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- PDB-4m56: The Structure of Wild-type MalL from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 4m56
TitleThe Structure of Wild-type MalL from Bacillus subtilis
ComponentsOligo-1,6-glucosidase 1Sucrase-isomaltase
KeywordsHYDROLASE / TIM barrel / Glucosidase
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 / 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 ...Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / 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 / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
D-glucose / Oligo-1,6-glucosidase 1
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.3 Å
AuthorsHobbs, J.K. / Jiao, W. / Easter, A.D. / Parker, E.J. / Schipper, L.A. / Arcus, V.L.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Change in heat capacity for enzyme catalysis determines temperature dependence of enzyme catalyzed rates.
Authors: Hobbs, J.K. / Jiao, W. / Easter, A.D. / Parker, E.J. / Schipper, L.A. / Arcus, V.L.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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)132,9677
Polymers132,3262
Non-polymers6415
Water16,520917
1
A: Oligo-1,6-glucosidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4353
Polymers66,1631
Non-polymers2722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Oligo-1,6-glucosidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5314
Polymers66,1631
Non-polymers3683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.650, 100.260, 101.490
Angle α, β, γ (deg.)90.00, 103.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 559
2010B1 - 559

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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: 66163.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. 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: Sugar ChemComp-GLO / D-glucose / D-GLUCOSE IN LINEAR FORM / Glucose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 917 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM LiSO4, 20% (w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9536 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.3→98.776 Å / Num. all: 53428 / Num. obs: 51131 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 4.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.372.50.5531.7186.8
9.48-34.192.90.0859197.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.04 Å32.93 Å
Translation6.04 Å32.93 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.1.27data scaling
PHASER2.5.1phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementResolution: 2.3→32.95 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.879 / SU B: 15.141 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.494 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2622 5.1 %RANDOM
Rwork0.187 ---
obs0.19 48488 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å2-0.13 Å2
2--1.62 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9108 0 41 917 10066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199423
X-RAY DIFFRACTIONr_bond_other_d0.0050.028732
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.93912768
X-RAY DIFFRACTIONr_angle_other_deg1.091319845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16551120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53424.402493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.338151583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8191550
X-RAY DIFFRACTIONr_chiral_restr0.0930.21301
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110735
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022279
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 34999 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 178 -
Rwork0.272 3235 -
obs--86.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7291-0.13790.5510.71280.03671.7611-0.0882-0.18090.17110.08190.0671-0.0669-0.21060.0820.02110.04980.00740.00250.0803-0.02440.063436.694211.50346.6528
22.2651-0.29540.06041.82840.56131.9949-0.0705-0.4533-0.0310.27070.05570.0560.0026-0.18590.01480.05190.01110.01980.24660.00790.019425.16496.210616.2663
31.4809-0.06680.38820.6006-0.27951.54120.0297-0.1094-0.18730.010.0081-0.02910.12570.0699-0.03780.0256-0.0040.01910.04750.01540.090628.3676-7.9452-2.0342
42.4536-0.4625-0.23161.98610.95961.9796-0.0293-0.1787-0.23110.0139-0.11110.38490.0278-0.07340.14040.0137-0.01690.02260.1880.06180.17953.9843-8.99630.1932
54.5714-8.35850.501415.2959-0.91080.05920.37910.0751-0.6414-0.8093-0.24511.14430.0437-0.0332-0.1340.1454-0.00450.03380.4830.02840.26673.269-14.7386-6.0616
61.237-0.06190.21650.980.27241.96020.04140.2780.1923-0.1058-0.08080.0698-0.4481-0.38130.03940.14750.14070.01370.3780.03490.041624.980424.160852.2407
71.2779-0.4462-0.37810.9751-0.59392.21080.09510.373-0.0552-0.1037-0.0885-0.0728-0.158-0.1611-0.00660.12670.08460.03340.33970.01890.027335.337116.532141.4375
810.696111.87840.892613.24881.03340.13890.22110.2241-0.72540.3734-0.0019-0.85740.1956-0.058-0.21921.01830.1011-0.19961.05980.02690.371228.137-3.382550.406
91.58210.0841-0.02850.73610.27151.39240.01370.1551-0.07290.0083-0.04790.0410.0458-0.18280.03420.01010.0090.00350.149-0.0150.012934.18847.270564.3161
102.5118-0.1722-0.13231.0127-0.32152.9641-0.0390.1944-0.0403-0.09230.0151-0.1216-0.04180.14850.02380.01550.00670.02130.1629-0.01910.068558.51074.152563.4941
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 214
2X-RAY DIFFRACTION2A215 - 292
3X-RAY DIFFRACTION3A293 - 471
4X-RAY DIFFRACTION4A472 - 538
5X-RAY DIFFRACTION5A539 - 561
6X-RAY DIFFRACTION6B3 - 202
7X-RAY DIFFRACTION7B203 - 288
8X-RAY DIFFRACTION8B289 - 300
9X-RAY DIFFRACTION9B301 - 474
10X-RAY DIFFRACTION10B475 - 561

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