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- PDB-1i8n: CRYSTAL STRUCTURE OF LEECH ANTI-PLATELET PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1i8n
TitleCRYSTAL STRUCTURE OF LEECH ANTI-PLATELET PROTEIN
ComponentsANTI-PLATELET PROTEIN
KeywordsTOXIN / PAN MODULE
Function / homologyHepatocyte Growth Factor / Hepatocyte Growth Factor / 3-Layer(bba) Sandwich / toxin activity / extracellular region / Alpha Beta / PROPIONAMIDE / Leech anti-platelet protein
Function and homology information
Biological speciesHaementeria officinalis (Mexican leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.2 Å
AuthorsHuizinga, E.G. / Schouten, A. / Connolly, T.M. / Kroon, J. / Sixma, J.J. / Gros, P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: The structure of leech anti-platelet protein, an inhibitor of haemostasis.
Authors: Huizinga, E.G. / Schouten, A. / Connolly, T.M. / Kroon, J. / Sixma, J.J. / Gros, P.
#1: Journal: J.Biol.Chem. / Year: 1992
Title: An inhibitor of Collagen-Stimulated Platelet Activation from the salivary glands of the Haementeria Officinalis Leech. I. Identification, Isolation, and Characterization
Authors: Connolly, T.M. / Jacobs, J.W. / Condra, C.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: An inhibitor of Collagen-Stimulated Platelet Activation from the salivary glands of the Haementeria Officinalis Leech. II. Cloning of the cDNA and Expression
Authors: Keller, P.M. / Schultz, L.D. / Condra, C. / Karczewski, J. / Connolly, T.M.
History
DepositionMar 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: ANTI-PLATELET PROTEIN
B: ANTI-PLATELET PROTEIN
C: ANTI-PLATELET PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5226
Polymers41,3033
Non-polymers2193
Water3,423190
1
A: ANTI-PLATELET PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8412
Polymers13,7681
Non-polymers731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ANTI-PLATELET PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8412
Polymers13,7681
Non-polymers731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ANTI-PLATELET PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8412
Polymers13,7681
Non-polymers731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.45, 73.45, 199.49
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11B-334-

HOH

21C-940-

HOH

31C-963-

HOH

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Components

#1: Protein ANTI-PLATELET PROTEIN


Mass: 13767.517 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haementeria officinalis (Mexican leech)
Gene: LAPP / Plasmid: PKH4 ALPHA 2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ1995 / References: UniProt: Q01747
#2: Chemical ChemComp-ROP / PROPIONAMIDE


Mass: 73.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: MPD, sodium citrate, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMsodium phosphate1drop
320 %(v/v)2-propanol1reservoir
40.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8825 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8825 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 27864 / Num. obs: 27864 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 4.4 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 35.6
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1822 / Rsym value: 0.253 / % possible all: 96.5
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
Lowest resolution: 2.23 Å / % possible obs: 96.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNS1refinement
RefinementMethod to determine structure: SIR / Resolution: 2.2→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2082 -RANDOM
Rwork0.215 ---
all0.216 27864 --
obs0.216 27864 97.1 %-
Solvent computationBsol: 42.9627 Å2 / ksol: 0.359435 e/Å3
Displacement parametersBiso mean: 41.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.29 Å25.29 Å2-10.58 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 15 190 2335
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.542
X-RAY DIFFRACTIONc_scbond_it2.92
X-RAY DIFFRACTIONc_scangle_it3.722.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.332 333 -
Rwork0.312 --
obs-4537 97.1 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.215 / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.332 / Rfactor Rwork: 0.312

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