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- PDB-2p32: Crystal structure of the C-terminal 10 kDa subdomain from C. eleg... -

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Basic information

Entry
Database: PDB / ID: 2p32
TitleCrystal structure of the C-terminal 10 kDa subdomain from C. elegans Hsp70
ComponentsHeat shock 70 kDa protein A
KeywordsCHAPERONE / Three-helix bundle
Function / homology
Function and homology information


GABA synthesis, release, reuptake and degradation / Regulation of HSF1-mediated heat shock response / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mRNA Splicing - Major Pathway / HSF1-dependent transactivation / Clathrin-mediated endocytosis / Neutrophil degranulation / retrograde transport, endosome to Golgi / chaperone cofactor-dependent protein refolding / heat shock protein binding ...GABA synthesis, release, reuptake and degradation / Regulation of HSF1-mediated heat shock response / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mRNA Splicing - Major Pathway / HSF1-dependent transactivation / Clathrin-mediated endocytosis / Neutrophil degranulation / retrograde transport, endosome to Golgi / chaperone cofactor-dependent protein refolding / heat shock protein binding / protein folding chaperone / determination of adult lifespan / ATP-dependent protein folding chaperone / response to heat / protein refolding / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / ATPase, nucleotide binding domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Heat shock protein hsp-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWorrall, L.J. / Walkinshaw, M.D.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Crystal structure of the C-terminal three-helix bundle subdomain of C. elegans Hsp70.
Authors: Worrall, L.J. / Walkinshaw, M.D.
History
DepositionMar 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 21, 2024Group: 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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 A
B: Heat shock 70 kDa protein A
C: Heat shock 70 kDa protein A
D: Heat shock 70 kDa protein A
E: Heat shock 70 kDa protein A
F: Heat shock 70 kDa protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,32012
Polymers77,7446
Non-polymers5766
Water00
1
A: Heat shock 70 kDa protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0532
Polymers12,9571
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Heat shock 70 kDa protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0532
Polymers12,9571
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Heat shock 70 kDa protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0532
Polymers12,9571
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Heat shock 70 kDa protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0532
Polymers12,9571
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: Heat shock 70 kDa protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0532
Polymers12,9571
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: Heat shock 70 kDa protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0532
Polymers12,9571
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-116 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.927, 138.927, 100.704
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth seq-ID: 533 - 614 / Label seq-ID: 13 - 94

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
DetailsThe biological assembly is a monomer.

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Components

#1: Protein
Heat shock 70 kDa protein A


Mass: 12957.294 Da / Num. of mol.: 6 / Fragment: C-terminal 10 kDa subdomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: hsp-1, hsp70a / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3) / References: UniProt: P09446
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4

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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: 3.12 Å3/Da / Density % sol: 60.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 55% ammonium sulphate, 0.5% PEG 400, 0.1M sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 4, 2006 / Details: Mirrors
RadiationMonochromator: Si 111 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionRedundancy: 8.74 % / Number: 146865 / Rmerge(I) obs: 0.136 / D res high: 3.2 Å / D res low: 35.99 Å
ReflectionResolution: 3.2→36 Å / Num. all: 16809 / Num. obs: 16809 / % possible obs: 99.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 103.1 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 12.9
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 2 / Num. measured all: 11782 / Num. unique all: 2399 / Rsym value: 0.936 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.2.17data scaling
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.7data extraction
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Preliminary model built using data from a mercury derivative crystal solved using MAD

Resolution: 3.2→36 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.225 / SU B: 66.939 / SU ML: 0.443 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.473 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2819 820 5.052 %RANDOM
Rwork0.2684 ---
all0.269 16809 --
obs-16232 96.694 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 89.409 Å2
Baniso -1Baniso -2Baniso -3
1-1.749 Å20 Å20 Å2
2--1.749 Å20 Å2
3----3.497 Å2
Refinement stepCycle: LAST / Resolution: 3.2→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3972 0 30 0 4002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224056
X-RAY DIFFRACTIONr_bond_other_d0.0040.022838
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.9945436
X-RAY DIFFRACTIONr_angle_other_deg1.10937038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1725486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.45827.353204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.53815834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg33.938156
X-RAY DIFFRACTIONr_chiral_restr0.1380.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024386
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02654
X-RAY DIFFRACTIONr_nbd_refined0.2960.21448
X-RAY DIFFRACTIONr_nbd_other0.2040.23063
X-RAY DIFFRACTIONr_nbtor_refined0.2160.21979
X-RAY DIFFRACTIONr_nbtor_other0.10.22173
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2530.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2230.216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0830.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.26
X-RAY DIFFRACTIONr_mcbond_it0.51.52642
X-RAY DIFFRACTIONr_mcbond_other0.0891.5984
X-RAY DIFFRACTIONr_mcangle_it0.81523930
X-RAY DIFFRACTIONr_mcangle_other0.40923306
X-RAY DIFFRACTIONr_scbond_it1.02731752
X-RAY DIFFRACTIONr_scbond_other0.30632244
X-RAY DIFFRACTIONr_scangle_it1.7194.51506
X-RAY DIFFRACTIONr_scangle_other0.7834.53732
Refine LS restraints NCS

Ens-ID: 1 / Number: 1135 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDRmsTypeWeight
1A0.03TIGHT POSITIONAL0.05
2B0.03TIGHT POSITIONAL0.05
3C0.03TIGHT POSITIONAL0.05
4D0.03TIGHT POSITIONAL0.05
5E0.05TIGHT POSITIONAL0.05
6F0.03TIGHT POSITIONAL0.05
1A0.04TIGHT THERMAL0.5
2B0.04TIGHT THERMAL0.5
3C0.04TIGHT THERMAL0.5
4D0.04TIGHT THERMAL0.5
5E0.04TIGHT THERMAL0.5
6F0.04TIGHT THERMAL0.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allNum. reflection obs% reflection obs (%)
3.2-3.2830.44560.42811420.42811981142100
3.283-3.3720.393610.3811180.38111791118100
3.372-3.4690.333550.37110890.36911441089100
3.469-3.5740.432510.39410770.39611281077100
3.574-3.690.675420.6927560.692105875675.425
3.69-3.8180.455330.4417540.441105975474.315
3.818-3.9610.462520.4739360.473101093697.822
3.961-4.1210.302460.2279340.231980934100
4.121-4.3010.336430.1939030.199946903100
4.301-4.5080.172480.1618630.161911863100
4.508-4.7480.145350.1768210.174856821100
4.748-5.030.274430.1667850.171828785100
5.03-5.370.192490.1697270.17776727100
5.37-5.790.186410.1896860.189727686100
5.79-6.3260.199440.2056270.205671627100
6.326-7.0450.234340.2165820.217616582100
7.045-8.0840.18250.1695270.17552527100
8.084-9.7780.166260.1594600.1648746099.795
9.778-13.3450.225240.163690.164393369100
13.345-360.297120.3572560.354268256100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.436-2.17416.215110.0481-6.382315.85040.099-1.5032-0.56030.43610.00030.1873-0.1577-0.7478-0.0994-0.2183-0.0919-0.4181-0.52470.2135-0.29783.7257-35.203637.7124
29.92783.48016.88937.83344.335412.09430.32760.0233-0.63980.5519-0.73760.76750.2084-1.23850.41-0.2910.0809-0.4648-0.5028-0.1968-0.1496-12.6511-51.415713.7753
33.9906-1.68070.108320.64660.02476.29970.4496-0.2284-0.03570.48630.20350.9577-0.669-0.6152-0.6531-0.05760.0092-0.3123-0.6879-0.0461-0.4954-12.3187-18.295114.1748
46.72972.5365.860710.83456.496315.25760.18441.642-0.6384-0.4823-0.1297-0.0517-0.13440.7387-0.0547-0.23560.1089-0.4146-0.5565-0.226-0.3071-3.7532-35.2907-3.5765
59.4967-3.43046.25068.7123-4.406111.21280.2452-0.0848-0.5557-0.4711-0.6835-0.7920.17851.2010.4383-0.2819-0.0735-0.4487-0.52640.1847-0.164712.5233-51.407320.4186
64.96771.60020.297321.4836-0.90455.31630.35470.30380.0462-0.17050.2946-0.9692-0.76780.5709-0.64930.01390.0081-0.3131-0.68610.0573-0.484212.2844-18.318219.8055
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 533 - 614 / Label seq-ID: 13 - 94

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC
44DD
55EE
66FF

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