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- PDB-4fd2: Crystal structure of the C-terminal domain of ClpB -

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Basic information

Entry
Database: PDB / ID: 4fd2
TitleCrystal structure of the C-terminal domain of ClpB
ComponentsChaperone protein ClpB
KeywordsCHAPERONE / AAA domain
Function / homology
Function and homology information


protein unfolding / cellular response to heat / protein refolding / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Chaperonin ClpB / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain ...Chaperonin ClpB / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / Helicase, Ruva Protein; domain 3 - #60 / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chaperone protein ClpB
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBiter, A.B. / Lee, S. / Sung, N. / Tsai, F.T.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for intersubunit signaling in a protein disaggregating machine.
Authors: Biter, A.B. / Lee, S. / Sung, N. / Tsai, F.T.
History
DepositionMay 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Chaperone protein ClpB
B: Chaperone protein ClpB
D: Chaperone protein ClpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0756
Polymers104,7943
Non-polymers1,2823
Water00
1
A: Chaperone protein ClpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3582
Polymers34,9311
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chaperone protein ClpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3582
Polymers34,9311
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: Chaperone protein ClpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3582
Polymers34,9311
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.775, 129.775, 129.401
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
12A
22B
32D
13A
23B
33D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A545 - 756
2114B545 - 756
3114D545 - 756
1124A757 - 852
2124B757 - 852
3124D757 - 852
1134A853
2134B853
3134D853

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Chaperone protein ClpB


Mass: 34931.223 Da / Num. of mol.: 3 / Fragment: UNP residues 545-852 / Mutation: E668A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: clpB, TTHA1487 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL CodonPlus / References: UniProt: Q9RA63
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 294 K / Method: hanging drop / pH: 5
Details: citric acid, isopropanol, pH 5.0, hanging drop, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.497
11h+k,-k,-l20.503
ReflectionResolution: 3→50 Å / Num. obs: 24567

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→42.48 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.882 / Occupancy max: 1 / Occupancy min: 1 / SU B: 72.784 / SU ML: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflection
Rfree0.298 1001 4.1 %
Rwork0.278 --
obs0.279 24567 98.8 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 109.45 Å2
Baniso -1Baniso -2Baniso -3
1--25.04 Å20 Å20 Å2
2---25.04 Å20 Å2
3---50.07 Å2
Refinement stepCycle: LAST / Resolution: 3→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7386 0 81 0 7467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227599
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5152.00110284
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7455921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02322.623366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.35151368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9581596
X-RAY DIFFRACTIONr_chiral_restr0.0920.21161
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215718
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7071.54599
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.22527431
X-RAY DIFFRACTIONr_scbond_it3.98533000
X-RAY DIFFRACTIONr_scangle_it7.4434.52853
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1702medium positional0.150.5
12B1702medium positional0.180.5
13D1702medium positional0.140.5
21A760medium positional0.120.5
22B760medium positional0.20.5
23D760medium positional0.150.5
31A27medium positional0.320.5
32B27medium positional0.40.5
33D27medium positional0.530.5
11A1702medium thermal1.52
12B1702medium thermal1.022
13D1702medium thermal0.842
21A760medium thermal1.42
22B760medium thermal1.242
23D760medium thermal0.592
31A27medium thermal0.22
32B27medium thermal0.292
33D27medium thermal0.212
LS refinement shellResolution: 3→3.08 Å
RfactorNum. reflection% reflection
Rfree0.325 81 -
Rwork0.355 1696 -
obs--97.53 %
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)
114.763513.4796-1.931323.4111-5.22741.03090.33740.9198-0.76410.4823-0.4809-0.70950.03010.37710.14350.41110.25690.03740.52260.02710.0436-48.4804-2.829541.3899
23.02390.82511.10282.47970.10191.83450.080.12870.2115-0.3104-0.17580.2051-0.2490.07960.09580.4081-0.01550.05410.54990.05790.1808-55.91727.332237.4749
37.9238-5.3171-6.610242.8971-8.82456.2052-0.7124-0.37632.073-4.3673.35733.65021.4961-0.6493-2.64491.9179-0.3563-0.66590.89760.25660.9235-67.600425.409430.4338
42.9666-24.37457.061868.8646-28.072115.8944-2.40431.3486-1.21156.9868-1.32221.5535-2.3902-0.44573.72661.10080.41550.50291.8312-0.1483.9076-68.600723.925420.9087
56.20411.02792.40811.525-1.24152.6271-0.1112-0.02050.80320.09050.01630.3068-0.2569-0.08040.09490.4480.10350.05550.54660.04640.2361-64.488413.17834.3742
630.2297-7.313917.03110.4819-3.844318.49360.2387-3.6177-0.63910.4823-0.59980.73110.6535-1.0340.36120.333-0.2120.1990.85020.01410.1044-54.898713.264957.0878
77.5611.2435-3.68660.501-0.50062.72820.0194-0.1726-0.28980.1142-0.1016-0.117-0.04160.18370.08220.43560.0105-0.03350.41980.09960.3181-29.267712.143136.1919
811.3328.58924.757615.07533.26321.6619-0.0088-0.05730.08060.7422-0.07080.6735-0.0176-0.21140.07950.51130.16130.08870.6207-0.16020.0875-43.1383-5.8435-37.0306
90.1931-0.0816-0.80213.567-0.99472.0445-0.04-0.0788-0.03590.341-0.0101-0.4432-0.12970.18650.05020.6720.00940.01650.6624-0.05030.5161-30.833-7.4677-32.8015
104.7765-5.7543-4.28214.46347.315955.0495-1.3872-0.6548-0.56461.19840.56580.1907-1.78154.12250.82150.7174-0.08480.071.36840.29571.7801-10.1777-9.8297-20.5239
115.6870.53160.96335.7287-0.92920.724-0.0788-0.0569-0.17730.11660.1417-0.98230.07730.4161-0.06290.58570.0732-0.0580.6937-0.09160.4747-21.672-12.9355-28.622
1223.7923-13.54139.933218.3518-8.72196.58580.28992.4456-0.0217-1.2721-0.7307-0.43070.55960.21940.44080.67390.13680.30360.9724-0.11570.1443-24.9725-2.3437-51.5397
132.452-0.4524-0.46942.32620.89962.9853-0.22020.18020.0473-0.2206-0.16640.4996-0.331-0.08340.38670.59720.0029-0.07620.6954-0.01430.4558-37.26486.5815-35.0756
143.4658-2.5609-0.98924.85160.67954.5955-0.13750.11130.379-0.03150.40010.26170.2049-0.1254-0.26260.6545-0.0962-0.04090.5413-0.05730.6137-41.379424.5318-29.075
1534.9651-2.55683.1625.93882.31171.01810.778-0.03040.9447-0.8053-0.8724-0.1529-0.3175-0.29490.09440.4548-0.1228-0.03580.29820.04810.0206-38.2017-3.1318-1.7965
162.8824-0.0001-0.80242.52130.65471.9315-0.00280.1611-0.5465-0.3085-0.03850.14450.2366-0.29750.04120.42810.0228-0.05390.4388-0.00650.1783-43.2464-14.6548-5.7228
171.005-2.72161.65444.1442-1.8016-0.03640.41740.5634-0.4214-0.9557-0.4280.30930.35720.2160.01061.3189-0.25780.0651.1511-0.20151.3305-52.1687-33.919-17.2652
183.0627-3.1135-0.68175.21353.19723.16950.26150.0994-0.9589-0.1153-0.29110.78660.3484-0.39770.02950.5731-0.0607-0.09390.4221-0.02040.2991-43.3478-25.4147-9.7066
1910.3035-2.23564.98825.343817.393417.7046-1.8868-1.8958-0.28141.09512.1743-1.4618-0.51340.7941-0.28750.42950.264-0.10420.69980.24080.595-49.4831-16.778813.2936
209.4105-6.33144.439512.4714-1.96654.751-0.3254-1.1149-0.12530.27340.31330.29930.041-0.27310.01210.3922-0.12230.13080.48580.03550.1003-48.1383-9.80324.9597
213.1978-2.57661.21233.5899-2.55634.83660.01740.00760.2812-0.1147-0.151-0.3097-0.2328-0.11050.13360.4211-0.0237-0.03090.4866-0.07190.3816-63.90439.9587-9.989
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A545 - 573
2X-RAY DIFFRACTION2A574 - 628
3X-RAY DIFFRACTION3A629 - 640
4X-RAY DIFFRACTION4A641 - 651
5X-RAY DIFFRACTION5A652 - 712
6X-RAY DIFFRACTION6A713 - 743
7X-RAY DIFFRACTION7A744 - 852
8X-RAY DIFFRACTION8B545 - 573
9X-RAY DIFFRACTION9B574 - 628
10X-RAY DIFFRACTION10B629 - 651
11X-RAY DIFFRACTION11B652 - 708
12X-RAY DIFFRACTION12B709 - 743
13X-RAY DIFFRACTION13B744 - 780
14X-RAY DIFFRACTION14B781 - 852
15X-RAY DIFFRACTION15D545 - 573
16X-RAY DIFFRACTION16D574 - 628
17X-RAY DIFFRACTION17D629 - 651
18X-RAY DIFFRACTION18D652 - 708
19X-RAY DIFFRACTION19D709 - 743
20X-RAY DIFFRACTION20D744 - 763
21X-RAY DIFFRACTION21D764 - 852

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