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- PDB-1vq0: Crystal structure of 33 kDa chaperonin (Heat shock protein 33 hom... -

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Basic information

Entry
Database: PDB / ID: 1vq0
TitleCrystal structure of 33 kDa chaperonin (Heat shock protein 33 homolog) (HSP33) (TM1394) from Thermotoga maritima at 2.20 A resolution
Components33 kDa chaperonin
KeywordsCHAPERONE / TM1394 / 33 KDA chaperonin (heat shock protein 33 homolog) (HSP33) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


protein folding chaperone / unfolded protein binding / protein refolding / cytoplasm
Similarity search - Function
HSP33 redox switch-like / Hsp33 domain / Hsp33 domain / Heat shock protein Hsp33 / Heat shock protein Hsp33, N-terminal / Heat shock protein Hsp33, C-terminal / Hsp33 protein / CBS domain Like / 3-Layer(bab) Sandwich / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / 33 kDa chaperonin
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 A resolution.
Authors: Jaroszewski, L. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Axelrod, H. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Deacon, A.M. / DiDonato, M. / ...Authors: Jaroszewski, L. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Axelrod, H. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Han, G.W. / Haugen, J. / Hornsby, M. / Klock, H.E. / Koesema, E. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Miller, M.D. / Moy, K. / Nigoghossian, E. / Paulsen, J. / Quijano, K. / Reyes, R. / Rife, C. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / White, A. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionNov 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_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 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 33 kDa chaperonin
B: 33 kDa chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,47611
Polymers68,0882
Non-polymers3889
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.213, 101.673, 113.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ZN / End label comp-ID: ZN / Refine code: 4 / Auth seq-ID: 1 - 300 / Label seq-ID: 13

Dom-IDAuth asym-IDLabel asym-ID
1AA - C
2BB - G

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 33 kDa chaperonin / Heat shock protein 33 homolog / HSP33


Mass: 34044.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: hslO, TM1394 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1B4

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Non-polymers , 5 types, 282 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 3.22 Å3/Da / Density % sol: 61.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 15.0% Glycerol, 8.5% iso-Propanol, 17.0% PEG-4000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979121
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2004 / Details: Flat mirror
RadiationMonochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979121 Å / Relative weight: 1
ReflectionResolution: 2.2→49.62 Å / Num. obs: 44233 / % possible obs: 97.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 43.5 Å2 / Rsym value: 0.09 / Net I/σ(I): 10.7
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2842 / Rsym value: 0.413 / % possible all: 86.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.1.9999refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I7F

1i7f


Resolution: 2.2→49.62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.015 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24079 2228 5 %RANDOM
Rwork0.19824 ---
obs0.20033 41981 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.973 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2---0.16 Å20 Å2
3---1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4570 0 42 273 4885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224687
X-RAY DIFFRACTIONr_bond_other_d0.0070.024403
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9656323
X-RAY DIFFRACTIONr_angle_other_deg0.903310221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3235578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92924.272213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19715848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.111532
X-RAY DIFFRACTIONr_chiral_restr0.1020.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02932
X-RAY DIFFRACTIONr_nbd_refined0.2220.2894
X-RAY DIFFRACTIONr_nbd_other0.2160.24215
X-RAY DIFFRACTIONr_nbtor_other0.110.22577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2214
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.211
X-RAY DIFFRACTIONr_mcbond_it1.9731.53150
X-RAY DIFFRACTIONr_mcbond_other0.2531.51186
X-RAY DIFFRACTIONr_mcangle_it1.88724642
X-RAY DIFFRACTIONr_scbond_it3.68931994
X-RAY DIFFRACTIONr_scangle_it5.2484.51681
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4415 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.110.5
medium thermal0.472
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 125 4.41 %
Rwork0.254 2707 -
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)
12.24510.0873-0.42921.77460.14611.9123-0.0756-0.1942-0.20260.1945-0.01260.11060.2360.0680.0882-0.0915-0.01160.0721-0.10110.0089-0.086415.169411.927945.7518
27.04920.27312.46284.4752-1.84769.5242-0.40111.15140.996-1.07150.35810.2039-0.81920.24810.0430.223-0.1754-0.08590.10710.11470.0806-0.752921.427415.4698
32.9021-0.35220.26222.445-0.211.6342-0.1097-0.32460.31940.30510.0382-0.0747-0.2252-0.12410.0715-0.07560.0096-0.0591-0.1007-0.0154-0.096223.033249.3645.5283
46.1691-0.1087-1.75713.95562.86818.9053-0.15410.8122-0.741-0.80370.23040.01080.51890.0218-0.07630.1117-0.06750.0183-0.0675-0.0176-0.021239.119239.48615.313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 232
2X-RAY DIFFRACTION2A233 - 287
3X-RAY DIFFRACTION3B-1 - 232
4X-RAY DIFFRACTION4B233 - 287

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