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- PDB-5a2c: Crystal Structure of Anoxybacillus Alpha-amylase Provides Insight... -

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Basic information

Entry
Database: PDB / ID: 5a2c
TitleCrystal Structure of Anoxybacillus Alpha-amylase Provides Insights into a New Glycosyl Hydrolase Subclass
ComponentsALPHA-AMYLASE
KeywordsHYDROLASE / CALCIUM-BINDING SITE / GEOBACILLUS / GLYCOSYL HYDROLASE
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / membrane
Similarity search - Function
: / Alpha-amylase C-terminal domain / 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 ...: / Alpha-amylase C-terminal domain / 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
alpha-maltose / alpha-amylase
Similarity search - Component
Biological speciesANOXYBACILLUS SP. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNg, C.L. / Chai, K.P. / Othman, N.F. / Teh, A.H. / Ho, K.L. / Chan, K.G. / Goh, K.M.
CitationJournal: Sci.Rep. / Year: 2016
Title: Crystal Structure of Anoxybacillus Alpha-Amylase Provides Insights Into Maltose Binding of a New Glycosyl Hydrolase Subclass.
Authors: Chai, K.P. / Othman, N.F.B. / Teh, A. / Ho, K.L. / Chan, K. / Shamsir, M.S. / Goh, K.M. / Ng, C.L.
History
DepositionMay 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_conn_angle / 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_atom_id / _atom_site.label_comp_id / _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.type / _pdbx_database_status.status_code_sf / _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_auth_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)58,6676
Polymers58,1641
Non-polymers5035
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.816, 63.532, 122.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALPHA-AMYLASE


Mass: 58164.398 Da / Num. of mol.: 1 / Fragment: TRUNCATED PROTEIN, RESIDUES 24-478
Source method: isolated from a genetically manipulated source
Details: CATALYTIC DOMAIN A WITH TIM BARREL FOLD (RESIDUES 26 TO 139,187 TO 393), DOMAIN B (RESIDUES 140 TO 186), AND DOMAIN C WITH AN ALL-ALPHA-BETA FOLD (RESIDUES 394 TO 475)
Source: (gene. exp.) ANOXYBACILLUS SP. (bacteria) / Strain: SK3-4 / Description: ISOLATED FROM SUNGAI KLAH HOT SPRING MALAYSIA / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I1VWH9, alpha-amylase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSIMILAR TO TASKA-APO. PDB ID 5A2A

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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: 2.27 Å3/Da / Density % sol: 45.7 % / Description: NONE
Crystal growpH: 6.5
Details: THE TASKA-MALTODP3 NAMELY TASKA-T COMPLEXES WAS CRYSTALLIZED USING THE STREAK SEEDING METHOD WITH A COMMERCIALLY AVAILABLE SEEDING TOOL, HAMPTON RESEARCH, USA. THE SEEDING TOOL WAS DIPPED ...Details: THE TASKA-MALTODP3 NAMELY TASKA-T COMPLEXES WAS CRYSTALLIZED USING THE STREAK SEEDING METHOD WITH A COMMERCIALLY AVAILABLE SEEDING TOOL, HAMPTON RESEARCH, USA. THE SEEDING TOOL WAS DIPPED INTO A DROP CONTAINING TASKA-APO,PDB ID 5A2A, CRYSTALS AND STREAKED ON THE DROPS THAT CONSISTED OF 0.3 UL 6 MG/ML TASKA PROTEIN AND 0.3 UL RESERVOIR SOLUTION 0.1 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, AND 18 % W/V POLYETHYLENE GLYCOL 8,000 WITH 20 MM MALTOTRIOSE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.548
DetectorType: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Jul 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.548 Å / Relative weight: 1
ReflectionResolution: 1.9→19.54 Å / Num. obs: 37601 / % possible obs: 96.7 % / Observed criterion σ(I): 1.9 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.9 / % possible all: 86.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E2O

4e2o


Resolution: 1.9→61.49 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.483 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20914 1861 5 %RANDOM
Rwork0.15585 ---
obs0.1585 35690 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.102 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---0.63 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.9→61.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3756 0 27 518 4301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193917
X-RAY DIFFRACTIONr_bond_other_d0.0020.023648
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.955316
X-RAY DIFFRACTIONr_angle_other_deg0.88438409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1385459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82124.143210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06115675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4181524
X-RAY DIFFRACTIONr_chiral_restr0.1150.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02950
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_it1.2921.4881809
X-RAY DIFFRACTIONr_mcbond_other1.2841.4871808
X-RAY DIFFRACTIONr_mcangle_it1.8752.2242262
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9911.752108
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
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 118 -
Rwork0.264 2366 -
obs--87.46 %
Refinement TLS params.Method: refined / Origin x: -14.551 Å / Origin y: -6.582 Å / Origin z: -19.909 Å
111213212223313233
T0.0063 Å20.0045 Å2-0.0024 Å2-0.0191 Å2-0.0037 Å2--0.0056 Å2
L0.7438 °20.0601 °20.4489 °2-0.2451 °2-0.05 °2--0.5197 °2
S0.0027 Å °-0.0012 Å °-0.016 Å °-0.0179 Å °0.0098 Å °-0.0129 Å °0.0008 Å °0.0314 Å °-0.0125 Å °

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