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- PDB-4f1k: Crystal structure of the MG2+ free VWA domain of plasmodium falci... -

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Basic information

Entry
Database: PDB / ID: 4f1k
TitleCrystal structure of the MG2+ free VWA domain of plasmodium falciparum trap protein
ComponentsThrombospondin related anonymous protein
KeywordsCELL ADHESION / Rossmann fold / DINUCLEOTIDE BINDING / MEMBRANE
Function / homology
Function and homology information


metal ion binding / plasma membrane
Similarity search - Function
Thrombospondin type 1 domain / von Willebrand factor, type A domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A ...Thrombospondin type 1 domain / von Willebrand factor, type A domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thrombospondin related anonymous protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.87 Å
AuthorsPihlajamaa, T. / Knuuti, J. / Kajander, T. / Sharma, A. / Permi, P.
CitationJournal: Biochem.J. / Year: 2013
Title: Structure of Plasmodium falciparum TRAP (thrombospondin-related anonymous protein) A domain highlights distinct features in apicomplexan von Willebrand factor A homologues.
Authors: Pihlajamaa, T. / Kajander, T. / Knuuti, J. / Horkka, K. / Sharma, A. / Permi, P.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thrombospondin related anonymous protein
B: Thrombospondin related anonymous protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,98723
Polymers45,5322
Non-polymers1,45421
Water5,062281
1
A: Thrombospondin related anonymous protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,46211
Polymers22,7661
Non-polymers69610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thrombospondin related anonymous protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,52412
Polymers22,7661
Non-polymers75811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.434, 89.434, 104.232
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A43 - 238
2115B43 - 238

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Components

#1: Protein Thrombospondin related anonymous protein / Thrombospondin-related adhesive protein


Mass: 22766.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: THROMBOSPONDIN RELATED ANONYMOUS PROTEIN (TRAP), TRAP / Plasmid: pRAT4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01502
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% PEG 3350, 0.1M HEPES, 0.2M lithium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 24, 2010
Details: THE OPTICAL ELEMENTS CONSIST OF A VERTICALLY COLLIMATING MIRROR (M1, FOCUS AT INFINITY) FOLLOWED BY A BARTELS MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS (DCCM) IN (+--+) GEOMETRY, AND A ...Details: THE OPTICAL ELEMENTS CONSIST OF A VERTICALLY COLLIMATING MIRROR (M1, FOCUS AT INFINITY) FOLLOWED BY A BARTELS MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS (DCCM) IN (+--+) GEOMETRY, AND A TOROIDAL MIRROR (M2) TO VERTICALLY AND HORIZONTALLY FOCUS THE BEAM AT THE SAMPLE POSITION (WITH 2:1 HORIZONTAL DEMAGNIFICATION)
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 66642 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.28 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.49
Reflection shellResolution: 1.87→1.99 Å / Redundancy: 4.18 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.24 / Num. unique all: 10559 / % possible all: 98

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.87→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.138 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23663 1767 5 %RANDOM
Rwork0.18769 ---
all0.19013 35374 --
obs0.19013 33607 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.87→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3074 0 84 281 3439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223214
X-RAY DIFFRACTIONr_bond_other_d0.0020.022150
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9684339
X-RAY DIFFRACTIONr_angle_other_deg1.0413.0035263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4285406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70525.211142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11415560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1831517
X-RAY DIFFRACTIONr_chiral_restr0.1070.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023519
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02586
X-RAY DIFFRACTIONr_nbd_refined0.2030.2689
X-RAY DIFFRACTIONr_nbd_other0.1990.22367
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21518
X-RAY DIFFRACTIONr_nbtor_other0.0860.21625
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.215
X-RAY DIFFRACTIONr_mcbond_it1.0181.52209
X-RAY DIFFRACTIONr_mcbond_other0.2721.5812
X-RAY DIFFRACTIONr_mcangle_it1.38923221
X-RAY DIFFRACTIONr_scbond_it2.37631307
X-RAY DIFFRACTIONr_scangle_it3.5224.51114
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1159medium positional0.090.5
1320loose positional0.45
1159medium thermal0.752
1320loose thermal1.1910
LS refinement shellResolution: 1.872→1.921 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 125 -
Rwork0.212 2367 -
obs-2367 100 %

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