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- PDB-4tpv: Crystal Structure of Hookworm Platelet Inhibitor -

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Basic information

Entry
Database: PDB / ID: 4tpv
TitleCrystal Structure of Hookworm Platelet Inhibitor
ComponentsPlatelet inhibitor
KeywordsBLOOD CLOTTING / cysteine-rich/antigen 5/pathogenesis-related 1 CAP platelet integrin
Function / homology
Function and homology information


Cysteine-rich secretory protein-related / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / CAP superfamily / Cysteine-rich secretory protein family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAncylostoma caninum (dog hookworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsAndersen, J.F. / Ma, D. / Francischetti, I.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: The structure of hookworm platelet inhibitor (HPI), a CAP superfamily member from Ancylostoma caninum.
Authors: Ma, D. / Francischetti, I.M. / Ribeiro, J.M. / Andersen, J.F.
History
DepositionJun 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jun 24, 2015Group: Database references
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_symm_contact / refine_hist / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Platelet inhibitor
B: Platelet inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2643
Polymers41,1722
Non-polymers921
Water6,666370
1
A: Platelet inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6782
Polymers20,5861
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Platelet inhibitor


Theoretical massNumber of molelcules
Total (without water)20,5861
Polymers20,5861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-10 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.158, 51.985, 73.940
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Platelet inhibitor


Mass: 20585.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ancylostoma caninum (dog hookworm) / Gene: HPI / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q962V9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

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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: 1.83 Å3/Da / Density % sol: 32.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30 % PEG 6000, 0.1 M HEPES, pH 7.0 / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.6→28.8 Å / Num. obs: 39309 / % possible obs: 99.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 3.4 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
PHASER2.1.4phasing
RefinementResolution: 1.6→28.8 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1936 1980 5.04 %
Rwork0.1501 --
obs0.1523 39309 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 6 370 3198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082926
X-RAY DIFFRACTIONf_angle_d1.0913940
X-RAY DIFFRACTIONf_dihedral_angle_d13.2411081
X-RAY DIFFRACTIONf_chiral_restr0.046407
X-RAY DIFFRACTIONf_plane_restr0.005520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.63680.23621200.17922492X-RAY DIFFRACTION92
1.6368-1.68110.23941360.16822620X-RAY DIFFRACTION98
1.6811-1.73050.19641350.16122637X-RAY DIFFRACTION100
1.7305-1.78640.22811550.16212687X-RAY DIFFRACTION100
1.7864-1.85020.20831460.15652662X-RAY DIFFRACTION100
1.8502-1.92430.19061490.1522668X-RAY DIFFRACTION100
1.9243-2.01180.22521480.14782645X-RAY DIFFRACTION100
2.0118-2.11790.18571390.15122668X-RAY DIFFRACTION100
2.1179-2.25050.18281270.15282720X-RAY DIFFRACTION100
2.2505-2.42420.20911350.14822686X-RAY DIFFRACTION100
2.4242-2.6680.18561380.15992690X-RAY DIFFRACTION100
2.668-3.05370.19121510.15492685X-RAY DIFFRACTION100
3.0537-3.84590.17931500.13452713X-RAY DIFFRACTION100
3.8459-28.80.17771510.14192756X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -8.5443 Å / Origin y: -12.8599 Å / Origin z: -17.8662 Å
111213212223313233
T0.0739 Å20.0032 Å2-0.0093 Å2-0.0908 Å20.0145 Å2--0.0847 Å2
L0.3051 °20.1546 °20.046 °2-0.8676 °20.399 °2--0.3781 °2
S-0.0108 Å °0.0332 Å °-0.0019 Å °-0.0206 Å °0.0298 Å °-0.0126 Å °0.0038 Å °0.0458 Å °-0.009 Å °
Refinement TLS groupSelection details: all

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