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- PDB-1w9x: Bacillus halmapalus alpha amylase -

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Basic information

Entry
Database: PDB / ID: 1w9x
TitleBacillus halmapalus alpha amylase
ComponentsALPHA AMYLASE
KeywordsHYDROLASE / AMYLASE / ACARBOSE / BACILLUS / GLYCOSIDE HYDROLASE
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / calcium ion binding
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #140 / Alpha-amylase, thermostable / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / 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 ...Elongation Factor Tu (Ef-tu); domain 3 - #140 / Alpha-amylase, thermostable / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / 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 / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBACILLUS HALMAPALUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDavies, G.J. / Brzozowski, A.M. / Dauter, Z. / Rasmussen, M.D. / Borchert, T.V. / Wilson, K.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of a Bacillus Halmapalus Family 13 Alpha-Amylase, Bha, in Complex with an Acarbose-Derived Nonasaccharide at 2.1 A Resolution
Authors: Davies, G.J. / Brzozowski, A.M. / Dauter, Z. / Rasmussen, M.D. / Borchert, T.V. / Wilson, K.S.
History
DepositionOct 20, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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
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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)56,8556
Polymers55,2771
Non-polymers1,5795
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.180, 75.847, 155.230
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: 55276.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ACARBOSE-DERIVED NONASACCHARIDE / Source: (gene. exp.) BACILLUS HALMAPALUS (bacteria) / Production host: BACILLUS SUBTILIS (bacteria) / References: UniProt: O82839*PLUS, alpha-amylase
#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1435.337 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/4,7,6/[a2122h-1b_1-5][a2122h-1a_1-5][a2122m-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2-3-2-2-2-4/a4-b1_b4-c1_c4n2-d1n1*1OC^RC^RC^SC^SN*2/6C=^ZCCO/10$3/5O/4O_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][non_ch_ring]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growpH: 7.5
Details: 30 MGML-1 IN 50 MM IMIDAZOLE, 5 MM CACL2, 25 MM ACARBOSE, PH 7.5 MIXED IN 1:1 RATIO WITH THE WELL SOLUTION CONSISTING OF 0.1 M IMIDAZOLE PH 7.5 100 MM MALTOSE, 5 MM CACL2, AND WITH 18% (W/V) ...Details: 30 MGML-1 IN 50 MM IMIDAZOLE, 5 MM CACL2, 25 MM ACARBOSE, PH 7.5 MIXED IN 1:1 RATIO WITH THE WELL SOLUTION CONSISTING OF 0.1 M IMIDAZOLE PH 7.5 100 MM MALTOSE, 5 MM CACL2, AND WITH 18% (W/V) MONOMETHYLETHER POLYETHYLENE GLYCOL 5K AS PRECIPITANT.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 30048 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E3X

1e3x


Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.781 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 699 2.1 %RANDOM
Rwork0.151 ---
obs0.152 33201 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2--1.2 Å20 Å2
3----2.26 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3908 0 102 290 4300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214138
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9235646
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2265480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69624.381226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67815604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7591520
X-RAY DIFFRACTIONr_chiral_restr0.1050.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023252
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21659
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22767
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2226
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.29
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8731.52376
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65323810
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.68331894
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0154.51836
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.244 41
Rwork0.193 2334

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