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- PDB-1aqm: ALPHA-AMYLASE FROM ALTEROMONAS HALOPLANCTIS COMPLEXED WITH TRIS -

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Basic information

Entry
Database: PDB / ID: 1aqm
TitleALPHA-AMYLASE FROM ALTEROMONAS HALOPLANCTIS COMPLEXED WITH TRIS
ComponentsALPHA-AMYLASE
KeywordsHYDROLASE / ALPHA-AMYLASE / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE / BETA-ALPHA-EIGHT BARREL / PSYCHROPHILIC ENZYME / GLYCOSIDASE INHIBITION
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsAghajari, N. / Haser, R.
Citation
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.
#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: 1996
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Alpha-Amylase from the Antarctic Psychrophile Alteromonas Haloplanctis A23
Authors: Aghajari, N. / Feller, G. / Gerday, C. / Haser, R.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Structure and Molecular Model Refinement of Pig Pancreatic Alpha-Amylase at 2.1 A Resolution
Authors: Qian, M. / Haser, R. / Payan, F.
History
DepositionJul 31, 1997Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / software / 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.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 / _software.name / _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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)49,5794
Polymers49,3811
Non-polymers1983
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.400, 138.900, 115.700
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: 49380.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas haloplanktis (bacteria)
Strain: A23 / Cell line: RR1 / Gene: AMY / Organ: PANCREAS / Cell line (production host): RR1 / 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.91 Å3/Da / Density % sol: 58 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 4, 20 ℃ / Method: vapor diffusion, hanging drop / Details: prtein to mother liquor ration was 2:1 / PH range low: 7.1 / PH range high: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160-70 %MPD1reservoir
20.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→43 Å / Num. obs: 42049 / % possible obs: 85.9 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.085 / Net I/σ(I): 8.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.499 / % possible all: 61.8
Reflection
*PLUS
Num. measured all: 153351 / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 61.8 % / Rmerge(I) obs: 0.499

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Processing

Software
NameVersionClassification
DENZOdata reduction
Agrovatadata reduction
AMoREphasing
X-PLOR3.843refinement
Agrovatadata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PORCINE PANCREAS ALPHA-AMYLASE (QIAN ET AL. J.MOL.BIOL. 231, 785-799 (1993))

Resolution: 1.85→43 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT REFINEMENT HAS BEEN APPLIED THROUGHOUT THE REFINEMENT PROCESS, TOPOLOGY AND PARAMETER INPUTS FOR THE TRIS ARE FOUND IN THE FIVE RESIDUES IN THE C-TERMINAL END OF THE ENZYME ARE ...Details: BULK SOLVENT REFINEMENT HAS BEEN APPLIED THROUGHOUT THE REFINEMENT PROCESS, TOPOLOGY AND PARAMETER INPUTS FOR THE TRIS ARE FOUND IN THE FIVE RESIDUES IN THE C-TERMINAL END OF THE ENZYME ARE NOT INCLUDED IN THE MODEL AS NO ELECTRON DENSITY WAS PRESENT FOR THESE RESIDUES. DOUBLE CONFORMATIONS HAVE BEEN ASSIGNED TO FOUR RESIDUES: THR 85, LEU 142, LEU 219 AND ARG 373. THE MISSING ATOMS OF GLU 118 IS DUE TO WEAK ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.186 -10 %RANDOM
Rwork0.157 ---
obs0.157 42016 87.6 %-
Refinement stepCycle: LAST / Resolution: 1.85→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3461 0 3 231 3695
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.28
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.86→1.94 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3809 --
Rwork0.334 2987 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3_MOD.CHO
X-RAY DIFFRACTION3GEN_ALT.INP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.28
LS refinement shell
*PLUS
Rfactor obs: 0.334

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