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- PDB-7d2w: Crystal structure of PHIT/PHISTa-like subfamily PF3D7_1372300 pro... -

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Basic information

Entry
Database: PDB / ID: 7d2w
TitleCrystal structure of PHIT/PHISTa-like subfamily PF3D7_1372300 protein from plasmodium falciparum
ComponentsPRESAN domain-containing protein
KeywordsPROTEIN BINDING / four-helix bundle structure
Function / homologyExported protein, PHISTa/b/c, conserved domain, Plasmodium / Plasmodium RESA, N-terminal / Plasmodium RESA, N-terminal helical domain superfamily / Plasmodium RESA N-terminal / : / Plasmodium RESA N-terminal domain-containing protein
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsGao, Y. / Yang, B.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No. 21736002, 31770827, 31961133015 China
CitationJournal: To Be Published
Title: Structural analysis of binding between Plasmodium falciparum PHIST and the parasite virulence factor PfEMP1 protein
Authors: Yang, B.L. / Gao, Y.
History
DepositionSep 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRESAN domain-containing protein
B: PRESAN domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1123
Polymers44,9112
Non-polymers2011
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-53 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.523, 78.523, 100.559
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein PRESAN domain-containing protein


Mass: 22455.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_1372300
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A143ZZR8
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 38.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 16% PEG 8000, 50mM KH2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.0082 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 31, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0082 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 24930 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 32.35 Å2 / CC1/2: 1 / Net I/σ(I): 45.45
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 20.5 % / Num. unique obs: 2472 / CC1/2: 0.972 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→40.43 Å / SU ML: 0.2055 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.3592 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1981 8.01 %Random selection
Rwork0.1716 22741 --
obs0.1742 24722 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.48 Å2
Refinement stepCycle: LAST / Resolution: 1.97→40.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 2 240 2290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682217
X-RAY DIFFRACTIONf_angle_d0.75873017
X-RAY DIFFRACTIONf_chiral_restr0.0375331
X-RAY DIFFRACTIONf_plane_restr0.0046388
X-RAY DIFFRACTIONf_dihedral_angle_d6.14651857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.020.26931410.21511565X-RAY DIFFRACTION96.11
2.02-2.070.28851420.19811571X-RAY DIFFRACTION97.83
2.07-2.130.26241350.1931623X-RAY DIFFRACTION98.82
2.13-2.20.23691400.18021620X-RAY DIFFRACTION99.44
2.2-2.280.21821370.18341636X-RAY DIFFRACTION99.55
2.28-2.370.26591450.17861610X-RAY DIFFRACTION99.55
2.37-2.480.24241460.18111627X-RAY DIFFRACTION99.66
2.48-2.610.20461410.18811643X-RAY DIFFRACTION99.94
2.61-2.770.23471400.18761641X-RAY DIFFRACTION99.94
2.77-2.990.20621410.1731618X-RAY DIFFRACTION100
2.99-3.290.21091390.18331646X-RAY DIFFRACTION100
3.29-3.770.1711470.15991642X-RAY DIFFRACTION99.94
3.77-4.740.17481410.1441642X-RAY DIFFRACTION99.94
4.74-40.430.18341460.17131657X-RAY DIFFRACTION99.07
Refinement TLS params.Method: refined / Origin x: 8.04585106279 Å / Origin y: 38.8152267928 Å / Origin z: 38.4751052902 Å
111213212223313233
T0.207290214153 Å20.0218140398213 Å2-0.010521790008 Å2-0.234381304731 Å2-0.019790610255 Å2--0.192548350823 Å2
L1.51692694321 °20.290065503077 °2-0.26281928581 °2-1.21503238648 °2-0.156067368622 °2--1.31190212964 °2
S-0.00808507486276 Å °0.038179189821 Å °-0.0164228618079 Å °-0.0410715156679 Å °0.0654362236042 Å °0.0484566396545 Å °-0.0434253882575 Å °-0.0367412412209 Å °-0.0471403183734 Å °
Refinement TLS groupSelection details: all

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