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- PDB-4o2x: Structure of a malarial protein -

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Basic information

Entry
Database: PDB / ID: 4o2x
TitleStructure of a malarial protein
ComponentsMaltose-binding periplasmic protein, ATP-dependent Clp protease adaptor protein ClpS containing protein chimeric construct
KeywordsTRANSPORT PROTEIN / ClpS / Proteolysis / Clp ATPase Protease / APICOPLAST
Function / homology
Function and homology information


endopeptidase Clp / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...endopeptidase Clp / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / protein catabolic process / peptidase activity / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / ATP-dependent Clp protease adapter protein ClpS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, molecular replacement / Resolution: 2.7 Å
AuthorsAhYoung, A.P. / Koehl, A. / Cascio, D. / Egea, P.F.
CitationJournal: Protein Sci. / Year: 2016
Title: Structure of a putative ClpS N-end rule adaptor protein from the malaria pathogen Plasmodium falciparum.
Authors: AhYoung, A.P. / Koehl, A. / Vizcarra, C.L. / Cascio, D. / Egea, P.F.
History
DepositionDec 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Aug 9, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
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: Maltose-binding periplasmic protein, ATP-dependent Clp protease adaptor protein ClpS containing protein chimeric construct
B: Maltose-binding periplasmic protein, ATP-dependent Clp protease adaptor protein ClpS containing protein chimeric construct


Theoretical massNumber of molelcules
Total (without water)112,9902
Polymers112,9902
Non-polymers00
Water00
1
A: Maltose-binding periplasmic protein, ATP-dependent Clp protease adaptor protein ClpS containing protein chimeric construct


Theoretical massNumber of molelcules
Total (without water)56,4951
Polymers56,4951
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose-binding periplasmic protein, ATP-dependent Clp protease adaptor protein ClpS containing protein chimeric construct


Theoretical massNumber of molelcules
Total (without water)56,4951
Polymers56,4951
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.850, 97.850, 298.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein Maltose-binding periplasmic protein, ATP-dependent Clp protease adaptor protein ClpS containing protein chimeric construct / MBP / MMBP


Mass: 56495.035 Da / Num. of mol.: 2 / Fragment: MBP residues, malarial ClpS residues 73-192
Mutation: A83D, A84K, A1733, A174N, A240K, A360E, A363K, A364D
Source method: isolated from a genetically manipulated source
Details: MBP fusion protein
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: k12 / Gene: malE, b4034, JW3994, MAL13P1.111 / Plasmid: pMAL-X / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P0AEX9, UniProt: Q8IEB2

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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: 3.74 Å3/Da / Density % sol: 67.13 %
Crystal growTemperature: 273 K / pH: 5
Details: Ammonium Sulfate 2 M, NaCl 1.8 M no buffer, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9793
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 9, 2013
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.699→73.703 Å / Num. obs: 43001 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 75 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 15.8

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Processing

Software
NameVersionClassification
APSdata collection
SHELXSphasing
PHENIX(phenix.refine: dev_1555)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD, molecular replacement
Starting model: PDB ID 3W3I, 1MG9, 1MBX and 3DNJ

3w3i
PDB Unreleased entry

1mg9

1mbx

3dnj


Resolution: 2.7→73.67 Å / SU ML: 0.4 / σ(F): 1.37 / Phase error: 26.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 3225 7.5 %
Rwork0.185 --
obs0.189 43001 97.3 %
all-44187 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→73.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6828 0 0 0 6828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096994
X-RAY DIFFRACTIONf_angle_d1.2329559
X-RAY DIFFRACTIONf_dihedral_angle_d13.4252409
X-RAY DIFFRACTIONf_chiral_restr0.0481089
X-RAY DIFFRACTIONf_plane_restr0.0061239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6992-2.73950.35581340.28431659X-RAY DIFFRACTION94
2.7395-2.78230.33571440.27421771X-RAY DIFFRACTION100
2.7823-2.82790.32341430.26851765X-RAY DIFFRACTION100
2.8279-2.87670.2691460.25291799X-RAY DIFFRACTION100
2.8767-2.9290.351410.26071737X-RAY DIFFRACTION99
2.929-2.98530.34881420.25981759X-RAY DIFFRACTION99
2.9853-3.04620.32131410.26431738X-RAY DIFFRACTION98
3.0462-3.11250.32631410.25011732X-RAY DIFFRACTION98
3.1125-3.18490.31021420.24991755X-RAY DIFFRACTION99
3.1849-3.26450.28191450.24561790X-RAY DIFFRACTION99
3.2645-3.35280.30571400.24221720X-RAY DIFFRACTION99
3.3528-3.45150.32451430.22351768X-RAY DIFFRACTION99
3.4515-3.56290.30091410.21791742X-RAY DIFFRACTION99
3.5629-3.69020.22771430.1941764X-RAY DIFFRACTION99
3.6902-3.83790.25561390.18091716X-RAY DIFFRACTION98
3.8379-4.01260.21821400.16211726X-RAY DIFFRACTION97
4.0126-4.22410.21241390.14691708X-RAY DIFFRACTION96
4.2241-4.48870.16811410.1411742X-RAY DIFFRACTION98
4.4887-4.83530.17691390.13531710X-RAY DIFFRACTION97
4.8353-5.32170.22331380.14931701X-RAY DIFFRACTION95
5.3217-6.09150.21471350.1741670X-RAY DIFFRACTION93
6.0915-7.67330.21661360.1871673X-RAY DIFFRACTION94
7.6733-73.70290.21371320.16631631X-RAY DIFFRACTION91
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)
11.7916-0.49661.87050.7532-1.26360.57560.0093-0.34190.17610.06910.138-0.1996-0.2131-0.22570.21490.4720.125-0.06550.8405-0.14530.599557.656347.294265.544
22.1312-0.03022.40350.95021.37281.0012-0.05110.39960.0842-0.08120.08920.2977-0.16710.12170.14860.4815-0.221-0.01330.88580.14240.604336.96748.0244108.0502
30.58360.11830.36290.63380.25270.30320.1147-0.2789-0.38790.50240.18670.23850.1633-0.4076-0.00050.7046-0.0113-0.11060.76440.2110.730234.510728.553448.9941
40.33480.03270.31640.5323-0.23660.3649-0.15870.6869-0.1829-0.4580.4431-0.36670.28970.10150.00740.878-0.17060.04580.8767-0.21830.801258.496927.2398124.9426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:383 )
2X-RAY DIFFRACTION2(CHAIN B AND RESID 5:382 )
3X-RAY DIFFRACTION3(CHAIN A AND RESID 406:483 )
4X-RAY DIFFRACTION4(CHAIN B AND RESID 407:482 )

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