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- PDB-3ni8: Crystal Structure of PFC0360w, an HSP90 activator from plasmodium... -

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Basic information

Entry
Database: PDB / ID: 3ni8
TitleCrystal Structure of PFC0360w, an HSP90 activator from plasmodium falciparum
ComponentsPFC0360w protein
KeywordsUNKNOWN FUNCTION / heat shock / malaria / ATPase / Structural Genomics Consortium / SGC
Function / homologyActivator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / ISOPROPYL ALCOHOL / PFC0360w protein
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsWernimont, A.K. / Hutchinson, A. / Sullivan, H. / MacKenzie, F. / Kozieradzki, I. / Cossar, D. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / MacKenzie, F. / Kozieradzki, I. / Cossar, D. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Pizzaro, J.C. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of PFC0360w, an HSP90 activator from plasmodium falciparum
Authors: Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / MacKenzie, F. / Kozieradzki, I. / Cossar, D. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Pizzaro, J.C. / Hills, T.
History
DepositionJun 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PFC0360w protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5914
Polymers18,3791
Non-polymers2123
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.658, 96.658, 44.288
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PFC0360w protein


Mass: 18378.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFC0360w / Plasmid: pet15mlh / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: Q689C4
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.25 Å3/Da / Density % sol: 62.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% isopropanol, 20% PEG 4000, 0.1M Na Citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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 SATURN A200 / Detector: CCD / Date: May 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→32.7 Å / Num. all: 8525 / Num. obs: 8517 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.6 % / Biso Wilson estimate: 48.5 Å2 / Rmerge(I) obs: 0.159 / Rsym value: 0.124 / Χ2: 0.378 / Net I/σ(I): 2.8
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 9 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 1.42 / Num. unique all: 410 / Χ2: 0.258 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→32.7 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.188 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.792 / SU B: 8.811 / SU ML: 0.205 / SU R Cruickshank DPI: 0.38 / SU Rfree: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.261 394 4.7 %RANDOM
Rwork0.224 ---
all0.226 8505 --
obs0.226 8402 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.81 Å2 / Biso mean: 29.609 Å2 / Biso min: 15.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.07 Å20 Å2
2---0.13 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 14 59 1210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221256
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9441708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7395155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37624.75461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64215216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.167154
X-RAY DIFFRACTIONr_chiral_restr0.1030.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021971
X-RAY DIFFRACTIONr_mcbond_it0.6091.5742
X-RAY DIFFRACTIONr_mcangle_it1.20121215
X-RAY DIFFRACTIONr_scbond_it1.8513514
X-RAY DIFFRACTIONr_scangle_it3.1754.5493
LS refinement shellResolution: 2.5→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 27 -
Rwork0.291 587 -
all-614 -
obs--99.84 %

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