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- PDB-1b9w: C-TERMINAL MEROZOITE SURFACE PROTEIN 1 FROM PLASMODIUM CYNOMOLGI -

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Basic information

Entry
Database: PDB / ID: 1b9w
TitleC-TERMINAL MEROZOITE SURFACE PROTEIN 1 FROM PLASMODIUM CYNOMOLGI
ComponentsPROTEIN (MEROZOITE SURFACE PROTEIN 1)
KeywordsSURFACE PROTEIN / MSP-1 / CANDIDATE MALARIA VACCINE / SURFACE ANTIGEN
Function / homology
Function and homology information


side of membrane / extracellular region / plasma membrane
Similarity search - Function
Merozoite surface 1, C-terminal / Merozoite surface protein, EGF domain 1 / Merozoite surface protein 1 (MSP1) C-terminus / MSP1 EGF domain 1 / EGF domain / Laminin / Laminin / Ribbon / Mainly Beta
Similarity search - Domain/homology
Merozoite surface protein 1
Similarity search - Component
Biological speciesPlasmodium cynomolgi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsBentley, G.A. / Chitarra, V. / Holm, I. / Longacre, S.
CitationJournal: Mol.Cell / Year: 1999
Title: The crystal structure of C-terminal merozoite surface protein 1 at 1.8 A resolution, a highly protective malaria vaccine candidate.
Authors: Chitarra, V. / Holm, I. / Bentley, G.A. / Petres, S. / Longacre, S.
History
DepositionFeb 15, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (MEROZOITE SURFACE PROTEIN 1)


Theoretical massNumber of molelcules
Total (without water)10,7951
Polymers10,7951
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.770, 43.770, 92.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PROTEIN (MEROZOITE SURFACE PROTEIN 1) / MSP1-19 / MSA1-19


Mass: 10795.188 Da / Num. of mol.: 1 / Fragment: TWO C-TERMINAL EGF-LIKE DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium cynomolgi (eukaryote) / Description: SYNTHETIC GENE / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q25659
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 40 %
Crystal growpH: 5.5 / Details: pH 5.50
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %(w/v)PEG400011
20.2 Mammonium acetate11
30.1 Msodium citrate11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 9965 / % possible obs: 100 % / Redundancy: 13.9 % / Biso Wilson estimate: 20.7 Å2 / Rsym value: 0.058
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 15 Å / % possible obs: 100 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.058 / Biso Wilson estimate: 20.7 Å2
Reflection shell
*PLUS
Rmerge(I) obs: 0.338

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 489 5 %RANDOM
Rwork0.212 ---
obs-9965 100 %-
Displacement parametersBiso mean: 27.2 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms701 0 0 65 766
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.01
X-RAY DIFFRACTIONp_angle_d0.0260.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.51.5
X-RAY DIFFRACTIONp_mcangle_it3.72.5
X-RAY DIFFRACTIONp_scbond_it4.22
X-RAY DIFFRACTIONp_scangle_it6.14
X-RAY DIFFRACTIONp_plane_restr0.0070.01
X-RAY DIFFRACTIONp_chiral_restr0.1770.1
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.150.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.33
X-RAY DIFFRACTIONp_staggered_tor2015
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor1125
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 15 Å / Rfactor obs: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS

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