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- PDB-4uv6: Crystal structure of apical membrane antigen 1 from Plasmodium kn... -

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Basic information

Entry
Database: PDB / ID: 4uv6
TitleCrystal structure of apical membrane antigen 1 from Plasmodium knowlesi
ComponentsAPICAL MEROZOITE ANTIGEN 1
KeywordsCELL INVASION / 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
Apical membrane antigen 1 / Apical membrane antigen 1
Similarity search - Component
Biological speciesPLASMODIUM KNOWLESI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsVulliez-Le Normand, B. / Saul, F.A. / Bentley, G.A.
CitationJournal: Plos One / Year: 2015
Title: Crystal Structure of Plasmodium Knowlesi Apical Membrane Antigen 1 and its Complex with an Invasion-Inhibitory Monoclonal Antibody.
Authors: Vulliez-Le Normand, B. / Faber, B.W. / Saul, F.A. / Van Der Eijk, M. / Thomas, A.W. / Singh, B. / Kocken, C.H.M. / Bentley, G.A.
History
DepositionAug 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APICAL MEROZOITE ANTIGEN 1
B: APICAL MEROZOITE ANTIGEN 1


Theoretical massNumber of molelcules
Total (without water)85,0232
Polymers85,0232
Non-polymers00
Water6,954386
1
A: APICAL MEROZOITE ANTIGEN 1


Theoretical massNumber of molelcules
Total (without water)42,5111
Polymers42,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: APICAL MEROZOITE ANTIGEN 1


Theoretical massNumber of molelcules
Total (without water)42,5111
Polymers42,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.320, 105.700, 104.750
Angle α, β, γ (deg.)90.00, 98.04, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.95306, 0.04609, -0.29926), (-0.04128, -0.9989, -0.02239), (-0.29996, -0.00899, 0.95391)
Vector: 51.59998, 60.96933, -44.41268)

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Components

#1: Protein APICAL MEROZOITE ANTIGEN 1 / AMA1


Mass: 42511.449 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 43-387 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM KNOWLESI (eukaryote) / Strain: H / Production host: PICHIA PASTORIS (fungus) / Strain (production host): KM71H / References: UniProt: B3L5E1, UniProt: A0A384KGX8*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O

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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: 2.93 Å3/Da / Density % sol: 58.07 % / Description: NONE
Crystal growpH: 8.4 / Details: 0.86M SODIUM CITRATE, 0.1M HEPES PH 8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.45→47.09 Å / Num. obs: 34848 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 42.45 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.7
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.9 / % possible all: 93.3

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W81

1w81


Resolution: 2.45→47.09 Å / Cor.coef. Fo:Fc: 0.9181 / Cor.coef. Fo:Fc free: 0.8668 / SU R Cruickshank DPI: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.307 / SU Rfree Blow DPI: 0.228 / SU Rfree Cruickshank DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 843 2.42 %RANDOM
Rwork0.1707 ---
obs0.172 34846 97.11 %-
Displacement parametersBiso mean: 45.48 Å2
Baniso -1Baniso -2Baniso -3
1--9.1418 Å20 Å23.2451 Å2
2---6.0957 Å20 Å2
3---15.2375 Å2
Refine analyzeLuzzati coordinate error obs: 0.281 Å
Refinement stepCycle: LAST / Resolution: 2.45→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5407 0 0 386 5793
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015554HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.157501HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1969SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes183HARMONIC2
X-RAY DIFFRACTIONt_gen_planes787HARMONIC5
X-RAY DIFFRACTIONt_it5554HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion20.2
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion696SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6649SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.52 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.3018 78 2.75 %
Rwork0.2525 2755 -
all0.2538 2833 -
obs--97.11 %

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