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

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Basic information

Entry
Database: PDB / ID: 4irf
TitlePreliminary structural investigations of a malarial protein secretion system
ComponentsMALARIAL CLPB2 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 / : ...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 / Clp repeat (R) domain profile. / 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: 1.65 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 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALARIAL CLPB2 ATPASE/HSP101 PROTEIN
B: MALARIAL CLPB2 ATPASE/HSP101 PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,6682
Polymers34,6682
Non-polymers00
Water4,017223
1
A: MALARIAL CLPB2 ATPASE/HSP101 PROTEIN


Theoretical massNumber of molelcules
Total (without water)17,3341
Polymers17,3341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MALARIAL CLPB2 ATPASE/HSP101 PROTEIN


Theoretical massNumber of molelcules
Total (without water)17,3341
Polymers17,3341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.780, 92.080, 96.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein MALARIAL CLPB2 ATPASE/HSP101 PROTEIN


Mass: 17333.771 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 273 K / pH: 9.4
Details: PEG 3350 20%, 0.1M CAPSO pH 9.4, 10% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2012
RadiationMonochromator: CRYOGENICALLY-COOLED SINGLE CRYSTAL SI(111) SIDE BOUNCE MONOCHROMATOR.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.645→66.78 Å / Num. obs: 35144 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 28.2 Å2 / Rsym value: 0.063 / Net I/σ(I): 15
Reflection shellResolution: 1.65→1.67 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.478 / % possible all: 94.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IOD

4iod


Resolution: 1.65→66.78 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 3513 10 %
Rwork0.214 --
obs0.216 35142 99 %
all-35142 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→66.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 0 223 2444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182280
X-RAY DIFFRACTIONf_angle_d1.9043085
X-RAY DIFFRACTIONf_dihedral_angle_d14.689852
X-RAY DIFFRACTIONf_chiral_restr0.097364
X-RAY DIFFRACTIONf_plane_restr0.008398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.645-1.66790.30351280.27221150X-RAY DIFFRACTION92
1.6679-1.69170.31441360.25811221X-RAY DIFFRACTION98
1.6917-1.7170.29121390.25791246X-RAY DIFFRACTION100
1.717-1.74380.32151400.25211265X-RAY DIFFRACTION100
1.7438-1.77240.32871400.24691258X-RAY DIFFRACTION99
1.7724-1.80290.27991380.23961237X-RAY DIFFRACTION100
1.8029-1.83570.28991380.26121244X-RAY DIFFRACTION99
1.8357-1.8710.31241400.25661254X-RAY DIFFRACTION98
1.871-1.90920.33091370.25161242X-RAY DIFFRACTION99
1.9092-1.95080.27611380.25371241X-RAY DIFFRACTION100
1.9508-1.99610.26781430.24511291X-RAY DIFFRACTION99
1.9961-2.04610.27631370.23691237X-RAY DIFFRACTION100
2.0461-2.10140.26081420.241273X-RAY DIFFRACTION100
2.1014-2.16320.26341400.22331258X-RAY DIFFRACTION100
2.1632-2.2330.26841410.22311267X-RAY DIFFRACTION100
2.233-2.31290.2661400.21691277X-RAY DIFFRACTION99
2.3129-2.40550.26391370.21571233X-RAY DIFFRACTION98
2.4055-2.5150.22831420.20771276X-RAY DIFFRACTION100
2.515-2.64760.2671430.21011304X-RAY DIFFRACTION100
2.6476-2.81340.2491390.22171254X-RAY DIFFRACTION100
2.8134-3.03070.25661440.21911293X-RAY DIFFRACTION100
3.0307-3.33560.21821450.20691301X-RAY DIFFRACTION100
3.3356-3.81830.18551410.18511281X-RAY DIFFRACTION97
3.8183-4.81040.19151480.17811331X-RAY DIFFRACTION100
4.8104-66.83050.21511570.23151395X-RAY DIFFRACTION98
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)
12.393-0.5712-0.0683.1599-0.30562.0133-0.08730.07790.3352-0.16820.0780.22740.0886-0.05140.04210.1833-0.021-0.12760.20980.03210.26190.4419-7.806123.0319
22.0577-0.8124-0.22045.0859-0.3683.3538-0.0415-0.2922-0.0930.50120.24550.3743-0.2169-0.3184-0.20930.32320.0085-0.0280.30.05990.1735-3.3601-25.210344.3974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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