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- PDB-6t4d: Crystal structure of Plasmodium falciparum Morn1 -

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Basic information

Entry
Database: PDB / ID: 6t4d
TitleCrystal structure of Plasmodium falciparum Morn1
ComponentsMorn1
KeywordsSTRUCTURAL PROTEIN / MORN repeat / MORN1 / Apicomplexa
Function / homologyPossible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / MORN motif / MORN repeat / metal ion binding / MORN repeat-containing protein 1 / MORN repeat-containing protein 1
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsGrishkovskaya, I. / Kostan, J. / Sajko, S. / Morriswood, B. / Djinovic-Carugo, K.
CitationJournal: Plos One / Year: 2020
Title: Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats.
Authors: Sajko, S. / Grishkovskaya, I. / Kostan, J. / Graewert, M. / Setiawan, K. / Trubestein, L. / Niedermuller, K. / Gehin, C. / Sponga, A. / Puchinger, M. / Gavin, A.C. / Leonard, T.A. / Svergun, ...Authors: Sajko, S. / Grishkovskaya, I. / Kostan, J. / Graewert, M. / Setiawan, K. / Trubestein, L. / Niedermuller, K. / Gehin, C. / Sponga, A. / Puchinger, M. / Gavin, A.C. / Leonard, T.A. / Svergun, D.I. / Smith, T.K. / Morriswood, B. / Djinovic-Carugo, K.
History
DepositionOct 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 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.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Morn1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7832
Polymers24,7171
Non-polymers651
Water21612
1
A: Morn1
hetero molecules

A: Morn1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5654
Polymers49,4352
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area1570 Å2
ΔGint-60 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.327, 79.175, 94.417
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-401-

ZN

21A-504-

HOH

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Components

#1: Protein Morn1


Mass: 24717.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFFCH_03839 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A024VKH2, UniProt: Q8IJ93*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2 mM divalents mix (0.5 mM MnCl3, 0.5 mM CoCl2, 0.5 mM NiCl2, 0.5 mM Zn(OAc)2, 0.1 M Buffer System 6, pH 8.5 (Gly-Gly, AMPD), and 50% precipitation Mix 7 (20 % PEG 8000, 40% 1,5-Pentanediol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.14→46.43 Å / Num. obs: 12148 / % possible obs: 99.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 59.97 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.024 / Rrim(I) all: 0.04 / Net I/σ(I): 17.5
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.065 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 985 / CC1/2: 0.467 / Rpim(I) all: 0.888 / Rrim(I) all: 1.394 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→41.67 Å / SU ML: 0.3556 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.3704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 635 5.25 %
Rwork0.2294 11466 -
obs0.2317 12101 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.65 Å2
Refinement stepCycle: LAST / Resolution: 2.14→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1625 0 1 12 1638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00181671
X-RAY DIFFRACTIONf_angle_d0.48162243
X-RAY DIFFRACTIONf_chiral_restr0.0439203
X-RAY DIFFRACTIONf_plane_restr0.0014289
X-RAY DIFFRACTIONf_dihedral_angle_d4.2093222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.310.42371120.38822252X-RAY DIFFRACTION98.05
2.31-2.540.40911310.33432245X-RAY DIFFRACTION99.75
2.54-2.90.4091390.2872283X-RAY DIFFRACTION99.79
2.9-3.660.34171340.25672291X-RAY DIFFRACTION99.47
3.66-41.670.20631190.18782395X-RAY DIFFRACTION99.05

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