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- PDB-3h80: Crystal structure of the amino-terminal domain of HSP90 from Leis... -

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Basic information

Entry
Database: PDB / ID: 3h80
TitleCrystal structure of the amino-terminal domain of HSP90 from Leishmania major, LmjF33.0312:M1-K213
ComponentsHeat shock protein 83-1Heat shock response
KeywordsCHAPERONE / Sleeping sickness / leishmania / heat shock protein / structural genomics / Stress response protein / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding ...ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm
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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases ...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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Heat shock protein 83-1
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWernimont, A.K. / Tempel, W. / Lin, Y.H. / Hutchinson, A. / Mackenzie, F. / Fairlamb, A. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. ...Wernimont, A.K. / Tempel, W. / Lin, Y.H. / Hutchinson, A. / Mackenzie, F. / Fairlamb, A. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Ferguson, M.A.J. / Hui, R. / Pizarro, J.C. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the amino-terminal domain of HSP90 from Leishmania major, LmjF33.0312:M1-K213
Authors: Wernimont, A.K. / Tempel, W. / Lin, Y.H. / Hutchinson, A. / Mackenzie, F. / Fairlamb, A. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / ...Authors: Wernimont, A.K. / Tempel, W. / Lin, Y.H. / Hutchinson, A. / Mackenzie, F. / Fairlamb, A. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Ferguson, M.A.J. / Hui, R. / Pizarro, J.C. / Hills, T.
History
DepositionApr 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein 83-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,10011
Polymers26,1101
Non-polymers98910
Water2,828157
1
A: Heat shock protein 83-1
hetero molecules

A: Heat shock protein 83-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,19922
Polymers52,2212
Non-polymers1,97920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area1270 Å2
ΔGint-9 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.431, 43.197, 50.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Heat shock protein 83-1 / Heat shock response


Mass: 26110.465 Da / Num. of mol.: 1 / Fragment: UNP residues 1-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin
Gene: LmjF33.0312, LmjF33.0314, LmjF33.0316, LmjF33.0320, LmjF33.0323, LmjF33.0326, LmjF33.0333, LmjF33.0336, LmjF33.0340, LmjF33.0343, LmjF33.0346, LmjF33.0350, LmjF33.0355, LmjF33.0360, LmjF33.0365
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRare2 / References: UniProt: Q4Q4I6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 0.1 M Ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 2 mM AMPPNP, 4 mM MgCl2, 2 mM TCEP, 25% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.96863 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 18169 / Num. obs: 18169 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 21.192 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.064 / Net I/σ(I): 34.588
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.42 / Num. unique all: 650 / Rsym value: 0.215 / % possible all: 69.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EKO

3eko


Resolution: 2→46.68 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.892 / SU B: 5.487 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27289 933 5.2 %RANDOM
Rwork0.19371 ---
all0.19762 17013 --
obs0.19762 17013 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.215 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 61 157 1889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221805
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9992443
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94124.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04115327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0191511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021323
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.2768
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21245
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0140.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1871.51125
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84821768
X-RAY DIFFRACTIONr_scbond_it2.6423771
X-RAY DIFFRACTIONr_scangle_it4.2814.5665
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 57 -
Rwork0.227 958 -
obs--74.14 %

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