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- PDB-8d20: Crystal structure of Plasmodium falciparum GRP78 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8d20
TitleCrystal structure of Plasmodium falciparum GRP78 in complex with 5'-Methylthioadenosine
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 ...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 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / Endoplasmic reticulum chaperone BIP
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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

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Assembly

Deposited unit
A: Chaperone DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8504
Polymers44,3601
Non-polymers4893
Water5,819323
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)84.322, 84.322, 291.748
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-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S / 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.: 323 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
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: CLSI / Beamline: 08B1-1 / Wavelength: 1.5212 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5212 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 44948 / % possible obs: 97.3 % / Redundancy: 19.2 % / Rrim(I) all: 0.52 / Rsym value: 0.08 / Net I/σ(I): 37.96
Reflection shellResolution: 1.95→2.06 Å / Num. unique obs: 136029 / Rrim(I) all: 0.52 / 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: 1.95→45.63 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.715 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22687 2172 4.8 %RANDOM
Rwork0.19391 ---
obs0.19552 42772 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.308 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å20 Å2
2--0.66 Å2-0 Å2
3----2.16 Å2
Refinement stepCycle: 1 / Resolution: 1.95→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 30 323 3304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133090
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172960
X-RAY DIFFRACTIONr_angle_refined_deg1.81.6564184
X-RAY DIFFRACTIONr_angle_other_deg1.4661.596882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2315390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37123.354161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95615571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.211519
X-RAY DIFFRACTIONr_chiral_restr0.0970.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02607
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_it2.3152.1891542
X-RAY DIFFRACTIONr_mcbond_other2.3142.1891540
X-RAY DIFFRACTIONr_mcangle_it2.9253.2661938
X-RAY DIFFRACTIONr_mcangle_other2.9253.2661938
X-RAY DIFFRACTIONr_scbond_it3.6042.6381547
X-RAY DIFFRACTIONr_scbond_other3.5942.6351539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4643.7742235
X-RAY DIFFRACTIONr_long_range_B_refined6.59327.3733516
X-RAY DIFFRACTIONr_long_range_B_other6.55827.0083439
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→1.997 Å
RfactorNum. reflection% reflection
Rfree0.249 146 -
Rwork0.202 3005 -
obs--94.37 %

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