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Open data
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Basic information
Entry | Database: PDB / ID: 1n1i | ||||||
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Title | The structure of MSP-1(19) from Plasmodium knowlesi | ||||||
![]() | Merozoite surface protein-1 | ||||||
![]() | CELL ADHESION / MSP1 / malaria / surface protein / surface antigen / glycoprotein / EGF domain | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Garman, S.C. / Simcoke, W.N. / Stowers, A.W. / Garboczi, D.N. | ||||||
![]() | ![]() 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 |
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Remark 999 | SEQUENCE 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 viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.5 KB | Display | ![]() |
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PDB format | ![]() | 68.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.4 KB | Display | ![]() |
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Full document | ![]() | 487.7 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b9wS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | There are four copies of the biological monomer in the asymmetric unit. |
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Components
#1: Protein | 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.) ![]() ![]() Species: Plasmodium knowlesi / Strain: MALAYAN H / Gene: MSP1 / Plasmid: YEpRPEU-3 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-HIS / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 68 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 23, 2000 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 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.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.5311 Å2 / ksol: 0.257708 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→20.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 50 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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