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- PDB-3n72: Crystal Structure of Aha-1 from plasmodium falciparum, PFC0270w -

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Basic information

Entry
Database: PDB / ID: 3n72
TitleCrystal Structure of Aha-1 from plasmodium falciparum, PFC0270w
Componentsputative activator of HSP90
Keywordschaperone activator / malaria / structural genomics / heat shock / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ATPase activator activity / Hsp90 protein binding / protein-folding chaperone binding
Similarity search - Function
Activator of 90kDa heat shock protein ATPase-like / Activator of Hsp90 ATPase Aha1, N-terminal domain / Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase, Aha1 / Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase, N-terminal / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / PFC0270w protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.77 Å
AuthorsWernimont, A.K. / Dong, A. / Hutchinson, A. / Sullivan, H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. ...Wernimont, A.K. / Dong, A. / Hutchinson, A. / Sullivan, H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Pizarro, J.C. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Aha-1 from plasmodium falciparum, PFC0270w
Authors: Wernimont, A.K. / Dong, A. / Hutchinson, A. / Sullivan, H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / ...Authors: Wernimont, A.K. / Dong, A. / Hutchinson, A. / Sullivan, H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Pizarro, J.C. / Hills, T.
History
DepositionMay 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: putative activator of HSP90
B: putative activator of HSP90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3563
Polymers39,2982
Non-polymers581
Water2,558142
1
B: putative activator of HSP90
hetero molecules

A: putative activator of HSP90


Theoretical massNumber of molelcules
Total (without water)39,3563
Polymers39,2982
Non-polymers581
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1460 Å2
ΔGint-9 kcal/mol
Surface area16950 Å2
MethodPISA
2
A: putative activator of HSP90


Theoretical massNumber of molelcules
Total (without water)19,6491
Polymers19,6491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: putative activator of HSP90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7072
Polymers19,6491
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.709, 63.709, 61.722
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Detailsunknown

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Components

#1: Protein putative activator of HSP90 / PFC0270w protein


Mass: 19649.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFC0270w / Plasmid: pet15mlh / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: Q689C6
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 mM Hepes, 30% PEG 2000 MME, 0.2 M Potassium thiocyanate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT11.5418
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEApr 19, 2010
RIGAKU SATURN A2002CCDMay 7, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 5.4 % / Av σ(I) over netI: 32.68 / Number: 145886 / Rmerge(I) obs: 0.063 / Χ2: 1.45 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 26949 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.885099.410.0564.4425.7
3.884.8810010.0472.6345.7
3.393.8810010.052.2395.6
3.083.3910010.0531.8635.6
2.863.0810010.0591.5885.5
2.692.8610010.0661.445.5
2.552.6910010.0751.3915.5
2.442.5510010.0761.2245.4
2.352.4410010.0781.0975.4
2.272.3510010.0891.1155.4
2.22.2799.910.1111.2845.3
2.132.210010.09715.3
2.082.1310010.1061.045.3
2.032.0810010.1241.0675.3
1.982.0310010.1250.9365.3
1.941.9810010.1441.015.3
1.91.9410010.1721.0095.3
1.861.910010.1730.7525.3
1.831.8610010.1850.7625.3
1.81.8310010.2030.7125.3
ReflectionResolution: 1.77→50 Å / Num. all: 27299 / Num. obs: 27245 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.059 / Χ2: 1.347 / Net I/σ(I): 12.8
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1318 / Χ2: 1.229 / % possible all: 96.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.834 / SU B: 6.385 / SU ML: 0.094 / SU R Cruickshank DPI: 0.396 / SU Rfree: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1368 5 %RANDOM
Rwork0.188 ---
all0.191 25909 --
obs0.191 25855 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.12 Å2 / Biso mean: 21.758 Å2 / Biso min: 8.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.77→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 3 142 2538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222570
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9513465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1695320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27625.299134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11715480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8831511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021986
X-RAY DIFFRACTIONr_mcbond_it1.1651.51550
X-RAY DIFFRACTIONr_mcangle_it2.02922484
X-RAY DIFFRACTIONr_scbond_it3.26231020
X-RAY DIFFRACTIONr_scangle_it5.0244.5981
X-RAY DIFFRACTIONr_rigid_bond_restr1.56932570
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 105 -
Rwork0.235 1873 -
all-1978 -
obs--98.26 %

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