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- PDB-4e2o: Crystal structure of alpha-amylase from Geobacillus thermoleovora... -

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Basic information

Entry
Database: PDB / ID: 4e2o
TitleCrystal structure of alpha-amylase from Geobacillus thermoleovorans, GTA, complexed with acarbose
ComponentsAlpha-amylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / tim barrel / calcium binding / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


alpha-amylase activity / membrane => GO:0016020 / carbohydrate metabolic process / calcium ion binding
Similarity search - Function
Alpha-amylase-like / 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-amylase-like / 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
Chem-ACI / Alpha-amylase
Similarity search - Component
Biological speciesGeobacillus thermoleovorans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.103 Å
AuthorsMok, S.C. / Teh, A.H. / Saito, J.A. / Najimudin, N. / Alam, M.
CitationJournal: Enzyme.Microb.Technol. / Year: 2013
Title: Crystal structure of a compact alpha-amylase from Geobacillus thermoleovorans.
Authors: Mok, S.C. / Teh, A.H. / Saito, J.A. / Najimudin, N. / Alam, M.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Structure summary
Revision 1.2Jul 23, 2014Group: Database references
Revision 2.0Oct 25, 2017Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _struct_conn.ptnr2_label_atom_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Nov 8, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3896
Polymers53,3461
Non-polymers1,0435
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.960, 122.960, 55.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-amylase


Mass: 53345.980 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 25-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermoleovorans (bacteria) / Strain: CCB_US3_UF5 / Gene: GTCCBUS3UF5_7870 / Plasmid: pET-17xb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: G8N704, alpha-amylase

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DQuipa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122m-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-4,6-deoxy-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-quinovopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DQuipa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122m-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-4,6-deoxy-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 338 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACI / 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL


Mass: 175.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13NO4 / Comment: antibiotic*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 15% PEG 6000, 0.1M sodium citrate, 20mM acarbose, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 1, 2011
RadiationMonochromator: varimax hf / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.07
ReflectionResolution: 2.1→30 Å / Num. obs: 27917 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.37 % / Biso Wilson estimate: 28.638 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.1-2.160.4970.3543.146438208220190.42497
2.16-2.220.4190.2963.786676201020020.35299.6
2.22-2.280.3860.2774.126381193419250.3399.5
2.28-2.350.3160.2255.026358190819030.26899.7
2.35-2.430.3070.2185.186199185318450.25999.6
2.43-2.510.2750.2065.635983178317760.24499.6
2.51-2.610.240.1746.435746171517100.20799.7
2.61-2.710.1950.1527.525624165416500.1899.8
2.71-2.840.1680.1368.585452160416000.16199.8
2.84-2.970.1370.10710.655183152615200.12899.6
2.97-3.130.0970.08713.384971146614560.10399.3
3.13-3.330.0790.07116.044665136913640.08499.6
3.33-3.550.0650.05520.34387130012860.06598.9
3.55-3.840.0490.04723.864052119411840.05699.2
3.84-4.210.0430.04126.583785111311070.04899.5
4.21-4.70.0370.03728.923469102510150.04399
4.7-5.430.0360.03727.7130298918900.04399.9
5.43-6.650.0430.0425.4825707607560.04899.5
6.65-9.40.0320.03329.9120376035940.03998.5
9.40.020.02238.5210313433150.02691.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entrY 7TAA

7taa


Resolution: 2.103→26.926 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.8674 / σ(F): 2 / Phase error: 20.98 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 1407 5.04 %random
Rwork0.1616 ---
obs0.1636 27917 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.367 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 53.44 Å2 / Biso mean: 23.2821 Å2 / Biso min: 10.57 Å2
Baniso -1Baniso -2Baniso -3
1-4.2991 Å2-0 Å2-0 Å2
2--4.2991 Å2-0 Å2
3----8.5982 Å2
Refinement stepCycle: LAST / Resolution: 2.103→26.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3699 0 66 335 4100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073888
X-RAY DIFFRACTIONf_angle_d1.0515282
X-RAY DIFFRACTIONf_chiral_restr0.067558
X-RAY DIFFRACTIONf_plane_restr0.005671
X-RAY DIFFRACTIONf_dihedral_angle_d13.0871424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1034-2.17850.27351390.21842600273993
2.1785-2.26570.23651370.20172631276895
2.2657-2.36870.25661370.19082654279195
2.3687-2.49350.24781380.18832628276695
2.4935-2.64960.21811440.18262658280295
2.6496-2.8540.19841380.18422650278895
2.854-3.14080.20781440.16912655279994
3.1408-3.59440.18961380.14612628276694
3.5944-4.52510.15041430.12552683282694
4.5251-26.92780.16431400.13922726286694

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