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- PDB-3nt8: Crystal Structure of Na-ASP-1 -

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Basic information

Entry
Database: PDB / ID: 3nt8
TitleCrystal Structure of Na-ASP-1
ComponentsAncylostoma secreted protein 1
KeywordsIMMUNE SYSTEM / PATHOGENESIS RELATED-1 PROTEIN / CYSTEINE-RICH SECRETORY PROTEIN / CAP DOMAIN
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Venom allergen 5-like / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family / CAP superfamily ...Venom allergen 5-like / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ancylostoma secreted protein 1
Similarity search - Component
Biological speciesNecator americanus (New World hookworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAsojo, O.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of a two-CAP-domain protein from the human hookworm parasite Necator americanus.
Authors: Asojo, O.A.
History
DepositionJul 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ancylostoma secreted protein 1
B: Ancylostoma secreted protein 1


Theoretical massNumber of molelcules
Total (without water)91,5682
Polymers91,5682
Non-polymers00
Water6,990388
1
A: Ancylostoma secreted protein 1


Theoretical massNumber of molelcules
Total (without water)45,7841
Polymers45,7841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ancylostoma secreted protein 1


Theoretical massNumber of molelcules
Total (without water)45,7841
Polymers45,7841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.780, 74.570, 84.740
Angle α, β, γ (deg.)90.00, 112.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ancylostoma secreted protein 1


Mass: 45784.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Necator americanus (New World hookworm)
Strain: NECATOR AMERICANUS / Gene: asp1, Human hookworm 51031 / Plasmid: PPICZALPHANA-ASP-1 / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: O76744
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 3UL (7.5 MG/ML) PROTEIN AND 1.5UL RESERVOIR SOLUTION CONTAINING 21% (W/V) PEG 6000 AND 200 MM, SODIUM CITRATE PH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 24, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.957
11-H, -K, H+L20.043
ReflectionResolution: 2.15→30.8 Å / Num. obs: 37195 / % possible obs: 93.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.107 / Rsym value: 0.115
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 4.7 / % possible all: 91.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U53

1u53


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.185 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23747 1880 5.1 %RANDOM
Rwork0.1934 ---
obs0.19568 35298 86.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.318 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20.5 Å2
2---0.04 Å20 Å2
3---1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6038 0 0 388 6426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0216201
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9348413
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3355798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93925.221272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50815984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5551520
X-RAY DIFFRACTIONr_chiral_restr0.110.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214792
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0251.53945
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77326296
X-RAY DIFFRACTIONr_scbond_it3.03832256
X-RAY DIFFRACTIONr_scangle_it4.534.52117
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.202 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.618 3 -
Rwork0.21 77 -
obs--2.53 %

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