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- PDB-4iod: Preliminary structural investigations of a malarial protein secre... -

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Basic information

Entry
Database: PDB / ID: 4iod
TitlePreliminary structural investigations of a malarial protein secretion system.
ComponentsMalarial CLP B2 atpase/HSP101 protein
KeywordsCHAPERONE / MALARIA / AAA+ ATPASE ClpB CHAPERONE / N-TERMINAL CARGO-BINDING DOMAIN / PROTEIN TRANSLOCATION AND UNFOLDING / PARASITOPHOROUS VACUOLE
Function / homology
Function and homology information


PTEX complex / apical complex / symbiont-containing vacuole / translocation of peptides or proteins into host cell cytoplasm / symbiont-containing vacuole membrane / response to unfolded protein / cellular response to heat / response to heat / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Double Clp-N motif / Clp, N-terminal domain / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. ...Double Clp-N motif / Clp, N-terminal domain / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Heat shock protein 101
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEgea, P.F.
CitationJournal: Protein Sci. / Year: 2015
Title: Structural mapping of the ClpB ATPases of Plasmodium falciparum: Targeting protein folding and secretion for antimalarial drug design.
Authors: AhYoung, A.P. / Koehl, A. / Cascio, D. / Egea, P.F.
History
DepositionJan 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
B: Malarial CLP B2 atpase/HSP101 protein
A: Malarial CLP B2 atpase/HSP101 protein
C: Malarial CLP B2 atpase/HSP101 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2906
Polymers52,0013
Non-polymers2883
Water6,684371
1
A: Malarial CLP B2 atpase/HSP101 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4302
Polymers17,3341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Malarial CLP B2 atpase/HSP101 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4302
Polymers17,3341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Malarial CLP B2 atpase/HSP101 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4302
Polymers17,3341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Malarial CLP B2 atpase/HSP101 protein
A: Malarial CLP B2 atpase/HSP101 protein
hetero molecules

B: Malarial CLP B2 atpase/HSP101 protein
A: Malarial CLP B2 atpase/HSP101 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7198
Polymers69,3354
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6520 Å2
ΔGint-84 kcal/mol
Surface area26870 Å2
MethodPISA
5
C: Malarial CLP B2 atpase/HSP101 protein
hetero molecules

C: Malarial CLP B2 atpase/HSP101 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8604
Polymers34,6682
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2320 Å2
ΔGint-33 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.180, 141.010, 91.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-336-

HOH

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Components

#1: Protein Malarial CLP B2 atpase/HSP101 protein


Mass: 17333.771 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF11_0175, PF3D7_1116800 / Plasmid: pCDF / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q8IIJ8
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 273 K / pH: 5.5
Details: 2.2M AMMONIUM SULFATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2012
RadiationMonochromator: CRYOGENICALLY-COOLED SINGLE CRYSTAL SI(220) SIDE BOUNCE MONOCHROMATOR.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→45 Å / Num. obs: 53488 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 9.9 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.071 / Net I/σ(I): 21.6

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Processing

Software
NameVersionClassification
CONSOLEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KHY AND 1QVR

1khy

1qvr


Resolution: 1.8→44.59 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 5334 9.97 %
Rwork0.17 --
obs0.175 53476 99.7 %
all-53488 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.28 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1112 Å20 Å2-0 Å2
2--1.3591 Å20 Å2
3----1.2479 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3407 0 15 371 3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143585
X-RAY DIFFRACTIONf_angle_d1.2314877
X-RAY DIFFRACTIONf_dihedral_angle_d14.951374
X-RAY DIFFRACTIONf_chiral_restr0.078576
X-RAY DIFFRACTIONf_plane_restr0.007628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.28041560.22711489X-RAY DIFFRACTION93
1.8205-1.84190.30341640.20961582X-RAY DIFFRACTION100
1.8419-1.86430.27191740.21615X-RAY DIFFRACTION100
1.8643-1.88790.29721880.19281573X-RAY DIFFRACTION100
1.8879-1.91280.27991940.18761574X-RAY DIFFRACTION100
1.9128-1.9390.25951660.17521618X-RAY DIFFRACTION100
1.939-1.96670.24481690.16531582X-RAY DIFFRACTION100
1.9667-1.9960.22551830.15711594X-RAY DIFFRACTION100
1.996-2.02720.21961770.15791612X-RAY DIFFRACTION100
2.0272-2.06050.22711740.15411570X-RAY DIFFRACTION100
2.0605-2.0960.21221800.15351603X-RAY DIFFRACTION100
2.096-2.13410.21541790.15041601X-RAY DIFFRACTION100
2.1341-2.17510.20061690.15421577X-RAY DIFFRACTION100
2.1751-2.21950.21391770.1471585X-RAY DIFFRACTION100
2.2195-2.26780.19171830.14211588X-RAY DIFFRACTION100
2.2678-2.32060.20151780.14371633X-RAY DIFFRACTION100
2.3206-2.37860.21981710.14521589X-RAY DIFFRACTION100
2.3786-2.44290.20431770.15551610X-RAY DIFFRACTION100
2.4429-2.51480.21781820.15741604X-RAY DIFFRACTION100
2.5148-2.59590.20531790.16811591X-RAY DIFFRACTION100
2.5959-2.68870.21351770.16321632X-RAY DIFFRACTION100
2.6887-2.79630.2111790.16941604X-RAY DIFFRACTION100
2.7963-2.92360.24261770.17241595X-RAY DIFFRACTION100
2.9236-3.07770.23621850.19531628X-RAY DIFFRACTION100
3.0777-3.27050.21631790.1971615X-RAY DIFFRACTION100
3.2705-3.52290.22161790.17751630X-RAY DIFFRACTION100
3.5229-3.87720.19591780.16511637X-RAY DIFFRACTION100
3.8772-4.43780.15481880.14811635X-RAY DIFFRACTION100
4.4378-5.58950.19291860.1651660X-RAY DIFFRACTION100
5.5895-44.60370.20291860.21621716X-RAY DIFFRACTION99
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)
10.2343-0.1930.16940.5892-0.56850.8432-0.068-0.0392-0.0550.08620.07080.0623-0.1009-0.058-0.01650.08060.0240.00370.05440.01730.0609-29.2135-15.248724.8367
20.5590.3641-0.16220.3469-0.30460.65630.0456-0.05780.02970.0647-0.0480.0466-0.07410.0848-0.01180.1088-0.01770.02980.0957-0.00640.1027-29.892616.50178.5833
30.7484-0.0191-0.70980.3347-0.06310.7714-0.0315-0.0695-0.01790.0531-0.0627-0.0840.08530.0477-0.04290.0886-0.01210.0140.1169-0.01240.1319-0.835731.2842-6.2022
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA10 - 422
2X-RAY DIFFRACTION2chain BB10 - 447
3X-RAY DIFFRACTION3chain CC11 - 402

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