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- PDB-6tlb: Plasmodium falciparum lipocalin (PF3D7_0925900) -

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Basic information

Entry
Database: PDB / ID: 6tlb
TitlePlasmodium falciparum lipocalin (PF3D7_0925900)
ComponentsSerine/threonine protein kinase
KeywordsUNKNOWN FUNCTION / Lipocalin / Malaria / Infection
Function / homologyCalycin / Parasitophorous vacuolar protein 5, putative
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SOLUTION SCATTERING / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsBurda, P.C. / Crosskey, T.D. / Lauk, K. / Wilmanns, M. / Gilberger, T.W.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Molecular Biology Organization Germany
CitationJournal: Cell Rep / Year: 2020
Title: Structure-Based Identification and Functional Characterization of a Lipocalin in the Malaria Parasite Plasmodium falciparum.
Authors: Burda, P.C. / Crosskey, T. / Lauk, K. / Zurborg, A. / Sohnchen, C. / Liffner, B. / Wilcke, L. / Pietsch, E. / Strauss, J. / Jeffries, C.M. / Svergun, D.I. / Wilson, D.W. / Wilmanns, M. / Gilberger, T.W.
History
DepositionDec 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine protein kinase
B: Serine/threonine protein kinase
C: Serine/threonine protein kinase
D: Serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,40211
Polymers88,9654
Non-polymers4377
Water70339
1
B: Serine/threonine protein kinase
D: Serine/threonine protein kinase
hetero molecules

A: Serine/threonine protein kinase
C: Serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,40211
Polymers88,9654
Non-polymers4377
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area9450 Å2
ΔGint-111 kcal/mol
Surface area31910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.993, 92.250, 214.502
Angle α, β, γ (deg.)90.00, 98.35, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
Serine/threonine protein kinase


Mass: 22241.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0925900 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I2Q0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
SOLUTION SCATTERING

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7
Details: 0.2 M magnesium chloride, 0.1 M Tris pH7, 2.5 M Sodium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.85→56.2 Å / Num. obs: 28936 / % possible obs: 99.75 % / Redundancy: 2 % / Biso Wilson estimate: 54.95 Å2 / CC1/2: 0.546 / Rmerge(I) obs: 0.1985 / Rrim(I) all: 0.2943 / Net I/σ(I): 3.69
Reflection shellResolution: 2.85→2.952 Å / Mean I/σ(I) obs: 1.19 / Num. unique obs: 2889 / CC1/2: 0.41 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MBT

3mbt


Resolution: 2.85→56.2 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 16.431 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R: 0.734 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23647 1428 4.9 %RANDOM
Rwork0.18886 ---
obs0.1912 27535 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.494 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å2-0.04 Å2
2--0.09 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.85→56.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5930 0 27 40 5997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136106
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175628
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.6378263
X-RAY DIFFRACTIONr_angle_other_deg1.2081.56913114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7755739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26524.919307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.812151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2761516
X-RAY DIFFRACTIONr_chiral_restr0.0640.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026721
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021203
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.335.5292968
X-RAY DIFFRACTIONr_mcbond_other4.3135.5292967
X-RAY DIFFRACTIONr_mcangle_it6.8958.2893703
X-RAY DIFFRACTIONr_mcangle_other6.8988.293704
X-RAY DIFFRACTIONr_scbond_it4.6546.0833138
X-RAY DIFFRACTIONr_scbond_other4.6046.0823138
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4688.934561
X-RAY DIFFRACTIONr_long_range_B_refined11.23463.7066355
X-RAY DIFFRACTIONr_long_range_B_other11.25163.7176355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 110 -
Rwork0.329 2058 -
obs--99.59 %

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