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- PDB-4xbi: Structure Of A Malarial Protein Involved in Proteostasis -

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Basic information

Entry
Database: PDB / ID: 4xbi
TitleStructure Of A Malarial Protein Involved in Proteostasis
ComponentsClpB protein, putative,Green fluorescent protein
KeywordsCHAPERONE / CLP Chaperone / AAA+ ATPase / Refoldase / Protein Metabolism
Function / homology
Function and homology information


apicoplast / bioluminescence / generation of precursor metabolites and energy / cellular response to heat / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
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 ...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 / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein / Chaperone protein ClpB1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.013 Å
AuthorsEgea, P.F. / Ah Young, A.P. / Cascio, D.
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
DepositionDec 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ClpB protein, putative,Green fluorescent protein
B: ClpB protein, putative,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0447
Polymers86,5642
Non-polymers4805
Water6,882382
1
A: ClpB protein, putative,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5704
Polymers43,2821
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ClpB protein, putative,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4743
Polymers43,2821
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.530, 127.530, 92.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein ClpB protein, putative,Green fluorescent protein /


Mass: 43281.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote), (gene. exp.) Aequorea victoria (jellyfish)
Strain: isolate 3D7 / Gene: PF08_0063, GFP / Plasmid: pRSF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q8IB03, UniProt: P42212
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.51 Å3/Da / Density % sol: 51.03 % / Description: bright yellow hexagonal shaped
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 2 M ammonium sulphate 100 mM Hepes pH=7 protein at 13-15 mg/ml
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.01→70.946 Å / Num. all: 55948 / Num. obs: 55948 / % possible obs: 98.6 % / Redundancy: 5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.94
Reflection shellResolution: 2.01→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.68 / % possible all: 90.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P, 4IOD and 4IRF

2b3p

4iod

4irf


Resolution: 2.013→70.946 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 2804 5.02 %Random selection
Rwork0.1668 ---
obs0.1685 55908 98.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.013→70.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5817 0 25 382 6224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075988
X-RAY DIFFRACTIONf_angle_d1.0358103
X-RAY DIFFRACTIONf_dihedral_angle_d13.2252190
X-RAY DIFFRACTIONf_chiral_restr0.043908
X-RAY DIFFRACTIONf_plane_restr0.0041039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0131-2.04790.27681010.22892334X-RAY DIFFRACTION86
2.0479-2.08510.23041340.19422665X-RAY DIFFRACTION100
2.0851-2.12520.23641750.18762650X-RAY DIFFRACTION100
2.1252-2.16860.22971530.18462650X-RAY DIFFRACTION100
2.1686-2.21570.21841430.17622690X-RAY DIFFRACTION100
2.2157-2.26730.24551290.17742679X-RAY DIFFRACTION100
2.2673-2.3240.22421410.17232698X-RAY DIFFRACTION100
2.324-2.38680.21791400.16992680X-RAY DIFFRACTION100
2.3868-2.45710.21611430.17612661X-RAY DIFFRACTION100
2.4571-2.53640.22891400.17912688X-RAY DIFFRACTION100
2.5364-2.6270.21421430.18082667X-RAY DIFFRACTION100
2.627-2.73220.21751400.18472680X-RAY DIFFRACTION100
2.7322-2.85660.2191420.19432673X-RAY DIFFRACTION99
2.8566-3.00720.25191400.19872668X-RAY DIFFRACTION99
3.0072-3.19560.23921440.17732678X-RAY DIFFRACTION99
3.1956-3.44230.20741400.17252674X-RAY DIFFRACTION99
3.4423-3.78870.17771410.15632665X-RAY DIFFRACTION99
3.7887-4.33690.17431360.1412673X-RAY DIFFRACTION98
4.3369-5.46370.17181380.13912664X-RAY DIFFRACTION98
5.4637-70.98960.17141410.16522667X-RAY DIFFRACTION97
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)
12.9742-0.2561-2.2691.7280.86643.94920.21340.0455-0.1475-0.4929-0.1958-0.0477-0.15830.1001-0.00380.68870.05610.08710.57220.01660.4939-0.117544.730965.0787
21.8032-0.26950.07191.420.11541.15570.0386-0.12730.07370.1259-0.04360.0339-0.1035-0.12610.00380.25780.0017-0.00980.2263-0.02440.196614.937527.910930.6248
32.3174-0.7186-0.20272.14570.36771.90280.0797-0.5530.7729-0.02590.0413-0.1463-0.0619-0.1495-0.12160.34240.00310.10630.5873-0.1260.702367.240127.06326.0582
43.2832-0.0204-0.13591.90130.28712.0313-0.03720.29330.367-0.09310.0653-0.1263-0.15220.266-0.05150.2933-0.0199-0.01540.27060.0110.296829.487446.136311.2314
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 7:148
2X-RAY DIFFRACTION2chain A and resseq 149:382
3X-RAY DIFFRACTION3chain B and resseq 5:149
4X-RAY DIFFRACTION4chain B and resseq 150:379

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