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- PDB-8d24: Crystal structure of Plasmodium falciparum GRP78-NBD in complex w... -

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Basic information

Entry
Database: PDB / ID: 8d24
TitleCrystal structure of Plasmodium falciparum GRP78-NBD in complex with VER155008
ComponentsChaperone DnaK
KeywordsCHAPERONE / ATPase
Function / homology
Function and homology information


non-chaperonin molecular chaperone ATPase / 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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Chem-3FD / Endoplasmic reticulum chaperone BIP
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMrozek, A. / Park, H.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Front Mol Biosci / Year: 2022
Title: A non-traditional crystal-based compound screening method targeting the ATP binding site of Plasmodium falciparum GRP78 for identification of novel nucleoside analogues.
Authors: Mrozek, A. / Antoshchenko, T. / Chen, Y. / Zepeda-Velazquez, C. / Smil, D. / Kumar, N. / Lu, H. / 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
Revision 1.2Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperone DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1094
Polymers44,3601
Non-polymers7493
Water5,441302
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)83.997, 83.997, 292.603
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 / Strain: isolate Palo Alto / Uganda / Gene: PFUGPA_02944 / Production host: Escherichia coli (E. coli) / References: UniProt: W4J0F1
#2: Chemical ChemComp-3FD / 4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile


Mass: 556.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H23Cl2N7O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 302 / 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: 3.36 Å3/Da / Density % sol: 63.38 %
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: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 62702 / % possible obs: 100 % / Redundancy: 19 % / Rrim(I) all: 0.06 / Rsym value: 0.06 / Net I/σ(I): 32.2
Reflection shellResolution: 1.75→1.86 Å / Num. unique obs: 9890 / Rrim(I) all: 0.53 / Rsym value: 0.51

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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: 1.75→48.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.954 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21699 3085 4.9 %RANDOM
Rwork0.20065 ---
obs0.20146 59614 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.202 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.38 Å20 Å2
2--0.75 Å2-0 Å2
3----2.44 Å2
Refinement stepCycle: 1 / Resolution: 1.75→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 48 302 3301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133184
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173026
X-RAY DIFFRACTIONr_angle_refined_deg1.861.6654323
X-RAY DIFFRACTIONr_angle_other_deg1.4911.5947045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1845405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46423.415164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53915585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7111519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023737
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02632
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_it2.2892.3611582
X-RAY DIFFRACTIONr_mcbond_other2.2812.361579
X-RAY DIFFRACTIONr_mcangle_it2.9193.5271999
X-RAY DIFFRACTIONr_mcangle_other2.9183.5272000
X-RAY DIFFRACTIONr_scbond_it3.872.8481600
X-RAY DIFFRACTIONr_scbond_other3.8642.8491593
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6944.0942313
X-RAY DIFFRACTIONr_long_range_B_refined6.69929.6143575
X-RAY DIFFRACTIONr_long_range_B_other6.6429.233513
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 224 -
Rwork0.232 4275 -
obs--99.93 %

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