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- PDB-1bvn: PIG PANCREATIC ALPHA-AMYLASE IN COMPLEX WITH THE PROTEINACEOUS IN... -

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Basic information

Entry
Database: PDB / ID: 1bvn
TitlePIG PANCREATIC ALPHA-AMYLASE IN COMPLEX WITH THE PROTEINACEOUS INHIBITOR TENDAMISTAT
Components
  • PROTEIN (ALPHA-AMYLASE)
  • PROTEIN (TENDAMISTAT)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / GLYCOSYLTRANSFERASE / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE / ALPHA-AMYLASE / PROTEINACEOUS ALPHA-AMYLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


alpha-amylase inhibitor activity / alpha-amylase / alpha-amylase activity / carbohydrate catabolic process / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space
Similarity search - Function
Alpha-amylase inhibitor / Alpha-amylase inhibitor / Alpha-amylase inhibitor superfamily / Alpha amylase inhibitor / Alpha amylase inhibitor / 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 inhibitor / Alpha-amylase inhibitor / Alpha-amylase inhibitor superfamily / Alpha amylase inhibitor / Alpha amylase inhibitor / 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
Pancreatic alpha-amylase / Alpha-amylase inhibitor HOE-467A
Similarity search - Component
Biological speciesSus scrofa (pig)
Streptomyces tendae (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsMachius, M. / Wiegand, G. / Epp, O. / Huber, R.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: The crystal structure of porcine pancreatic alpha-amylase in complex with the microbial inhibitor Tendamistat.
Authors: Wiegand, G. / Epp, O. / Huber, R.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Carbohydrate and Protein-Based Inhibitors of Porcine Pancreatic Alpha-Amylase: Structure Analysis and Comparison of Their Binding Characteristics
Authors: Machius, M. / Vertesy, L. / Huber, R. / Wiegand, G.
#2: Journal: Protein Sci. / Year: 1995
Title: Carbohydrate Binding Sites in a Pancreatic Alpha-Amylase-Substrate Complex, Derived from X-Ray Structure Analysis at 2.1 Angstrom Resolution
Authors: Qian, M. / Haser, R. / Payan, F.
#3: Journal: J.Mol.Biol. / Year: 1994
Title: Refined Molecular Structure of Pig Pancreatic Alpha-Amylase at 2.1 A Resolution
Authors: Larson, S.B. / Greenwood, A. / Cascio, D. / Day, J. / McPherson, A.
#4: Journal: Biochemistry / Year: 1994
Title: The Active Center of a Mammalian Alpha-Amylase. Structure of the Complex of a Pancreatic Alpha-Amylase with a Carbohydrate Inhibitor Refined to 2.2-A Resolution
Authors: Qian, M. / Haser, R. / Buisson, G. / Duee, E. / Payan, F.
#5: 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
DepositionSep 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 23, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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.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_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

Downloads & links

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Assembly

Deposited unit
P: PROTEIN (ALPHA-AMYLASE)
T: PROTEIN (TENDAMISTAT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4624
Polymers63,3862
Non-polymers762
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.700, 77.700, 359.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein PROTEIN (ALPHA-AMYLASE) / 1 / 4-GLUCAN-4-GLUCANOHYDROLASE / GLYCOSYLTRANSFERASE


Mass: 55418.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00690, alpha-amylase
#2: Protein PROTEIN (TENDAMISTAT)


Mass: 7967.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces tendae (bacteria) / Strain: 4158 / References: UniProt: P01092
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE DISCREPANCIES ARE DESCRIBED IN THE CITED REFERENCES GLN1: THIS RESIDUE IS REPORTED TO ...THE SEQUENCE DISCREPANCIES ARE DESCRIBED IN THE CITED REFERENCES GLN1: THIS RESIDUE IS REPORTED TO BE PYROGLUTAMATE IN OTHER STRUCTURES OF PIG PANCREATIC AND SIMILAR ALPHA-AMYLASES. ALTHOUGH AMINO ACID SEQUENCING INDICATED THAT THE N-TERMINUS WAS BLOCKED IN THE MATERIAL WHICH WAS USED FOR CRYSTALLIZATION IN THE PRESENTED STUDY, THE QUALITY OF THE ELECTRON DENSITY DID NOT ALLOW TO UNAMBIGOUSLY IDENTIFY THE NATURE OF THIS RESIDUE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.5 %
Crystal growpH: 8
Details: PROTEIN: 12 MG/ML IN 50 MM TRIS/HCL, PH 8.0, MIXED 5:1 WITH 40% (W/V) PEG 1000; RESERVOIR: 0.18-0.20 M SODIUM PHOSPHATE, PH 8.0 HARVESTED IN: 3 M SODIUM ACETATE, PH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
250 mMTris-HCl1drop
340 %(w/v)PEG1reservoir
40.18-0.20 Msodium potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: KODAK / Detector: FILM / Details: NI-FILTER, DOUBLE-FOCUSING MIRROR SYSTEM
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→29.39 Å / Num. obs: 19789 / % possible obs: 81.3 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.0602
Reflection shellResolution: 2.5→2.61 Å / % possible all: 42.4
Reflection
*PLUS
Num. measured all: 54641
Reflection shell
*PLUS
Rmerge(I) obs: 0.352

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Processing

Software
NameVersionClassification
FILMEdata collection
PROTEINdata reduction
PROTEINmodel building
X-PLOR3.185refinement
FILMEdata reduction
PROTEINdata scaling
PROTEINphasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→29.4 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 2 / Details: FINAL RMS COORD. SHIFT 0.0 ANGSTROMS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1889 5 %RANDOM
Rwork0.166 ---
obs0.166 17259 73.7 %-
Displacement parametersBiso mean: 26.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4443 0 2 161 4606
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_deg1.49
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.51
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.714
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.366 134 5 %
Rwork0.25 1059 -
obs--37.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETERTIP3P.TOPOLOGY
X-RAY DIFFRACTION3PARAMETER.ELEMENTSTOPOLOGY.ELEMENTS
Software
*PLUS
Name: X-PLOR / Version: 3.185 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 29.4 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.51
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.714
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.366 / % reflection Rfree: 5 % / Rfactor Rwork: 0.25

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