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- PDB-3s6u: Caclcium-bound Ac-ASP-7 -

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Basic information

Entry
Database: PDB / ID: 3s6u
TitleCaclcium-bound Ac-ASP-7
ComponentsAc-ASP-7
KeywordsUNKNOWN FUNCTION / PR domain / CAP domain / SCP/TAPS
Function / homologyPathogenesis-related Protein p14a / CAP / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesAncylostoma caninum (dog hookworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOsman, A. / Wang, C.K. / Winter, A. / Loukas, A. / Tribolet, L. / Gasser, R. / Hofmann, A.
CitationJournal: Biotechnol Adv
Title: Hookworm SCP/TAPS protein structure--A key to understanding host-parasite interactions and developing new interventions.
Authors: Osman, A. / Wang, C.K. / Winter, A. / Loukas, A. / Tribolet, L. / Gasser, R.B. / Hofmann, A.
History
DepositionMay 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Ac-ASP-7
B: Ac-ASP-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0633
Polymers47,0232
Non-polymers401
Water1,802100
1
A: Ac-ASP-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5522
Polymers23,5111
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ac-ASP-7


Theoretical massNumber of molelcules
Total (without water)23,5111
Polymers23,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.834, 77.958, 96.318
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ac-ASP-7


Mass: 23511.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ancylostoma caninum (dog hookworm) / Production host: Pichia pastoris (fungus)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAS PER THE THE AUTHORS THERE IS AN UNEXPLAINED SEQUENCE MISMATCH BETWEEN THE GENBANK SEQUENCE AND ...AS PER THE THE AUTHORS THERE IS AN UNEXPLAINED SEQUENCE MISMATCH BETWEEN THE GENBANK SEQUENCE AND THE SEQUENCE IN IS STRUCTURE. THE DNA SEQUENCING DATA IS UNAMBIGUOUS AND THE ELECTRON DENSITY CLEARLY SUPPORTS THE AUTHORS ASSIGNMENT

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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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% MPD, 0.1 M TRIS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.3778 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3778 Å / Relative weight: 1
ReflectionResolution: 2.7→61 Å / Num. obs: 23262 / % possible obs: 99.2 % / Redundancy: 14.1 % / Biso Wilson estimate: 54.2 Å2 / Rsym value: 0.063
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 14.9 / Num. unique all: 1777 / Rsym value: 0.169 / % possible all: 98.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXautomr (Phaser)model building
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXautomr (Phaser)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3S6S

3s6s


Resolution: 2.7→24.78 Å / SU ML: 0.35 / σ(F): 1.6 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 1124 4.83 %random
Rwork0.1804 ---
obs0.1834 23262 99.1 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.588 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.091 Å2-0 Å2-0 Å2
2---0.9095 Å20 Å2
3----5.1815 Å2
Refinement stepCycle: LAST / Resolution: 2.7→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 1 100 2843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082808
X-RAY DIFFRACTIONf_angle_d1.1573768
X-RAY DIFFRACTIONf_dihedral_angle_d17.1861028
X-RAY DIFFRACTIONf_chiral_restr0.079379
X-RAY DIFFRACTIONf_plane_restr0.004503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.82290.33471310.21822747X-RAY DIFFRACTION98
2.8229-2.97150.32381510.20772754X-RAY DIFFRACTION99
2.9715-3.15740.27231510.20792748X-RAY DIFFRACTION99
3.1574-3.40060.25391550.16932744X-RAY DIFFRACTION99
3.4006-3.74170.24261370.16962772X-RAY DIFFRACTION99
3.7417-4.28080.19581200.15182823X-RAY DIFFRACTION99
4.2808-5.38420.1961400.15862766X-RAY DIFFRACTION100
5.3842-24.78290.24741390.21192784X-RAY DIFFRACTION100

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