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- PDB-4jle: Structure of the P. falciparum PFI1780w PHIST domain -

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Basic information

Entry
Database: PDB / ID: 4jle
TitleStructure of the P. falciparum PFI1780w PHIST domain
ComponentsPHIST
KeywordsPROTEIN BINDING / 3-helix bundle / Protein interaction module / PfEMP1 ATS domain / Human P. falciparum-infected erythrocytes
Function / homology
Function and homology information


Maurer's cleft / adhesion of symbiont to microvasculature / host cell cytosol / host cell cytoplasm / host cell plasma membrane / membrane
Similarity search - Function
Plasmodium RESA, N-terminal helical domain / Exported protein, PHISTa/b/c, conserved domain, Plasmodium / Plasmodium RESA, N-terminal / Plasmodium RESA, N-terminal helical domain superfamily / Plasmodium RESA N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special
Similarity search - Domain/homology
ACETATE ION / Plasmodium RESA N-terminal domain-containing protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsSlater, L. / Vakonakis, I.
CitationJournal: Faseb J. / Year: 2014
Title: A Plasmodium falciparum PHIST protein binds the virulence factor PfEMP1 and comigrates to knobs on the host cell surface.
Authors: Oberli, A. / Slater, L.M. / Cutts, E. / Brand, F. / Mundwiler-Pachlatko, E. / Rusch, S. / Masik, M.F. / Erat, M.C. / Beck, H.P. / Vakonakis, I.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHIST
B: PHIST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3099
Polymers41,0372
Non-polymers2727
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-161 kcal/mol
Surface area19370 Å2
MethodPISA
2
B: PHIST
hetero molecules

B: PHIST
hetero molecules

A: PHIST
hetero molecules

A: PHIST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,61818
Polymers82,0754
Non-polymers54414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
crystal symmetry operation3_564-x+y,-x+1,z-1/31
crystal symmetry operation4_566y,x+1,-z+11
Buried area8310 Å2
ΔGint-146 kcal/mol
Surface area53190 Å2
MethodPISA
3
A: PHIST
B: PHIST
hetero molecules

A: PHIST
B: PHIST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,61818
Polymers82,0754
Non-polymers54414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area26810 Å2
ΔGint-343 kcal/mol
Surface area34690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.030, 71.030, 146.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe asymmetric unit contains one helix-swapped protein dimer, however in solution under physiological conditions the protein is a monomer

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Components

#1: Protein PHIST


Mass: 20518.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: P. falciparum 3D7 / Gene: PFI1780w / Plasmid: PGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I2F2
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.0M Sodium Chloride 0.1M Sodium Acetate 22.5% Glycerol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2011
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→146.4 Å / Num. all: 18438 / Num. obs: 18438 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 53.38 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 11.8
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2646 / Rsym value: 0.494 / % possible all: 100

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.35→56.71 Å / Cor.coef. Fo:Fc: 0.9337 / Cor.coef. Fo:Fc free: 0.8976 / SU R Cruickshank DPI: 0.295
Isotropic thermal model: Isotropic thermal model with 1 TLS group per chain
Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 947 5.14 %RANDOM
Rwork0.2068 ---
all0.2092 18437 --
obs0.2092 18437 99.82 %-
Displacement parametersBiso mean: 66.53 Å2
Baniso -1Baniso -2Baniso -3
1--7.5734 Å20 Å20 Å2
2---7.5734 Å20 Å2
3---15.1469 Å2
Refine analyzeLuzzati coordinate error obs: 0.369 Å
Refinement stepCycle: LAST / Resolution: 2.35→56.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 10 47 2735
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012756HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.963664HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1371SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes84HARMONIC2
X-RAY DIFFRACTIONt_gen_planes380HARMONIC5
X-RAY DIFFRACTIONt_it2756HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion3.4
X-RAY DIFFRACTIONt_chiral_improper_torsion329SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3261SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.49 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2579 137 4.68 %
Rwork0.2285 2790 -
all0.23 2927 -
obs-2927 99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4129-0.501-0.06350.66350.45161.62840.01160.00110.06610.05030.1695-0.1481-0.19280.1944-0.1811-0.2315-0.03750.0859-0.4673-0.0129-0.4453.205757.545767.1634
20.1177-0.15770.36010.19310.02751.83350.24180.05540.0628-0.02260.00720.03550.036-0.2024-0.249-0.46540.00610.0287-0.59490.0339-0.6492-10.675844.999352.4065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|19 - A|167 }A19 - 167
2X-RAY DIFFRACTION2{ B|6 - B|164 }B6 - 164

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