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- PDB-1n81: Crystal structure of Pfg27 from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 1n81
TitleCrystal structure of Pfg27 from Plasmodium falciparum
Componentsplasmodium falciparum gamete antigen 27/25
KeywordsUNKNOWN FUNCTION / Gametocyte / helical / helix-turn-helix / pxxp
Function / homologyGametocyte protein Pfg27 / Gametocyte protein Pfg27 / Gamete antigen, Plasmodium species / Gametocyte protein Pfg27 superfamily / Pfg27 / protein dimerization activity / Orthogonal Bundle / Mainly Alpha / Gamete antigen 27/25
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsSharma, A. / Sharma, I. / Kogkasuriyachai, D. / Kumar, N.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structure of a gametocyte protein essential for sexual development in Plasmodium falciparum
Authors: Sharma, A. / Sharma, I. / Kogkasuriyachai, D. / Kumar, N.
History
DepositionNov 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 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: plasmodium falciparum gamete antigen 27/25


Theoretical massNumber of molelcules
Total (without water)22,5211
Polymers22,5211
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.880, 113.190, 91.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein plasmodium falciparum gamete antigen 27/25


Mass: 22520.742 Da / Num. of mol.: 1 / Fragment: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: Pfg27 / Plasmid: pMalp / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8IEU2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.17 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, MES, Glucose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / Details: Hendrickson, W.A., (1990) EMBO J., 9, 1665.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 %(w/v)glucose1reservoir
20.050 mg/mlcarbenicillin1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 13, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 18053 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 37.3
Reflection shellResolution: 2.1→15 Å / Redundancy: 4 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 3.4 / Num. unique all: 18053 / Rsym value: 0.282 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 25 Å / % possible obs: 99 %
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→14.83 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1353 7.8 %RANDOM
Rwork0.207 ---
all0.207 18053 --
obs0.207 17272 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.973 Å2 / ksol: 0.376104 e/Å3
Displacement parametersBiso mean: 52.2 Å2
Baniso -1Baniso -2Baniso -3
1--7.12 Å20 Å20 Å2
2---4.02 Å20 Å2
3---11.14 Å2
Refine analyzeLuzzati coordinate error free: 0.35 Å / Luzzati sigma a free: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.1→14.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 0 131 1717
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_mcbond_it4.831.5
X-RAY DIFFRACTIONc_mcangle_it6.122
X-RAY DIFFRACTIONc_scbond_it7.482
X-RAY DIFFRACTIONc_scangle_it9.632.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 208 7.6 %
Rwork0.261 2513 -
obs--91.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 25 Å / % reflection Rfree: 7.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06

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