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- PDB-3ied: Crystal structure of N-terminal domain of Plasmodium falciparum H... -

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Basic information

Entry
Database: PDB / ID: 3ied
TitleCrystal structure of N-terminal domain of Plasmodium falciparum Hsp90 (PF14_0417) in complex with AMPPN
ComponentsHeat shock protein
KeywordsCHAPERONE / Hsp90 / Plasmodium / Structural Genomics / Structural Genomics Consortium / SGC / Stress response
Function / homology
Function and homology information


HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity ...HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / plasma membrane / cytosol
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase/HSP90-like ATPase superfamily ...Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AMP PHOSPHORAMIDATE / Heat shock protein 90, putative
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsPizarro, J.C. / Wernimont, A.K. / Lew, J. / Hutchinson, A. / Artz, J.D. / Amaya, M.F. / Plotnikova, O. / Vedadi, M. / Kozieradzki, I. / Weigelt, J. ...Pizarro, J.C. / Wernimont, A.K. / Lew, J. / Hutchinson, A. / Artz, J.D. / Amaya, M.F. / Plotnikova, O. / Vedadi, M. / Kozieradzki, I. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Botchkarev, A. / Hui, R. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of N-terminal domain of Plasmodium falciparum Hsp90 (PF14_0417) in complex with AMPPN
Authors: Pizarro, J.C. / Wernimont, A.K. / Lew, J. / Hutchinson, A. / Artz, J.D. / Amaya, M.F. / Plotnikova, O. / Vedadi, M. / Kozieradzki, I. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / ...Authors: Pizarro, J.C. / Wernimont, A.K. / Lew, J. / Hutchinson, A. / Artz, J.D. / Amaya, M.F. / Plotnikova, O. / Vedadi, M. / Kozieradzki, I. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Botchkarev, A. / Hui, R. / Hills, T. / Structural Genomics Consortium (SGC)
History
DepositionJul 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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: Heat shock protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9262
Polymers31,4991
Non-polymers4261
Water1,47782
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.236, 69.462, 71.382
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heat shock protein /


Mass: 31499.467 Da / Num. of mol.: 1 / Fragment: N-terminal domain: UNP residues 97-347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF14_0417 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IL32
#2: Chemical ChemComp-AN2 / AMP PHOSPHORAMIDATE


Mass: 426.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N6O9P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5M Ammonium sulfate, 1M Lithium sulfate, 0.1M Na citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 102 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 28, 2009 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 21647 / % possible obs: 98.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 53.4 Å2 / Rmerge(I) obs: 0.067 / Χ2: 1.378 / Net I/σ(I): 11
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.916 / Num. unique all: 1903 / Χ2: 1.235 / % possible all: 88.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.98 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.78 Å
Translation2.5 Å49.78 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H80

3h80


Resolution: 2.01→19.67 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.741 / SU B: 12.947 / SU ML: 0.16 / SU R Cruickshank DPI: 0.188 / SU Rfree: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1104 5.1 %RANDOM
Rwork0.232 ---
obs0.234 21619 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 130.46 Å2 / Biso mean: 38.657 Å2 / Biso min: 21.88 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.01→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 27 82 1893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221925
X-RAY DIFFRACTIONr_bond_other_d0.0190.021729
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.9882610
X-RAY DIFFRACTIONr_angle_other_deg2.05834073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2575244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33826.04491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88715378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.733156
X-RAY DIFFRACTIONr_chiral_restr0.0520.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022107
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02367
X-RAY DIFFRACTIONr_mcbond_it0.4381.51144
X-RAY DIFFRACTIONr_mcbond_other0.0561.5471
X-RAY DIFFRACTIONr_mcangle_it0.80921856
X-RAY DIFFRACTIONr_scbond_it0.9253781
X-RAY DIFFRACTIONr_scangle_it1.5914.5742
LS refinement shellResolution: 2.01→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 65 -
Rwork0.4 1297 -
all-1362 -
obs--87.14 %
Refinement TLS params.Method: refined / Origin x: 23.8299 Å / Origin y: 33.6834 Å / Origin z: 12.3565 Å
111213212223313233
T0.0053 Å2-0.012 Å2-0.0045 Å2-0.0433 Å20.002 Å2--0.0332 Å2
L0.999 °2-0.1228 °2-0.1675 °2-1.6975 °20.0834 °2--1.3514 °2
S-0.0429 Å °0.0911 Å °0.0987 Å °0.0178 Å °-0.0525 Å °0.0339 Å °0.0401 Å °-0.0576 Å °0.0954 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A89 - 337
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION1A501 - 582

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