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- PDB-1kzq: crystal structure of a parasite protein -

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Basic information

Entry
Database: PDB / ID: 1kzq
Titlecrystal structure of a parasite protein
ComponentsMajor Surface Antigen P30
KeywordsIMMUNE SYSTEM / SAG1 / major surface antigen / Toxoplasma Gondii / parasite invasion / MAD
Function / homology
Function and homology information


symbiont-containing vacuole / membrane
Similarity search - Function
SRS domain / Protozoan surface antigen, SAG1 family / SRS domain / SRS domain / SRS domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major surface antigen p30
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsHe, X. / Grigg, M.E. / Boothroyd, J.C. / Garcia, K.C.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structure of the immunodominant surface antigen from the Toxoplasma gondii SRS superfamily.
Authors: He, X.L. / Grigg, M.E. / Boothroyd, J.C. / Garcia, K.C.
History
DepositionFeb 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS HAVE FUNCTIONAL DATA SHOWING THE DIMER IS ACTIVE, AND BIOCHEMICAL DATA SHOWING A MIXTURE OF DIMER AND MONOMER IN SOLUTION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major Surface Antigen P30
B: Major Surface Antigen P30


Theoretical massNumber of molelcules
Total (without water)59,6602
Polymers59,6602
Non-polymers00
Water12,124673
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-8 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.840, 101.840, 125.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Major Surface Antigen P30


Mass: 29829.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: SAG1 / Cell line (production host): High 5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P13664
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Ammonium Sulfide, sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
135 mg/mlprotein1drop
22.8 Mammonium sulfate1reservoir
30.1 Msodium acetate1reservoirpH5.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.9197
SYNCHROTRONALS 5.0.220.9191,0.9194,0.9056
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDNov 28, 2001
ADSC QUANTUM 42CCDDec 9, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91971
20.91911
30.91941
40.90561
ReflectionResolution: 1.7→50 Å / Num. all: 72621 / Num. obs: 72621 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 7.5
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 10 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 1.9 / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 138104
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3660 -RANDOM
Rwork0.2 ---
all0.201 72602 --
obs0.201 72602 99.6 %-
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.119 Å20 Å20 Å2
2---0.119 Å20 Å2
3---0.237 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3702 0 0 673 4375
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 1.7→1.8 Å / Rfactor Rfree error: 0.004 /
Rfactor% reflection
Rfree0.277 -
Rwork0.254 -
obs-99.4 %
Refinement
*PLUS
Lowest resolution: 50 Å / Num. reflection obs: 138104 / % reflection Rfree: 5 % / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.76 Å

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