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- PDB-4m8u: The Structure of MalL mutant enzyme V200A from Bacillus subtilus -

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Basic information

Entry
Database: PDB / ID: 4m8u
TitleThe Structure of MalL mutant enzyme V200A from Bacillus subtilus
ComponentsOligo-1,6-glucosidase 1Sucrase-isomaltase
KeywordsHYDROLASE / TIM barrel / alpha 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
Oligo-1,6-glucosidase 1
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 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 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,5387
Polymers66,0071
Non-polymers5316
Water11,025612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.650, 100.330, 61.360
Angle α, β, γ (deg.)90.000, 112.590, 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: 66007.000 Da / Num. of mol.: 1 / Mutation: V200A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU34560, malL, yvdL / Plasmid: pPROEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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.: 4 / 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.: 612 / 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: 2.09 Å3/Da / Density % sol: 41.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris pH 7.5, 22% (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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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: Apr 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 1.45→56.639 Å / Num. all: 95977 / Num. obs: 95401 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 21.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.45-1.4713.40.6314.862646466097.3
7.94-18.9212.70.0548.3713856092.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.45 Å18.92 Å
Translation1.45 Å18.92 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.1.27data scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→27.28 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.1573 / WRfactor Rwork: 0.133 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9251 / SU B: 1.766 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0565 / SU Rfree: 0.0586 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1638 4782 5 %RANDOM
Rwork0.1381 ---
all0.1394 90709 --
obs0.1394 90709 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.39 Å2 / Biso mean: 12.8324 Å2 / Biso min: 4.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.22 Å2
2--0.39 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.45→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4627 0 33 612 5272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194838
X-RAY DIFFRACTIONr_bond_other_d0.0010.024398
X-RAY DIFFRACTIONr_angle_refined_deg2.1121.946556
X-RAY DIFFRACTIONr_angle_other_deg0.947310142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3575578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64324.466262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07515828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2621528
X-RAY DIFFRACTIONr_chiral_restr0.1390.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025526
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021174
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 354 -
Rwork0.187 6541 -
all-6895 -
obs--97.32 %
Refinement TLS params.Method: refined / Origin x: 2.511 Å / Origin y: -5.1573 Å / Origin z: 18.4919 Å
111213212223313233
T0.0039 Å20.0053 Å2-0.0078 Å2-0.0083 Å2-0.0132 Å2--0.0416 Å2
L0.4088 °20.0783 °2-0.059 °2-0.6875 °2-0.3642 °2--0.8988 °2
S0.0228 Å °0.0164 Å °-0.0313 Å °-0.002 Å °-0.0178 Å °-0.016 Å °-0.0312 Å °-0.034 Å °-0.005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 561
2X-RAY DIFFRACTION1A601 - 606
3X-RAY DIFFRACTION1A701 - 1312

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