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- PDB-4apl: Crystal Structure of AMA1 from Neospora caninum -

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Basic information

Entry
Database: PDB / ID: 4apl
TitleCrystal Structure of AMA1 from Neospora caninum
ComponentsAPICAL MEMBRANE ANTIGEN 1
KeywordsMEMBRANE PROTEIN / APICOMPLEXA / MOVING JUNCTION / INVASION
Function / homology
Function and homology information


Complement Module; domain 1 - #70 / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / Complement Module; domain 1 / 3-Layer(bba) Sandwich / Ribbon / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Apical membrane antigen 1
Similarity search - Component
Biological speciesNEOSPORA CANINUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTonkin, M.L. / Crawford, J. / Lebrun, M.L. / Boulanger, M.J.
CitationJournal: Protein Sci. / Year: 2013
Title: Babesia Divergens and Neospora Caninum Apical Membrane Antigen 1 (Ama1) Structures Reveal Selectivity and Plasticity in Apicomplexan Parasite Host Cell Invasion.
Authors: Tonkin, M.L. / Crawford, J. / Lebrun, M.L. / Boulanger, M.J.
History
DepositionApr 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 13, 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: APICAL MEMBRANE ANTIGEN 1
B: APICAL MEMBRANE ANTIGEN 1
D: APICAL MEMBRANE ANTIGEN 1
E: APICAL MEMBRANE ANTIGEN 1


Theoretical massNumber of molelcules
Total (without water)191,9724
Polymers191,9724
Non-polymers00
Water2,558142
1
A: APICAL MEMBRANE ANTIGEN 1


Theoretical massNumber of molelcules
Total (without water)47,9931
Polymers47,9931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: APICAL MEMBRANE ANTIGEN 1


Theoretical massNumber of molelcules
Total (without water)47,9931
Polymers47,9931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: APICAL MEMBRANE ANTIGEN 1


Theoretical massNumber of molelcules
Total (without water)47,9931
Polymers47,9931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: APICAL MEMBRANE ANTIGEN 1


Theoretical massNumber of molelcules
Total (without water)47,9931
Polymers47,9931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)251.560, 51.000, 145.340
Angle α, β, γ (deg.)90.00, 90.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
APICAL MEMBRANE ANTIGEN 1


Mass: 47993.102 Da / Num. of mol.: 4 / Fragment: DOMAINS I/II/III, RESIDUES 59-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEOSPORA CANINUM (eukaryote) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: A2A114
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.36 % / Description: NONE
Crystal growDetails: 20% PEG3350, 300 MM SODIUM CITRATE PH 4.2 AND 10 MM ZINC CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 41269 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.8
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.4 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X2Z

2x2z


Resolution: 2.9→48.44 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.861 / SU B: 16.873 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27097 2078 5 %RANDOM
Rwork0.19265 ---
obs0.19663 39156 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.656 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.04 Å2
2--0.05 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12477 0 0 142 12619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212882
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.93817499
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.38651573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.89824.923646
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.522152071
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7611554
X-RAY DIFFRACTIONr_chiral_restr0.0850.21784
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110105
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 138 -
Rwork0.273 2650 -
obs--95.54 %

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