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- PDB-5jkq: Crystal structure of Plasmodium falciparum Pf3D7_0606800 (PfVFT1) -

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Basic information

Entry
Database: PDB / ID: 5jkq
TitleCrystal structure of Plasmodium falciparum Pf3D7_0606800 (PfVFT1)
ComponentsPfVFT1
KeywordsSOLUTE BINDING PROTEIN / Venus Fly Trap (VFT) domain / solute binding protein (SBP) / bi-lobed
Function / homologyVFT protein
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsParker, M.L. / Boulanger, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)Discovery Grant Canada
CitationJournal: Protein Sci. / Year: 2017
Title: The structure of Plasmodium falciparum 3D7_0606800 reveals a bi-lobed architecture that supports re-annotation as a Venus Flytrap protein.
Authors: Parker, M.L. / Ramaswamy, R. / van Gordon, K. / Powell, C.J. / Bosch, J. / Boulanger, M.J.
History
DepositionApr 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PfVFT1
B: PfVFT1
D: PfVFT1
C: PfVFT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,56610
Polymers129,9894
Non-polymers5766
Water4,378243
1
A: PfVFT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5932
Polymers32,4971
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PfVFT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5932
Polymers32,4971
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: PfVFT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6893
Polymers32,4971
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: PfVFT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6893
Polymers32,4971
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: PfVFT1
B: PfVFT1
hetero molecules

A: PfVFT1
B: PfVFT1
hetero molecules

D: PfVFT1
hetero molecules

D: PfVFT1
hetero molecules

C: PfVFT1
hetero molecules

C: PfVFT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,13120
Polymers259,9788
Non-polymers1,15312
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_456-x-1,-y,z+11
Buried area20760 Å2
ΔGint-234 kcal/mol
Surface area93320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.770, 201.430, 77.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-524-

HOH

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Components

#1: Protein
PfVFT1


Mass: 32497.281 Da / Num. of mol.: 4 / Mutation: S31A, S75A, T146A
Source method: isolated from a genetically manipulated source
Details: Three NxS/T glycosylation sites mutated to NxA
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PFF0335c / Plasmid: pAcGP67b / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C6KSR6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris:HCl pH 6.5, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2015 / Details: Rh coated focusing mirror
RadiationMonochromator: Side scattering I-beam bent single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.35→84.77 Å / Num. obs: 55998 / % possible obs: 99.8 % / Redundancy: 4.3 % / Biso Wilson estimate: 25.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.125 / Net I/σ(I): 8.6
Reflection shellResolution: 2.35→2.42 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
Blu-Icedata collection
Aimlessdata scaling
SHELXphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.35→61.45 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.57
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 2705 4.83 %Random selection
Rwork0.2038 ---
obs0.2066 55958 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.21 Å2 / Biso mean: 26.4042 Å2 / Biso min: 6.49 Å2
Refinement stepCycle: final / Resolution: 2.35→61.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8852 0 30 243 9125
Biso mean--38.65 22.74 -
Num. residues----1099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039063
X-RAY DIFFRACTIONf_angle_d0.72112268
X-RAY DIFFRACTIONf_chiral_restr0.0321384
X-RAY DIFFRACTIONf_plane_restr0.0031555
X-RAY DIFFRACTIONf_dihedral_angle_d13.3533331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.39280.30231410.245227082849100
2.3928-2.43880.32961220.242528052927100
2.4388-2.48860.2641310.239127922923100
2.4886-2.54270.33481510.236627302881100
2.5427-2.60180.30561490.237427932942100
2.6018-2.66690.31611480.2427792927100
2.6669-2.7390.29241520.236127552907100
2.739-2.81960.281350.232227722907100
2.8196-2.91060.30231420.234428042946100
2.9106-3.01460.29491440.236427902934100
3.0146-3.13530.28071550.237227792934100
3.1353-3.2780.27651480.215227992947100
3.278-3.45080.28861340.198927952929100
3.4508-3.6670.2611310.185628382969100
3.667-3.95010.24021450.171828052950100
3.9501-4.34750.20891410.153628202961100
4.3475-4.97640.18721490.15392849299899
4.9764-6.26870.22391350.19422871300699
6.2687-61.47120.22971520.20272969312198

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