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- PDB-1z1y: Crystal structure of Methylated Pvs25, an ookinete protein from P... -

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Basic information

Entry
Database: PDB / ID: 1z1y
TitleCrystal structure of Methylated Pvs25, an ookinete protein from Plasmodium vivax
Componentsookinete surface protein Pvs25
KeywordsCELL ADHESION / Four EGF-like domains
Function / homology
Function and homology information


calcium ion binding / cell surface / membrane
Similarity search - Function
Plasmodium vivax P25 fold / Plasmodium vivax P25 domain / Ookinete surface antigen, EGF domain / Pvs28 EGF domain / Orthogonal Prism / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. ...Plasmodium vivax P25 fold / Plasmodium vivax P25 domain / Ookinete surface antigen, EGF domain / Pvs28 EGF domain / Orthogonal Prism / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / Mainly Beta
Similarity search - Domain/homology
YTTERBIUM (III) ION / Ookinete surface protein
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSaxena, A.K. / Singh, K. / Su, H.P. / Klein, M.M. / Stowers, A.W. / Saul, A.J. / Long, C.A. / Garboczi, D.N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: The essential mosquito-stage P25 and P28 proteins from Plasmodium form tile-like triangular prisms
Authors: Saxena, A.K. / Singh, K. / Su, H.P. / Klein, M.M. / Stowers, A.W. / Saul, A.J. / Long, C.A. / Garboczi, D.N.
History
DepositionMar 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Database references / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_symm_contact ...pdbx_struct_conn_angle / pdbx_validate_symm_contact / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ookinete surface protein Pvs25
B: ookinete surface protein Pvs25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,62811
Polymers42,0702
Non-polymers1,5579
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.164, 43.700, 65.650
Angle α, β, γ (deg.)90.00, 103.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ookinete surface protein Pvs25


Mass: 21035.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Plasmid: YEpRPEU-3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): S. cerevisiae VK1
Keywords: Plasmodium vivax ookinete surface protein Lacking N-terminal signal sequence and C-terminal GPI linker Reductively Methylated Protein
References: UniProt: O96555
#2: Chemical
ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Yb
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.9 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG1500, sodium accetate, ammonium accetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.09524 / Wavelength: 1.09524 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09524 Å / Relative weight: 1
ReflectionResolution: 2→28.6 Å / Num. all: 21617 / Num. obs: 21346 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 5.2 / Num. unique all: 21346 / Rsym value: 0.187 / % possible all: 98.1

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2 Å / D res low: 28.64 Å / FOM acentric: 0.413 / FOM centric: 0.169 / Reflection acentric: 19856 / Reflection centric: 1321
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_100228.64198561321
ANO_10.7180228.64197880
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_18.56-28.640015553
ISO_16.19-8.560037771
ISO_15.09-6.190051768
ISO_14.43-5.090061465
ISO_13.97-4.430069373
ISO_13.63-3.970078963
ISO_13.37-3.630085965
ISO_13.15-3.370090971
ISO_12.97-3.150099560
ISO_12.82-2.9700102765
ISO_12.69-2.8200108762
ISO_12.58-2.6900113360
ISO_12.48-2.5800119464
ISO_12.39-2.4800122262
ISO_12.31-2.3900130070
ISO_12.23-2.3100132572
ISO_12.17-2.2300136072
ISO_12.11-2.1700140169
ISO_12.05-2.1100143458
ISO_12-2.0500146578
ANO_18.56-28.640.44201290
ANO_16.19-8.560.40303690
ANO_15.09-6.190.39605120
ANO_14.43-5.090.44806120
ANO_13.97-4.430.51406890
ANO_13.63-3.970.56107890
ANO_13.37-3.630.60208580
ANO_13.15-3.370.6509090
ANO_12.97-3.150.6809950
ANO_12.82-2.970.735010270
ANO_12.69-2.820.775010870
ANO_12.58-2.690.797011330
ANO_12.48-2.580.841011940
ANO_12.39-2.480.886012210
ANO_12.31-2.390.914013000
ANO_12.23-2.310.932013240
ANO_12.17-2.230.952013580
ANO_12.11-2.170.952013990
ANO_12.05-2.110.962014300
ANO_12-2.050.963014530
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
13.43331.42910.501YB01.67
2-2.17627.919.454YB01.9
329.15919.27.271YB01.73
427.83923.73328.698YB00.89
526.69723.16332.005YB00.68
624.81225.16430.01YB01.27
746.89920.2415.089YB01.12
817.249-0.29234.397YB01.11
9-5.71216.33961.903YB00.65
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
8.56-28.640.6460.29415553
6.19-8.560.6720.24337771
5.09-6.190.6670.2651768
4.43-5.090.6210.20161465
3.97-4.430.5740.17469373
3.63-3.970.5520.17678963
3.37-3.630.5340.16185965
3.15-3.370.510.19190971
2.97-3.150.510.19499560
2.82-2.970.4920.218102765
2.69-2.820.4630.155108762
2.58-2.690.4460.233113360
2.48-2.580.4130.153119464
2.39-2.480.3690.159122262
2.31-2.390.3560.143130070
2.23-2.310.3170.118132572
2.17-2.230.2990.096136072
2.11-2.170.2780.096140169
2.05-2.110.2530.081143458
2-2.050.2490.076146578

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Processing

Software
NameVersionClassificationNB
SHARPphasing
SOLOMONphasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.6data extraction
HKL-2000data reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→28.6 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.887 / SU B: 5.455 / SU ML: 0.157 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1095 5.1 %RANDOM
Rwork0.244 ---
all0.245 21346 --
obs0.245 20249 98.75 %-
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 31.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20.56 Å2
2---0.42 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 9 88 2829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222786
X-RAY DIFFRACTIONr_angle_refined_deg1.3642.0323768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0385350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07128.033122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48115368
X-RAY DIFFRACTIONr_chiral_restr0.0820.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022004
X-RAY DIFFRACTIONr_nbd_refined0.2260.21080
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21879
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2138
X-RAY DIFFRACTIONr_metal_ion_refined0.1210.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3050.2153
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.216
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1880.210
X-RAY DIFFRACTIONr_mcbond_it0.7511.51785
X-RAY DIFFRACTIONr_mcangle_it1.20322798
X-RAY DIFFRACTIONr_scbond_it1.82631086
X-RAY DIFFRACTIONr_scangle_it3.0694.5970
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 73 -
Rwork0.251 1485 -
obs-1485 98.48 %

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