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- PDB-1n1i: The structure of MSP-1(19) from Plasmodium knowlesi -

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Basic information

Entry
Database: PDB / ID: 1n1i
TitleThe structure of MSP-1(19) from Plasmodium knowlesi
ComponentsMerozoite surface protein-1
KeywordsCELL ADHESION / MSP1 / malaria / surface protein / surface antigen / glycoprotein / EGF domain
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
HISTIDINE / IMIDAZOLE / Merozoite surface protein 1
Similarity search - Component
Biological speciesPlasmodium knowlesi strain H (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGarman, S.C. / Simcoke, W.N. / Stowers, A.W. / Garboczi, D.N.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of the C-terminal domains of merozoite surface protein-1 from Plasmodium knowlesi reveals a novel histidine binding site
Authors: Garman, S.C. / Simcoke, W.N. / Stowers, A.W. / Garboczi, D.N.
History
DepositionOct 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The first five residues of the crystallized protein (GLU-ALA-GLU-ALA-SER) are non-native; ...SEQUENCE The first five residues of the crystallized protein (GLU-ALA-GLU-ALA-SER) are non-native; they are the remains of the yeast alpha mating factor secretory signal

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Merozoite surface protein-1
B: Merozoite surface protein-1
C: Merozoite surface protein-1
D: Merozoite surface protein-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0977
Polymers45,8034
Non-polymers2943
Water5,513306
1
A: Merozoite surface protein-1


Theoretical massNumber of molelcules
Total (without water)11,4511
Polymers11,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Merozoite surface protein-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5202
Polymers11,4511
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Merozoite surface protein-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6072
Polymers11,4511
Non-polymers1561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Merozoite surface protein-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5202
Polymers11,4511
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.880, 106.460, 62.690
Angle α, β, γ (deg.)90.00, 102.05, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThere are four copies of the biological monomer in the asymmetric unit.

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Components

#1: Protein
Merozoite surface protein-1


Mass: 11450.643 Da / Num. of mol.: 4 / Fragment: C-terminal EGF-LIKE DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium knowlesi strain H (eukaryote)
Species: Plasmodium knowlesi / Strain: MALAYAN H / Gene: MSP1 / Plasmid: YEpRPEU-3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): VK1 / References: UniProt: Q9GSQ9
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 6000, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
230 %PEG60001reservoir
3100 mMHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 23, 2000 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 16555 / Num. obs: 16555 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 47.8 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 14.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1565 / Rsym value: 0.315 / % possible all: 93.7
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 16570 / % possible obs: 97.7 % / Num. measured all: 56495
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 93.7 % / Num. unique obs: 1565 / Num. measured obs: 4653

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B9W

1b9w


Resolution: 2.4→20.59 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: 300 KCAL/MOL/A^2 NCS RESTRAINTS APPLIED TO ALL ATOMS IN EARLY ROUNDS OF REFINEMENT AND RELAXED IN LATER ROUNDS.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 860 5.2 %SHELLS
Rwork0.234 ---
all0.234 16555 --
obs0.234 16555 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.5311 Å2 / ksol: 0.257708 e/Å3
Displacement parametersBiso mean: 55.4 Å2
Baniso -1Baniso -2Baniso -3
1-29.47 Å20 Å2-0.93 Å2
2---15.54 Å20 Å2
3----13.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.4→20.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2716 0 20 306 3042
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it3.523
X-RAY DIFFRACTIONc_mcangle_it5.684
X-RAY DIFFRACTIONc_scbond_it5.464
X-RAY DIFFRACTIONc_scangle_it7.955
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 129 5 %
Rwork0.378 2429 -
obs-2558 91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMCARBOHYDRATE.TOP
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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