van der Kamp, M.W. / Prentice, E.J. / Kraakman, K.L. / Connolly, M. / Mulholland, A.J. / Arcus, V.L.
History
DepositionJul 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: 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 / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)139,0747
Polymers138,4712
Non-polymers6035
Water22,8071266
1
A: Oligo-1,6-glucosidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5834
Polymers69,2351
Non-polymers3473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oligo-1,6-glucosidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4913
Polymers69,2351
Non-polymers2552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.585, 98.835, 101.345
Angle α, β, γ (deg.)90.00, 103.08, 90.00
Int Tables number4
Space group name H-MP1211

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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: 69235.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: malL, yvdL, BSU34560 / Plasmid: pPROEX HTB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O06994, oligo-1,6-glucosidase
#2: Chemical ChemComp-NOJ / 1-DEOXYNOJIRIMYCIN / MORANOLINE


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: inhibitor*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1266 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 10 % (v/v) Tacsimate, 0.1 M MES monohydrate, 25 % (w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.58→46.78 Å / Num. obs: 159542 / % possible obs: 99 % / Redundancy: 9 % / Biso Wilson estimate: 14.63 Å2 / Rsym value: 0.078 / Net I/σ(I): 16.4
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.681 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
SCALA3.3.21data scaling
PDB_EXTRACT3.22data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M56

4m56


Resolution: 1.58→46.778 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1974 8008 5.02 %
Rwork0.1698 --
obs0.1712 159495 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→46.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9061 0 40 1266 10367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069390
X-RAY DIFFRACTIONf_angle_d0.80612723
X-RAY DIFFRACTIONf_dihedral_angle_d7.867700
X-RAY DIFFRACTIONf_chiral_restr0.0551288
X-RAY DIFFRACTIONf_plane_restr0.0061652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5797-1.59770.29682600.26024601X-RAY DIFFRACTION91
1.5977-1.61640.26272710.24644954X-RAY DIFFRACTION97
1.6164-1.63620.31332510.24374910X-RAY DIFFRACTION97
1.6362-1.65690.26452480.23375024X-RAY DIFFRACTION97
1.6569-1.67870.26112520.22964961X-RAY DIFFRACTION98
1.6787-1.70170.27992550.22455011X-RAY DIFFRACTION98
1.7017-1.7260.25682510.2214990X-RAY DIFFRACTION98
1.726-1.75170.26722530.21245009X-RAY DIFFRACTION98
1.7517-1.77910.23012790.20294973X-RAY DIFFRACTION98
1.7791-1.80830.21252650.1995042X-RAY DIFFRACTION98
1.8083-1.83950.2412700.19775033X-RAY DIFFRACTION99
1.8395-1.87290.26122770.20145053X-RAY DIFFRACTION99
1.8729-1.90890.22392590.18535082X-RAY DIFFRACTION99
1.9089-1.94790.21552910.19165008X-RAY DIFFRACTION99
1.9479-1.99030.21482950.18065065X-RAY DIFFRACTION99
1.9903-2.03660.21672790.17765069X-RAY DIFFRACTION100
2.0366-2.08750.19972850.17475038X-RAY DIFFRACTION99
2.0875-2.14390.20262390.17485107X-RAY DIFFRACTION99
2.1439-2.2070.22242740.17515118X-RAY DIFFRACTION100
2.207-2.27830.18942580.16915078X-RAY DIFFRACTION99
2.2783-2.35970.21222870.16955090X-RAY DIFFRACTION100
2.3597-2.45420.18862530.175081X-RAY DIFFRACTION100
2.4542-2.56580.21362490.1695130X-RAY DIFFRACTION100
2.5658-2.70110.19272950.16875095X-RAY DIFFRACTION100
2.7011-2.87030.19792540.16385139X-RAY DIFFRACTION100
2.8703-3.09190.18382580.16065173X-RAY DIFFRACTION100
3.0919-3.4030.17822750.15665127X-RAY DIFFRACTION100
3.403-3.89520.14822460.13755180X-RAY DIFFRACTION100
3.8952-4.90670.1372960.12445117X-RAY DIFFRACTION100
4.9067-46.79860.17562830.155229X-RAY DIFFRACTION100

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