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- PDB-4mb1: The Structure of MalL mutant enzyme G202P from Bacillus subtilus -

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Basic information

Entry
Database: PDB / ID: 4mb1
TitleThe Structure of MalL mutant enzyme G202P from Bacillus subtilus
ComponentsOligo-1,6-glucosidase 1
KeywordsHYDROLASE / TIM barrel / alpha glucosidase
Function / homology
Function and homology information


oligo-1,6-glucosidase activity / oligo-1,6-glucosidase / 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: 1.4 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 19, 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)66,3653
Polymers66,2031
Non-polymers1622
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.500, 101.070, 61.850
Angle α, β, γ (deg.)90.000, 112.860, 90.000
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: 66203.242 Da / Num. of mol.: 1 / Mutation: G202P
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: 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-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris pH 7.5, 24% (w/v) PEG 4000, 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: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.4→56.992 Å / Num. all: 107544 / Num. obs: 104533 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.4-1.4270.5843.335437504294.9
7.67-20.666.40.04335.6423165795.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.69 Å
Translation2.5 Å44.69 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.1.27data scaling
PHASER2.3.0phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→20.67 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.772 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 5251 5 %RANDOM
Rwork0.173 ---
all0.1744 109746 --
obs0.1744 104495 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.27 Å2 / Biso mean: 10.8088 Å2 / Biso min: 2.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å2-0.18 Å2
2--0.67 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4613 0 9 498 5120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0194788
X-RAY DIFFRACTIONr_bond_other_d0.0010.024352
X-RAY DIFFRACTIONr_angle_refined_deg2.1421.9376493
X-RAY DIFFRACTIONr_angle_other_deg0.962310038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8295571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24324.5260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40615824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7991527
X-RAY DIFFRACTIONr_chiral_restr0.1420.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215481
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021166
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 353 -
Rwork0.235 7169 -
all-7522 -
obs--94.69 %
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)
10.5558-0.16180.21920.799-0.41070.68310.03660.0154-0.08020.0279-0.00520.04290.0513-0.0067-0.03140.072-0.00270.01190.0011-0.00670.0779-3.6587-15.9826.8146
22.7496-0.76352.11987.90254.2636.6062-0.05870.0619-0.04180.56450.2465-0.91060.11660.4423-0.18780.1285-0.0048-0.08260.1471-0.01150.228520.2469-13.684139.2847
30.39440.44670.53594.26752.65583.8413-0.0291-0.0027-0.0160.03890.1227-0.2967-0.09320.4415-0.09360.09240.0138-0.00020.09220.00760.131914.3488-16.742628.5404
40.50820.20380.0360.7648-0.13180.66550.02380.0066-0.03130.0097-0.0251-0.07690.02520.07920.00130.06190.00510.0130.02360.00040.06466.7076-1.512416.6449
51.8149-0.16880.94150.2399-0.14291.03550.0059-0.10510.08450.0847-0.01070.0104-0.0895-0.03090.00480.0965-0.00130.03190.0106-0.00920.0753-5.92487.357128.3159
62.419-0.4086-0.75010.72710.39320.9623-0.04160.2427-0.0864-0.06370.0173-0.01660.0436-0.03980.02420.10470.0020.01370.04840.01660.05154.56383.63140.902
72.0927-0.3587-0.69581.23630.07342.3594-0.00320.12990.0552-0.11920.0751-0.1204-0.05360.0314-0.07190.1048-0.00820.02480.05750.01170.086111.8110.0306-4.2346
86.5699-1.73463.49090.4731-0.92441.870.54390.9266-0.5635-0.1308-0.21940.24160.21670.4113-0.32450.74290.16970.12580.80390.07360.63117.537415.8557-8.6295
91.8262-0.4559-1.02463.15584.73927.2201-0.00960.2110.0146-0.21930.1434-0.0507-0.28930.1543-0.13380.1286-0.00840.00650.0710.02560.12039.121113.2525-2.8565
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 206
2X-RAY DIFFRACTION2A207 - 214
3X-RAY DIFFRACTION3A215 - 240
4X-RAY DIFFRACTION4A241 - 388
5X-RAY DIFFRACTION5A389 - 452
6X-RAY DIFFRACTION6A453 - 500
7X-RAY DIFFRACTION7A501 - 537
8X-RAY DIFFRACTION8A538 - 543
9X-RAY DIFFRACTION9A544 - 559

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