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- PDB-5a2a: Crystal Structure of Anoxybacillus Alpha-amylase Provides Insight... -

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Basic information

Entry
Database: PDB / ID: 5a2a
TitleCrystal Structure of Anoxybacillus Alpha-amylase Provides Insights into a New Glycosyl Hydrolase Subclass
ComponentsAPO FORM OF ANOXYBACILLUS ALPHA-AMYLASES
KeywordsHYDROLASE / ANOXYBACILLUS / ALPHA-AMYLASE / 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-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
ACETATE ION / 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 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: APO FORM OF ANOXYBACILLUS ALPHA-AMYLASES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7057
Polymers53,4261
Non-polymers2786
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.429, 63.443, 122.758
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 APO FORM OF ANOXYBACILLUS ALPHA-AMYLASES


Mass: 53426.195 Da / Num. of mol.: 1
Fragment: 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-ALPAH-BETA FOLD (RESIDUES 394 TO 475)
Source method: isolated from a genetically manipulated source
Details: TRUNCATED PROTEIN WITH 23 RESIDUES AT THE N-TERMINUS (1 TO 23) AND 27 RESIDUES AT THE C-TERMINUS (RESIDUES 479 TO 505) REMOVED.
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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#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.: 405 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCOMPARE TO 1VWH9 SEQUENCE, TASKA HAS 23 RESIDUES AT THE N- TERMINUS AND 27 RESIDUES AT THE C- ...COMPARE TO 1VWH9 SEQUENCE, TASKA HAS 23 RESIDUES AT THE N- TERMINUS AND 27 RESIDUES AT THE C-TERMINUS TRUNCATED.

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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: 2.24 Å3/Da / Density % sol: 45.2 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE (PH 6.5) 18% (W/V) POLYETHYLENE GLYCOL 8, 000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV / Date: Jul 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.875
11K, H, -L20.125
ReflectionResolution: 1.95→19.42 Å / Num. obs: 34971 / % possible obs: 98.1 % / Observed criterion σ(I): 2.5 / Redundancy: 2.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.5 / % possible all: 93.4

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Processing

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

4e2o


Resolution: 1.9→19.99 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.883 / SU B: 6.306 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COMPARE TO FULL LENGTH ASKA SEQUENCES, TASKA HAS 23 RESIDUES AT THE N-TERMINUS AND 27 RESIDUES AT THE C- TERMINUS TRUNCATED.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1785 5.1 %RANDOM
Rwork0.17689 ---
obs0.1799 33142 89.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.166 Å2
Baniso -1Baniso -2Baniso -3
1--9.21 Å20 Å20 Å2
2---9.71 Å20 Å2
3---18.92 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3768 0 12 405 4185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193889
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2321.9455270
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2535455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36824.211209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40115668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5951523
X-RAY DIFFRACTIONr_chiral_restr0.1570.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213023
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1060.8731813
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.681.2992263
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5271.0192076
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: 1.895→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0 0 -
obs--0 %
Refinement TLS params.Method: refined / Origin x: 16.51 Å / Origin y: -6.411 Å / Origin z: -19.595 Å
111213212223313233
T0.161 Å20.0029 Å2-0.0057 Å2-0.128 Å20.0044 Å2--0.0022 Å2
L0.5866 °20.0828 °20.368 °2-0.2578 °2-0.0768 °2--0.4193 °2
S0.0011 Å °-0.0222 Å °-0.023 Å °-0.0282 Å °0.0064 Å °-0.0167 Å °-0.0085 Å °0.0205 Å °-0.0075 Å °

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