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- PDB-8d1w: Crystal structure of Plasmodium falciparum GRP78 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8d1w
TitleCrystal structure of Plasmodium falciparum GRP78 in complex with (2R,3R,4S,5R)-2-(6-amino-8-((2-chlorobenzyl)amino)-9H-purin-9-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol
ComponentsChaperone DnaK
KeywordsCHAPERONE / ATPase
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / endoplasmic reticulum / ATP binding
Similarity search - Function
Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, nucleotide binding domain
Similarity search - Domain/homology
8-{[(2-chlorophenyl)methyl]amino}adenosine / Chaperone DnaK
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMrozek, A. / Chen, Y. / Antoshchenko, T. / Park, H.W. / Smil, D. / Zepeda, C.A.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Frontiers in Molecular Bioscience / Year: 2022
Title: Targeting Plasmodium falciparum GRP78: nucleoside analogues as agents against the malaria chaperone
Authors: Mrozek, A. / Park, H.W.
History
DepositionMay 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9594
Polymers44,3601
Non-polymers5993
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.288, 84.288, 292.218
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Chaperone DnaK


Mass: 44360.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate Palo Alto / Uganda / Gene: PFUGPA_02944 / Production host: Escherichia coli (E. coli) / References: UniProt: W4J0F1
#2: Chemical ChemComp-HFY / 8-{[(2-chlorophenyl)methyl]amino}adenosine


Mass: 406.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19ClN6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.59 Å3/Da / Density % sol: 65.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.7 M (NH4)2SO4, 1.2 M Li2SO4, 0.1 M NaCitrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 36996 / % possible obs: 100 % / Redundancy: 18.9 % / Rrim(I) all: 0.1 / Rsym value: 0.09 / Net I/σ(I): 28.9
Reflection shellResolution: 2.1→2.23 Å / Num. unique obs: 5825 / Rrim(I) all: 0.51 / Rsym value: 0.49 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UMB

5umb


Resolution: 2.1→45.66 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.481 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22145 1824 4.9 %RANDOM
Rwork0.1897 ---
obs0.19131 35168 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.561 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20.5 Å20 Å2
2--1 Å2-0 Å2
3----3.24 Å2
Refinement stepCycle: 1 / Resolution: 2.1→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 38 266 3255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133058
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172925
X-RAY DIFFRACTIONr_angle_refined_deg1.781.6434136
X-RAY DIFFRACTIONr_angle_other_deg1.4171.5916803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24123.654156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70415563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7431517
X-RAY DIFFRACTIONr_chiral_restr0.090.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023495
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2273.1721524
X-RAY DIFFRACTIONr_mcbond_other3.2273.1721524
X-RAY DIFFRACTIONr_mcangle_it3.9394.7361907
X-RAY DIFFRACTIONr_mcangle_other3.9384.7351908
X-RAY DIFFRACTIONr_scbond_it4.9583.8231533
X-RAY DIFFRACTIONr_scbond_other4.9333.8161525
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4025.4652218
X-RAY DIFFRACTIONr_long_range_B_refined8.54439.0753383
X-RAY DIFFRACTIONr_long_range_B_other8.52938.6343321
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 134 -
Rwork0.213 2520 -
obs--99.89 %

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