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- PDB-3dc0: Crystal structure of native alpha-amylase from Bacillus sp. KR-8104 -

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Basic information

Entry
Database: PDB / ID: 3dc0
TitleCrystal structure of native alpha-amylase from Bacillus sp. KR-8104
Componentsalpha-amylase
KeywordsHYDROLASE / native alpha-amylase
Function / homology
Function and homology information


alpha-amylase activity => GO:0004556 / alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Starch-binding module 26 / Starch-binding module 26 / Alpha-amylase, C-terminal domain / Aamy_C / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Starch-binding module 26 / Starch-binding module 26 / Alpha-amylase, C-terminal domain / Aamy_C / Alpha amylase / 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 fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus sp. KR8104 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.78 Å
AuthorsAlikhajeh, J. / Khajeh, K. / Ranjbar, B. / Naderi-Manesh, M. / Naderi-Manesh, H. / Chen, C.J.
CitationJournal: to be published
Title: Crystal structure of native alpha-amylase from Bacillus sp. KR-8104
Authors: Alikhajeh, J. / Khajeh, K. / Ranjbar, B. / Naderi-Manesh, M. / Naderi-Manesh, H. / Chen, C.J.
History
DepositionJun 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7614
Polymers46,6411
Non-polymers1203
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.176, 163.141, 73.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein alpha-amylase /


Mass: 46640.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. KR8104 (bacteria) / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B3GQD0, alpha-amylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 4.53 Å3/Da / Density % sol: 72.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG 8000, 100mM Imidazole, 200mM Ca(OAC)2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Sep 28, 2007
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.78→30 Å / Num. all: 21308 / Num. obs: 20572 / % possible obs: 96.5 % / Redundancy: 4.2 % / Rsym value: 0.115 / Net I/σ(I): 28.2
Reflection shellResolution: 2.78→2.89 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 20572 / Rsym value: 0.115 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementStarting model: 1ua7

1ua7


Resolution: 2.78→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 2002 9.4 %random
Rwork0.1956 ---
all-21308 --
obs-20572 96.5 %-
Solvent computationBsol: 16.382 Å2
Displacement parametersBiso mean: 22.142 Å2
Baniso -1Baniso -2Baniso -3
1-5.862 Å20 Å20 Å2
2--4.336 Å20 Å2
3----10.198 Å2
Refinement stepCycle: LAST / Resolution: 2.78→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 3 142 3435
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.21
LS refinement shell
Resolution (Å)Rfactor RfreeRfactor RworkRefine-IDRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.78-2.890.4160.346X-RAY DIFFRACTION0.992388100
5.76-300.0550.05X-RAY DIFFRACTION1.009257499.8
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param

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