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- PDB-3bcd: Alpha-amylase B in complex with maltotetraose and alpha-cyclodextrin -

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Basic information

Entry
Database: PDB / ID: 3bcd
TitleAlpha-amylase B in complex with maltotetraose and alpha-cyclodextrin
ComponentsAlpha amylase, catalytic region
KeywordsHYDROLASE / alpha-amylase / maltotetraose / alpha-cyclodextrin / thermostable / halophilic / N domain / raw starch binding
Function / homology
Function and homology information


glucan 1,4-alpha-maltohexaosidase / glucan 1,4-alpha-maltohexaosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #140 / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / Immunoglobulin-like - #1220 / Copper resistance protein CopC/internalin, immunoglobulin-like / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Elongation Factor Tu (Ef-tu); domain 3 ...Elongation Factor Tu (Ef-tu); domain 3 - #140 / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / Immunoglobulin-like - #1220 / Copper resistance protein CopC/internalin, immunoglobulin-like / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Elongation Factor Tu (Ef-tu); domain 3 / Glycosyl hydrolase, all-beta / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltotetraose / alpha-cyclodextrin / Alpha amylase / :
Similarity search - Component
Biological speciesHalothermothrix orenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsTan, T.-C. / Mijts, B.N. / Swaminathan, K. / Patel, B.K.C. / Divne, C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structure of the Polyextremophilic alpha-Amylase AmyB from Halothermothrix orenii: Details of a Productive Enzyme-Substrate Complex and an N Domain with a Role in Binding Raw Starch
Authors: Tan, T.-C. / Mijts, B.N. / Swaminathan, K. / Patel, B.K.C. / Divne, C.
History
DepositionNov 12, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Alpha amylase, catalytic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,20812
Polymers68,5811
Non-polymers2,62811
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)228.700, 78.050, 50.640
Angle α, β, γ (deg.)90.00, 98.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha amylase, catalytic region / amyb


Mass: 68580.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothermothrix orenii (bacteria) / Strain: H 168 / Gene: amyb / Plasmid: pET-19B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q2ADF2, UniProt: B8CZ54*PLUS, alpha-amylase

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Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide Cyclohexakis-(1-4)-(alpha-D-glucopyranose) / alpha-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: alpha-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,6,6/[a2122h-1a_1-5]/1-1-1-1-1-1/a1-f4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0

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Non-polymers , 3 types, 267 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M sodium acetate, 0.1M Mes-OH, 20% (w/v) PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0412 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 27, 2007 / Details: mirrors
RadiationMonochromator: Bent germanium crystal, horizontally focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0412 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 47080 / Num. obs: 47080 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.057 / Net I/σ(I): 18
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.463 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3BC9

3bc9


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 12.833 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24008 898 2 %RANDOM
Rwork0.19595 ---
obs0.19685 43089 98.15 %-
all-43089 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.137 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.38 Å2
2--1.16 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4747 0 164 259 5170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225089
X-RAY DIFFRACTIONr_bond_other_d0.0010.023271
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.9626903
X-RAY DIFFRACTIONr_angle_other_deg1.59737932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.775585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66725.055273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55615751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6891520
X-RAY DIFFRACTIONr_chiral_restr0.1150.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025596
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021053
X-RAY DIFFRACTIONr_nbd_refined0.2180.2964
X-RAY DIFFRACTIONr_nbd_other0.2070.23396
X-RAY DIFFRACTIONr_nbtor_refined0.1950.22474
X-RAY DIFFRACTIONr_nbtor_other0.0950.22499
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2252
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0440.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2990.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1710.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0131.52934
X-RAY DIFFRACTIONr_mcbond_other0.2281.51199
X-RAY DIFFRACTIONr_mcangle_it1.49324670
X-RAY DIFFRACTIONr_scbond_it2.35232278
X-RAY DIFFRACTIONr_scangle_it3.5264.52233
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 78 -
Rwork0.268 3106 -
obs--97.97 %
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)
111.9639-9.1864-1.444712.02871.092.80160.2751-0.03570.5943-0.5385-0.1425-0.7649-0.8960.2244-0.13270.11590.040.03220.0464-0.0077-0.09282.54945.436929.6919
21.1923-1.4794-0.10742.45880.33382.6285-0.1-0.1167-0.07430.2246-0.0210.1010.0015-0.26920.121-0.0252-0.04170.01820.0846-0.0165-0.01080.6197-4.689536.3655
32.7096-3.0528-0.43035.83760.50311.90590.1513-0.1281-0.1136-0.1353-0.05070.2105-0.1622-0.287-0.10070.00590.00330.02970.09090.0088-0.0384-1.7338-1.116836.163
49.6746-5.929-3.41533.74741.6323.0726-0.2747-0.55210.20050.28230.2822-0.05520.26030.4088-0.00750.0221-0.049-0.01010.05750.00560.084221.352-15.048229.5063
51.88080.0916-0.69643.9523-1.21650.9740.4236-0.41710.36680.1664-0.38840.5647-0.20740.2263-0.03520.0265-0.10440.06570.0099-0.18190.071331.59959.049121.9412
64.43982.1555-1.45234.9065-1.121911.70850.4055-0.5710.05520.5001-0.41270.06940.08070.2640.0071-0.0332-0.11590.00270.0396-0.1247-0.022433.119-1.063626.1735
71.15490.9483-1.10891.5479-0.21452.32240.3095-0.53420.30540.216-0.28830.1187-0.21830.3561-0.02120.0524-0.1883-0.01420.0457-0.13360.042945.05110.878621.6818
82.67872.2977-1.30942.2817-1.11481.3409-0.10880.1223-0.0178-0.01030.09590.1031-0.10020.30460.01290.0155-0.0899-0.0432-0.0059-0.0910.11752.973118.1864-2.1111
90.45060.7697-0.84752.3521-0.7692.03860.1224-0.02610.06040.0075-0.10390.1277-0.21980.5417-0.0184-0.0363-0.1157-0.01760.0657-0.06010.098154.754116.69091.8692
103.03411.28130.60811.6246-1.13422.3172-0.0906-0.0898-0.040.0139-0.0164-0.056-0.07270.39130.107-0.0236-0.0406-0.02360.0088-0.07260.048652.10314.56718.1645
110.6977-1.2270.65152.5546-2.7677.6692-0.1233-0.16580.1251-0.0223-0.1091-0.2270.0570.3590.2324-0.02770.0045-0.04470.018-0.02990.102352.1889-2.9997.3967
129.377-3.48287.65562.4145-4.85729.8678-0.3127-0.39960.3005-0.18770.0723-0.2620.3716-0.24770.24040.034-0.0159-0.0206-0.0771-0.04890.025341.4929-3.13928.5083
132.79910.47780.2391.2718-1.88873.40660.10030.2280.0419-0.018-0.0634-0.14380.3666-0.1843-0.03690.03180.0087-0.0034-0.0227-0.04260.072740.7131-7.62741.1138
141.34350.7330.05710.49940.24840.4767-0.114-0.03680.04170.00940.0882-0.15760.2158-0.2790.02570.029-0.0455-0.00190.0139-0.01680.043725.5325-9.37081.7754
151.0211-0.38320.69552.8445-2.37712.13180.1322-0.15970.1676-0.1423-0.13870.0063-0.18720.10420.00650.0928-0.07730.0002-0.0469-0.08950.11529.26914.77637.2575
161.13490.566-0.34182.1895-0.80451.7180.1609-0.27590.03930.0337-0.0346-0.0398-0.0959-0.2474-0.1263-0.0031-0.0508-0.0051-0.0155-0.0640.061323.3553-2.253815.9529
170.93670.86-2.87850.7895-2.64278.8459-0.2523-0.58910.00880.07090.1914-0.25480.2645-0.13970.0609-0.0134-0.0181-0.03770.0772-0.02990.06425.5393-14.035522.8601
180.8262-0.84632.11532.2923-3.44139.3186-0.16060.0703-0.3229-0.00380.19080.12930.36590.0794-0.03030.0441-0.05590.0264-0.0356-0.03750.06421.0425-21.127712.5064
191.6617-0.29220.50081.6543-0.88272.3989-0.1753-0.079-0.0958-0.03550.15470.07560.3904-0.53170.02070.0115-0.10720.01710.0570.0040.026210.9667-19.450616.2208
203.4474-1.74451.23283.0606-1.88091.6873-0.1306-0.0409-0.16690.23590.123-0.01890.048-0.56810.00760.0356-0.10040.02480.1624-0.007-0.03511.7414-16.204915.8966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 2715 - 27
2X-RAY DIFFRACTION2AA28 - 6428 - 64
3X-RAY DIFFRACTION3AA65 - 10365 - 103
4X-RAY DIFFRACTION4AA104 - 120104 - 120
5X-RAY DIFFRACTION5AA121 - 153121 - 153
6X-RAY DIFFRACTION6AA154 - 169154 - 169
7X-RAY DIFFRACTION7AA170 - 226170 - 226
8X-RAY DIFFRACTION8AA227 - 258227 - 258
9X-RAY DIFFRACTION9AA259 - 308259 - 308
10X-RAY DIFFRACTION10AA309 - 350309 - 350
11X-RAY DIFFRACTION11AA351 - 373351 - 373
12X-RAY DIFFRACTION12AA374 - 383374 - 383
13X-RAY DIFFRACTION13AA384 - 405384 - 405
14X-RAY DIFFRACTION14AA406 - 437406 - 437
15X-RAY DIFFRACTION15AA438 - 459438 - 459
16X-RAY DIFFRACTION16AA460 - 496460 - 496
17X-RAY DIFFRACTION17AA497 - 506497 - 506
18X-RAY DIFFRACTION18AA507 - 537507 - 537
19X-RAY DIFFRACTION19AA538 - 576538 - 576
20X-RAY DIFFRACTION20AA577 - 599577 - 599

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