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- PDB-4okv: Crystal structure of anopheline anti-platelet protein with Fab an... -

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Basic information

Entry
Database: PDB / ID: 4okv
TitleCrystal structure of anopheline anti-platelet protein with Fab antibody
Components
  • Anti-platelet aggregation protein
  • heavy chain of 8H7 mAb
  • light chain of 8H7 mAb
KeywordsBLOOD CLOTTING / malaria vector mosquito / collagen binding protein
Function / homology
Function and homology information


IgE binding / toxin activity / extracellular region
Similarity search - Function
Helix Hairpins - #1890 / Salivary gland allergen Aed3 / Helix Hairpins / Helix non-globular / Special / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Aegyptin-like protein
Similarity search - Component
Biological speciesAnopheles stephensi (Asian malaria mosquito)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.802 Å
AuthorsPark, S.Y. / Sugiyama, K.
CitationJournal: To be Published
Title: The crystal structure of anopheles anti-platelet protein, a powerful anti-coagulant, in complex with an antibody
Authors: Sugiyama, K. / Iyori, M. / Sawaguchi, A. / Akashi, S. / Tame, J.R.H. / Yoshida, S. / Park, S.Y.
History
DepositionJan 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: heavy chain of 8H7 mAb
B: light chain of 8H7 mAb
C: heavy chain of 8H7 mAb
D: light chain of 8H7 mAb
E: Anti-platelet aggregation protein
F: Anti-platelet aggregation protein


Theoretical massNumber of molelcules
Total (without water)109,3726
Polymers109,3726
Non-polymers00
Water12,574698
1
A: heavy chain of 8H7 mAb
B: light chain of 8H7 mAb
F: Anti-platelet aggregation protein


Theoretical massNumber of molelcules
Total (without water)54,6863
Polymers54,6863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: heavy chain of 8H7 mAb
D: light chain of 8H7 mAb
E: Anti-platelet aggregation protein


Theoretical massNumber of molelcules
Total (without water)54,6863
Polymers54,6863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.810, 99.426, 166.033
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody heavy chain of 8H7 mAb


Mass: 23085.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: hybridoma cells / Source: (natural) Mus musculus (house mouse)
#2: Antibody light chain of 8H7 mAb


Mass: 24015.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: hybridoma cells / Source: (natural) Mus musculus (house mouse)
#3: Protein Anti-platelet aggregation protein / GE rich salivary gland protein


Mass: 7584.399 Da / Num. of mol.: 2 / Fragment: UNP residues 201-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles stephensi (Asian malaria mosquito)
Gene: ansg-1, aapp / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7YT37
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 3.54 Å3/Da / Density % sol: 65.25 % / Mosaicity: 0.281 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 15% PEG 20000, pH 7.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 6, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 135319 / % possible obs: 94.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 17.15 Å2 / Rmerge(I) obs: 0.093 / Χ2: 1.499 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.8320.43357130.70580.8
1.83-1.862.20.43660110.72184.9
1.86-1.92.40.42562280.75887.9
1.9-1.942.60.40963870.8190.1
1.94-1.982.70.39265320.8792
1.98-2.032.90.36866310.90293.3
2.03-2.083.10.34566850.96794.3
2.08-2.133.30.3267631.01895.1
2.13-2.23.40.28867841.02995.4
2.2-2.273.60.2668041.05695.9
2.27-2.353.80.23469051.08796.5
2.35-2.443.90.21268971.10296.7
2.44-2.554.10.1869401.16497.3
2.55-2.694.40.15569741.24797.3
2.69-2.864.70.12470141.37998
2.86-3.0850.170731.69298.3
3.08-3.395.30.08471092.14298.7
3.39-3.885.60.06671972.59499.2
3.88-4.885.60.04872402.29298.8
4.88-505.80.03874321.86997.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.14data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.802→47.624 Å / FOM work R set: 0.8172 / SU ML: 0.25 / σ(F): 1.42 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 6799 5.03 %
Rwork0.2183 --
obs0.2198 135285 94.31 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.356 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 104.5 Å2 / Biso mean: 25.16 Å2 / Biso min: 9.12 Å2
Baniso -1Baniso -2Baniso -3
1--3.1285 Å2-0 Å20 Å2
2---1.6614 Å2-0 Å2
3---4.7899 Å2
Refinement stepCycle: LAST / Resolution: 1.802→47.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7653 0 0 698 8351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077835
X-RAY DIFFRACTIONf_angle_d1.13410635
X-RAY DIFFRACTIONf_chiral_restr0.0761204
X-RAY DIFFRACTIONf_plane_restr0.0041356
X-RAY DIFFRACTIONf_dihedral_angle_d14.3452845
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8024-1.82280.39941890.40663387357676
1.8228-1.84430.37721800.38093741392182
1.8443-1.86680.39582180.36913794401285
1.8668-1.89040.37142190.36563894411388
1.8904-1.91530.37962120.34794053426589
1.9153-1.94150.35862220.32524047426990
1.9415-1.96930.31612000.31654090429091
1.9693-1.99870.3532100.3084200441093
1.9987-2.02990.33112120.2964244445694
2.0299-2.06320.31722290.28014230445994
2.0632-2.09870.30382170.26254274449195
2.0987-2.13690.29262200.24774309452995
2.1369-2.1780.27842440.24634303454796
2.178-2.22250.30162090.23614314452396
2.2225-2.27080.26182340.22254331456596
2.2708-2.32360.26972370.2174329456696
2.3236-2.38170.27512570.22894356461397
2.3817-2.44610.26942500.22334373462397
2.4461-2.51810.28162500.21864366461697
2.5181-2.59940.25812400.21284411465198
2.5994-2.69230.24852290.20644455468497
2.6923-2.80.25432210.20954432465398
2.8-2.92750.24732260.1994499472598
2.9275-3.08180.20942290.19124488471798
3.0818-3.27480.21242330.18824494472799
3.2748-3.52760.20922410.18674551479299
3.5276-3.88240.2042250.1744582480799
3.8824-4.44390.19952440.16374576482099
4.4439-5.59740.1722540.1534611486599
5.5974-47.64070.18332480.17864752500098

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