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- PDB-1wp6: Crystal structure of maltohexaose-producing amylase from alkaloph... -

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Basic information

Entry
Database: PDB / ID: 1wp6
TitleCrystal structure of maltohexaose-producing amylase from alkalophilic Bacillus sp.707.
ComponentsGlucan 1,4-alpha-maltohexaosidase
KeywordsHYDROLASE / Alpha-Amylase / Maltohexaose
Function / homology
Function and homology information


glucan 1,4-alpha-maltohexaosidase / glucan 1,4-alpha-maltohexaosidase activity / starch catabolic process / alpha-amylase activity / calcium ion binding / extracellular region
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 / 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, thermostable / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / Alpha amylase / 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
PHOSPHATE ION / Glucan 1,4-alpha-maltohexaosidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKanai, R. / Haga, K. / Akiba, T. / Yamane, K. / Harata, K.
Citation
Journal: Biochemistry / Year: 2004
Title: Biochemical and crystallographic analyses of maltohexaose-producing amylase from alkalophilic Bacillus sp. 707
Authors: Kanai, R. / Haga, K. / Akiba, T. / Yamane, K. / Harata, K.
#1: Journal: Appl.Microbiol.Biotechnol. / Year: 1988
Title: Cloning of a gene for maltohexaose producing amylase of an alkalophilic Bacillus and hyper-production of the enzyme in Bacillus subtilis cells
Authors: Kimura, K. / Tsukamoto, A. / Ishii, Y. / Takano, T. / Yamane, K.
History
DepositionAug 31, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucan 1,4-alpha-maltohexaosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7997
Polymers55,4391
Non-polymers3606
Water5,080282
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.620, 82.800, 127.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glucan 1,4-alpha-maltohexaosidase / G6-amylase / Maltohexaose-producing amylase / Exo-maltohexaohydrolase


Mass: 55438.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: 707 / Plasmid: pTUB812 / Production host: Bacillus subtilis (bacteria) / Strain (production host): 207-25
References: UniProt: P19571, glucan 1,4-alpha-maltohexaosidase

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Non-polymers , 5 types, 288 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: MPD, TrisHCl, Ammonium Phosphate, Calcium chloride, Sodium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 33308 / Num. obs: 33010 / % possible obs: 99.6 % / Observed criterion σ(I): 12.8 / Redundancy: 2.6 % / Rmerge(I) obs: 0.091
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 1.65 % / Rmerge(I) obs: 0.248 / % possible all: 97.8

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BVN

1bvn


Resolution: 2.1→6 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 2583 -RANDOM
Rwork0.1658 ---
all-27718 --
obs-26098 90.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3893 0 17 282 4192
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_deg23.48
X-RAY DIFFRACTIONc_improper_deg0.688
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
2.1-2.230.2293800.176385681.4
2.23-2.390.2324290.167408585.8
2.39-2.610.2283920.166423589.6
2.61-2.950.2334440.177442692.7
2.95-3.580.2094630.17466096.9
3.58-60.1834750.155483698.1

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