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- PDB-3s6v: Manganese-bound Ac-ASP-7 -

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Basic information

Entry
Database: PDB / ID: 3s6v
TitleManganese-bound Ac-ASP-7
ComponentsAc-ASP-7
KeywordsUNKNOWN FUNCTION / Pathogenesis-related Protein / CAP / 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: 2.6 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)47,0783
Polymers47,0232
Non-polymers551
Water1,40578
1
A: Ac-ASP-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5662
Polymers23,5111
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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
MethodPISA
Unit cell
Length a, b, c (Å)59.047, 78.688, 95.332
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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 THIS 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: 2.32 Å3/Da / Density % sol: 47.02 %
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: 1.378 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: 1.378 Å / Relative weight: 1
ReflectionResolution: 2.6→61 Å / Num. obs: 25918 / % possible obs: 99.9 % / Redundancy: 14.1 % / Biso Wilson estimate: 60.2 Å2 / Rsym value: 0.081
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 6.8 / Rsym value: 0.376 / % possible all: 99.4

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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: 2.6→24.93 Å / SU ML: 0.36 / σ(F): 1.38 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 1309 4.97 %
Rwork0.1899 --
obs0.1932 14201 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.865 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.92 Å20 Å2-0 Å2
2--1.6385 Å20 Å2
3----7.5585 Å2
Refinement stepCycle: LAST / Resolution: 2.6→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 1 78 2812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082799
X-RAY DIFFRACTIONf_angle_d1.183757
X-RAY DIFFRACTIONf_dihedral_angle_d16.1261021
X-RAY DIFFRACTIONf_chiral_restr0.088377
X-RAY DIFFRACTIONf_plane_restr0.004503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6002-2.70420.32431410.2642773X-RAY DIFFRACTION99
2.7042-2.82710.39981490.23542785X-RAY DIFFRACTION100
2.8271-2.97590.26881530.22472799X-RAY DIFFRACTION100
2.9759-3.1620.30171550.2112768X-RAY DIFFRACTION100
3.162-3.40550.27981330.19722792X-RAY DIFFRACTION100
3.4055-3.74720.30291530.19642766X-RAY DIFFRACTION100
3.7472-4.2870.21391580.16842787X-RAY DIFFRACTION100
4.287-5.39190.22261290.15442790X-RAY DIFFRACTION100
5.3919-24.72230.21491380.18632780X-RAY DIFFRACTION100

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