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- PDB-1l0p: CRYSTAL STRUCTURE ANALYSIS OF THE COMPLEX BETWEEN PSYCHROPHILIC A... -

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Basic information

Entry
Database: PDB / ID: 1l0p
TitleCRYSTAL STRUCTURE ANALYSIS OF THE COMPLEX BETWEEN PSYCHROPHILIC ALPHA AMYLASE FROM PSEUDOALTEROMONAS HALOPLANCTIS AND NITRATE
ComponentsALPHA-AMYLASE
KeywordsHYDROLASE / BETA-ALPHA-8-BARREL / 3 DOMAIN STRUCTURE
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
NITRATE ION / Alpha-amylase
Similarity search - Component
Biological speciesPseudoalteromonas haloplanktis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsAghajari, N. / Haser, R.
CitationJournal: Protein Sci. / Year: 2002
Title: Structural basis of alpha-amylase activation by chloride.
Authors: Aghajari, N. / Feller, G. / Gerday, C. / Haser, R.
History
DepositionFeb 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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_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
Revision 1.4Oct 30, 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)49,0503
Polymers48,9471
Non-polymers1022
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.3, 138.4, 114.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ALPHA-AMYLASE


Mass: 48947.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudoalteromonas haloplanktis (bacteria) / 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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, Hepes, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
pH: 7 / Details: Aghajari, N., (1996) Protein Sci., 5, 2128.
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: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 28, 1998
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→42.6 Å / Num. all: 29937 / Num. obs: 29641 / % possible obs: 89.3 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.15
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.5 % / % possible all: 90.5
Reflection
*PLUS
Num. measured all: 149687 / Rmerge(I) obs: 0.15
Reflection shell
*PLUS
% possible obs: 90.5 %

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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: 2.1→42.56 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: FINAL CYCLE OF REFINEMENT WAS CARRIED OUT USING CNS.
RfactorNum. reflectionSelection details
Rfree0.1801 2956 RANDOM
Rwork0.1461 --
obs0.156 29614 -
Refinement stepCycle: LAST / Resolution: 2.1→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4227 0 5 651 4883
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.27
Refinement
*PLUS
Highest resolution: 2.1 Å / Num. reflection obs: 29641
Solvent computation
*PLUS
Displacement parameters
*PLUS

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