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- PDB-4zgc: Crystal Structure Analysis of Kelch protein (with disulfide bond)... -

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Basic information

Entry
Database: PDB / ID: 4zgc
TitleCrystal Structure Analysis of Kelch protein (with disulfide bond) from Plasmodium falciparum
ComponentsKelch protein
KeywordsSTRUCTURAL GENOMICS / Structural Genomics Consortium / SGC / Putative Kelch Protein / K13 / Disulfide Bond
Function / homology
Function and homology information


: / Antigen processing: Ubiquitination & Proteasome degradation / response to xenobiotic stimulus => GO:0009410 / protein homooligomerization
Similarity search - Function
Galactose oxidase, central domain / Kelch-type beta propeller / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Kelch / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller ...Galactose oxidase, central domain / Kelch-type beta propeller / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Kelch / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / 6 Propeller / Neuraminidase / SKP1/BTB/POZ domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Kelch protein / Kelch protein K13
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / He, H. / Ravichandran, M. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / He, H. / Ravichandran, M. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / El Bakkouri, M. / Senisterra, G. / Osman, K.T. / Lovato, D.V. / Hui, R. / Hutchinson, A. / Lin, Y.H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of kelch protein with disulfide bond from Plasmodium falciparum.
Authors: Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / He, H. / Ravichandran, M. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / El Bakkouri, M. / Senisterra, G. ...Authors: Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / He, H. / Ravichandran, M. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / El Bakkouri, M. / Senisterra, G. / Osman, K.T. / Lovato, D.V. / Hutchinson, A. / Lin, Y.H.
History
DepositionApr 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references / Structure summary
Revision 1.2Sep 27, 2017Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_detector / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch protein
B: Kelch protein


Theoretical massNumber of molelcules
Total (without water)88,46838
Polymers88,4682
Non-polymers036
Water2,234124
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-12 kcal/mol
Surface area29590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.942, 117.634, 74.508
Angle α, β, γ (deg.)90.000, 113.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ILE / End label comp-ID: ILE

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRTHRchain AAA350 - 72613 - 389
2METMETchain BBB351 - 72614 - 389
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein Kelch protein


Mass: 44234.012 Da / Num. of mol.: 2 / Fragment: UNP residues 338-726
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF13_0238 / Plasmid: PFBOH-MH / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: A0A077LQB4, UniProt: Q8IDQ2*PLUS
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 36 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 33667 / % possible obs: 98.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 35.72 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.091 / Rrim(I) all: 0.154 / Χ2: 4.522 / Net I/av σ(I): 13.941 / Net I/σ(I): 8.9 / Num. measured all: 88485
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.542.60.58916190.6460.4360.7351.63696.7
2.54-2.592.60.54916460.6650.4080.6861.62497.1
2.59-2.642.60.45916530.7720.340.5731.67497.5
2.64-2.692.60.42316690.7290.3130.5291.72797.1
2.69-2.752.60.34216690.8320.2540.4281.78397.9
2.75-2.822.70.30716660.8640.2280.3841.8397.9
2.82-2.892.60.25516670.8930.1890.3191.75797.4
2.89-2.962.60.23616870.9070.1740.2942.1598.3
2.96-3.052.60.19416510.9320.1440.2422.49898.3
3.05-3.152.60.16916990.9570.1260.2122.18598.4
3.15-3.262.70.14716720.9590.1090.1842.17798.4
3.26-3.392.70.12816900.9670.0940.163.29198.7
3.39-3.552.60.11716860.9690.0870.1463.29999
3.55-3.732.60.10116920.9770.0750.1263.71598.8
3.73-3.972.70.09117140.980.0670.1144.46699.5
3.97-4.272.60.08416870.9730.0620.1056.72399.4
4.27-4.72.60.08117160.9710.060.10112.23799.2
4.7-5.382.60.08217190.9760.0610.1028.4599.8
5.38-6.782.60.09117240.9740.0670.1147.78799.9
6.78-502.50.08617410.9650.0640.10819.55398.9

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4YY8

4yy8


Resolution: 2.5→36.486 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2531 1667 4.96 %
Rwork0.1916 31968 -
obs0.1948 33635 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.4 Å2 / Biso mean: 37.2524 Å2 / Biso min: 12.15 Å2
Refinement stepCycle: final / Resolution: 2.5→36.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5714 0 36 124 5874
Biso mean--29.47 31.83 -
Num. residues----745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095889
X-RAY DIFFRACTIONf_angle_d1.1398021
X-RAY DIFFRACTIONf_chiral_restr0.049881
X-RAY DIFFRACTIONf_plane_restr0.0061048
X-RAY DIFFRACTIONf_dihedral_angle_d12.3522067
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3068X-RAY DIFFRACTION6.262TORSIONAL
12B3068X-RAY DIFFRACTION6.262TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.5760.38081250.2832540266595
2.576-2.65910.39411240.26592651277597
2.6591-2.75410.31211120.25472651276398
2.7541-2.86430.2961130.23272698281198
2.8643-2.99460.28911380.2262627276598
2.9946-3.15240.28921520.21612646279898
3.1524-3.34980.27951500.20632662281299
3.3498-3.60820.24631340.19632689282399
3.6082-3.9710.27741380.17892699283799
3.971-4.54460.21221530.14562672282599
4.5446-5.72220.19271550.149327292884100
5.7222-36.48940.21891730.17812704287799

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