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- PDB-1w81: Crystal structure of apical membrane antigen 1 from Plasmodium vivax -

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Basic information

Entry
Database: PDB / ID: 1w81
TitleCrystal structure of apical membrane antigen 1 from Plasmodium vivax
ComponentsAPICAL MEMBRANE ANTIGEN 1
KeywordsANTIGEN / PLASMODIUM ANTIGEN / MALARIA VACCINE CANDIDATE
Function / homology
Function and homology information


Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Apical merozoite antigen 1 / Apical membrane antigen 1
Similarity search - Component
Biological speciesPLASMODIUM VIVAX (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.01 Å
AuthorsPizarro, J.C. / Vulliez-Le Normand, B. / Chesne-Seck, M.-L. / Kocken, C.H.M. / Thomas, A.W. / Bentley, G.A.
CitationJournal: Science / Year: 2005
Title: Crystal Structure of the Malaria Vaccine Candidate Apical Membrane Antigen 1
Authors: Pizarro, J.C. / Vulliez-Le Normand, B. / Chesne-Seck, M.-L. / Collins, C. / Withers-Martinez, C. / Hackett, F. / Blackman, M. / Faber, B. / Remarque, E. / Kocken, C.H.M. / Thomas, A.W. / Bentley, G.A.
History
DepositionSep 15, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6662
Polymers51,5971
Non-polymers691
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.097, 76.096, 103.925
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 APICAL MEMBRANE ANTIGEN 1


Mass: 51597.047 Da / Num. of mol.: 1 / Fragment: ECTOPLASMIC REGION, RESIDUES 1-445 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM VIVAX (malaria parasite P. vivax)
Strain: SAL I / Production host: PICHIA PASTORIS (fungus) / References: UniProt: Q9TY14, UniProt: O61130*PLUS
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A, SER 178 TO ASN ENGINEERED MUTATION IN CHAIN A, ASN 226 TO ASP ...ENGINEERED MUTATION IN CHAIN A, SER 178 TO ASN ENGINEERED MUTATION IN CHAIN A, ASN 226 TO ASP ENGINEERED MUTATION IN CHAIN A, ASN 441 TO GLN
Has protein modificationY
Sequence detailsSEQUENCE EXPRESSED COMPRISES RESIDUES 1 TO 445. MUTATIONS S136N, N184D AND N399Q HAVE BEEN ...SEQUENCE EXPRESSED COMPRISES RESIDUES 1 TO 445. MUTATIONS S136N, N184D AND N399Q HAVE BEEN INTRODUCED TO ELIMINATE POTENTIAL N-GLYCOSYLATION SITE.

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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 Å3/Da / Density % sol: 38 %
Crystal growpH: 6.5
Details: THE CRYSTALLISATION MIXTURE CONSISTED OF 10-12% (W/V) PEG3350, 100-200MM IMIDAZOLE, PH 7.0, 5-10% (V/V) ISOPROPANOL, AND 1% (V/V) DMF OR 3% (V/V) T-BUTANOL. THE PROTEIN SOLUTION WAS DILUTED ...Details: THE CRYSTALLISATION MIXTURE CONSISTED OF 10-12% (W/V) PEG3350, 100-200MM IMIDAZOLE, PH 7.0, 5-10% (V/V) ISOPROPANOL, AND 1% (V/V) DMF OR 3% (V/V) T-BUTANOL. THE PROTEIN SOLUTION WAS DILUTED BY 40 - 60% WITH THE CRYSTALLISATION BUFFER, GIVING A FINAL CONCENTRATION OF 4-6 MG. ML-1 IN SUSPENDED DROPS OF VOLUME 2 - 3 PERCENT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.07197
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07197 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 147056 / % possible obs: 88.7 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.8 / % possible all: 53.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.01→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.564 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1347 5.2 %RANDOM
Rwork0.194 ---
obs0.198 24739 88.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2--0.21 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.01→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 5 288 3228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223014
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.661.9434057
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3325359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36824.522157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6315549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7011522
X-RAY DIFFRACTIONr_chiral_restr0.1270.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022304
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.21408
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22025
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.2277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.14221886
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.46842938
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.98741293
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.64261119
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: 2.01→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 53 -
Rwork0.225 1036 -
obs--51.78 %

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