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- PDB-3fe1: Crystal structure of the human 70kDa heat shock protein 6 (Hsp70B... -

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Basic information

Entry
Database: PDB / ID: 3fe1
TitleCrystal structure of the human 70kDa heat shock protein 6 (Hsp70B') ATPase domain in complex with ADP and inorganic phosphate
ComponentsHeat shock 70 kDa protein 6
KeywordsCHAPERONE / mixed beta-sheet / ATP-binding / Nucleotide-binding / Polymorphism / Stress response / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


neutrophil degranulation / misfolded protein binding / chaperone cofactor-dependent protein refolding / response to unfolded protein / Regulation of HSF1-mediated heat shock response / cellular response to unfolded protein / protein folding chaperone / vesicle-mediated transport / heat shock protein binding / centriole ...neutrophil degranulation / misfolded protein binding / chaperone cofactor-dependent protein refolding / response to unfolded protein / Regulation of HSF1-mediated heat shock response / cellular response to unfolded protein / protein folding chaperone / vesicle-mediated transport / heat shock protein binding / centriole / unfolded protein binding / cellular response to heat / protein refolding / blood microparticle / secretory granule lumen / ficolin-1-rich granule lumen / ubiquitin protein ligase binding / Neutrophil degranulation / enzyme binding / ATP hydrolysis activity / extracellular exosome / extracellular region / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily ...Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TRIETHYLENE GLYCOL / PHOSPHATE ION / Heat shock 70 kDa protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsWisniewska, M. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Wisniewska, M. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wikstrom, M. / Schueler, H. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: Crystal structures of the ATPase domains of four human Hsp70 isoforms: HSPA1L/Hsp70-hom, HSPA2/Hsp70-2, HSPA6/Hsp70B', and HSPA5/BiP/GRP78
Authors: Wisniewska, M. / Karlberg, T. / Lehtio, L. / Johansson, I. / Kotenyova, T. / Moche, M. / Schueler, H.
History
DepositionNov 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _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 70 kDa protein 6
B: Heat shock 70 kDa protein 6
C: Heat shock 70 kDa protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,16914
Polymers133,3443
Non-polymers1,82511
Water5,999333
1
A: Heat shock 70 kDa protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9954
Polymers44,4481
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock 70 kDa protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1806
Polymers44,4481
Non-polymers7325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heat shock 70 kDa protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9954
Polymers44,4481
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)236.450, 105.400, 73.590
Angle α, β, γ (deg.)90.000, 101.040, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Heat shock 70 kDa protein 6 / HSP70B' / Heat shock 70 kDa protein B'


Mass: 44448.078 Da / Num. of mol.: 3 / Fragment: ATP-ase domain, residues 6-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA6, HSP70B' / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3pRARE / References: UniProt: P17066

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Non-polymers , 6 types, 344 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.2
Details: 0.1M citric acid, 16% PEG 300, 0.1M di-sodium hydrogen phosphate, pH 3.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 30, 2008
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. all: 89951 / Num. obs: 88612 / % possible obs: 98.5 % / Redundancy: 3.86 % / Net I/σ(I): 10.54
Reflection shellResolution: 2.2→2.26 Å / % possible all: 95

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.5.0044refinement
PDB_EXTRACT3.006data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E88

2e88


Resolution: 2.2→33.69 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.428 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.238 4430 5 %RANDOM
Rwork0.199 ---
obs0.201 88609 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.38 Å2 / Biso mean: 25.411 Å2 / Biso min: 6.25 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.02 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8868 0 110 333 9311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229126
X-RAY DIFFRACTIONr_bond_other_d0.0010.026227
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.97112350
X-RAY DIFFRACTIONr_angle_other_deg0.853315100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65851158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54923.491424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.897151551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5011583
X-RAY DIFFRACTIONr_chiral_restr0.080.21389
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021927
X-RAY DIFFRACTIONr_mcbond_it1.04725695
X-RAY DIFFRACTIONr_mcbond_other0.24422358
X-RAY DIFFRACTIONr_mcangle_it1.96439127
X-RAY DIFFRACTIONr_scbond_it3.02343431
X-RAY DIFFRACTIONr_scangle_it4.87163216
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 324 -
Rwork0.23 6156 -
all-6480 -
obs--100 %

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