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- PDB-1jd9: CRYSTAL STRUCTURE ANALYSIS OF THE MUTANT K300Q OF PSEUDOALTEROMON... -

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Basic information

Entry
Database: PDB / ID: 1jd9
TitleCRYSTAL STRUCTURE ANALYSIS OF THE MUTANT K300Q OF PSEUDOALTEROMONAS HALOPLANCTIS ALPHA-AMYLASE
ComponentsALPHA-AMYLASE
KeywordsHYDROLASE / ALPHA-BETA BARREL / GLYCOSYL HYDROLASE / ALLOSTERIC ACTIVATION
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / 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 / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudoalteromonas haloplanktis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsAghajari, N. / Haser, R.
Citation
Journal: PROTEIN SCI. / Year: 2002
Title: Structural basis of alpha-amylase activation by chloride
Authors: Aghajari, N. / Feller, G. / Gerday, C. / Haser, R.
#1: Journal: Structure / Year: 1998
Title: Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level
Authors: Aghajari, N. / Feller, G. / Gerday, C. / Haser, R.
#2: Journal: Protein Sci. / Year: 1998
Title: Crystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor
Authors: Aghajari, N. / Feller, G. / Gerday, C. / Haser, R.
History
DepositionJun 13, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)49,4202
Polymers49,3801
Non-polymers401
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.500, 138.400, 115.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1429-

HOH

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Components

#1: Protein ALPHA-AMYLASE


Mass: 49379.789 Da / Num. of mol.: 1 / Mutation: K300Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas haloplanktis (bacteria)
Strain: A23 / Gene: AMY / Plasmid: PAH12WT / Gene (production host): HB101 / Production host: Escherichia coli (E. coli) / References: UniProt: P29957, alpha-amylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, Hepes, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 29, 1997 / Details: collimator
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→43.03 Å / Num. all: 16759 / Num. obs: 16759 / % possible obs: 81.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 3.4 % / Biso Wilson estimate: 32.92 Å2 / Rmerge(I) obs: 0.216 / Net I/σ(I): 3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.564 / Num. unique all: 1146 / % possible all: 39.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLOR3.843refinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1AQH

1aqh


Resolution: 2.5→42.7 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1680 -random
Rwork0.18 ---
all-16727 --
obs-16727 82.4 %-
Refinement stepCycle: LAST / Resolution: 2.5→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3443 0 1 190 3634
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.267
LS refinement shellResolution: 2.5→2.53 Å /
RfactorNum. reflection
Rfree0.364 23
Rwork0.335 -
obs-205

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