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- PDB-1kxq: Camelid VHH Domain in Complex with Porcine Pancreatic alpha-Amylase -

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Basic information

Entry
Database: PDB / ID: 1kxq
TitleCamelid VHH Domain in Complex with Porcine Pancreatic alpha-Amylase
Components
  • alpha-amylase, pancreatic
  • antibody VHH fragment CABAMD9
KeywordsHYDROLASE / IMMUNE SYSTEM / ALPHA 8 BETA 8 / BETA BARREL
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate catabolic process / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Pancreatic alpha-amylase
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDesmyter, A. / Spinelli, S. / Payan, F. / Lauwereys, M. / Wyns, L. / Muyldermans, S. / Cambillau, C.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Three camelid VHH domains in complex with porcine pancreatic alpha-amylase. Inhibition and versatility of binding topology.
Authors: Desmyter, A. / Spinelli, S. / Payan, F. / Lauwereys, M. / Wyns, L. / Muyldermans, S. / Cambillau, C.
#1: Journal: EMBO J. / Year: 1998
Title: Potent enzyme inhibitors derived from dromedary heavy-chain antibodies.
Authors: Lauwereys, M. / Arbabi Ghahroudi, M. / Desmyter, A. / Kinne, J. / Holzer, W. / De Genst, E. / Wyns, L. / Muyldermans, S.
#2: 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
DepositionFeb 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Aug 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The discrepancy between the sequence of this entry and the database reference is explained ...SEQUENCE The discrepancy between the sequence of this entry and the database reference is explained in reference 2 given above. An appropriate sequence database reference for the antibody VHH fragment CABAMD9, chains E, F, G, and H, was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha-amylase, pancreatic
B: alpha-amylase, pancreatic
C: alpha-amylase, pancreatic
D: alpha-amylase, pancreatic
E: antibody VHH fragment CABAMD9
F: antibody VHH fragment CABAMD9
G: antibody VHH fragment CABAMD9
H: antibody VHH fragment CABAMD9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,21816
Polymers273,9168
Non-polymers3028
Water50,5682807
1
A: alpha-amylase, pancreatic
H: antibody VHH fragment CABAMD9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5554
Polymers68,4792
Non-polymers762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha-amylase, pancreatic
G: antibody VHH fragment CABAMD9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5554
Polymers68,4792
Non-polymers762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: alpha-amylase, pancreatic
F: antibody VHH fragment CABAMD9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5554
Polymers68,4792
Non-polymers762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: alpha-amylase, pancreatic
E: antibody VHH fragment CABAMD9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5554
Polymers68,4792
Non-polymers762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-32 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.170, 100.920, 103.740
Angle α, β, γ (deg.)79.31, 72.63, 86.11
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
alpha-amylase, pancreatic / 1 / 4-ALPHA-D-GLUCAN GLUCANOHYDROLASE


Mass: 55462.836 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Pancreatic enzyme / Source: (natural) Sus scrofa (pig) / References: UniProt: P00690, alpha-amylase
#2: Protein
antibody VHH fragment CABAMD9


Mass: 13016.225 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 2807 / 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: 2.34 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Phosphate buffer 0.8 M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris1droppH7.5
2100 mM1dropNaCl
30.8 Mphosphate buffer1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 2000 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 383526 / Num. obs: 383526 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 5
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 1.7 / % possible all: 70
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 99.8 % / Num. measured all: 3531130
Reflection shell
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 1.75 Å / % possible obs: 99.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JFH, PDB ENTRY 1QD0

1jfh

1qd0


Resolution: 1.6→29.79 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1735909.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 9426 3 %RANDOM
Rwork0.197 ---
all-317086 --
obs-317086 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.6817 Å2 / ksol: 0.376787 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.49 Å2-2.22 Å2-2.35 Å2
2---1.66 Å20.85 Å2
3----1.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-10 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.6→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19304 0 8 2807 22119
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.278 913 3 %
Rwork0.258 29934 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / % reflection Rfree: 3 % / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
LS refinement shell
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 1.75 Å / Rfactor obs: 0.258

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