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

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Basic information

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


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 repeat (R) N-terminal domain / : / 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 repeat (R) N-terminal domain / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / 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: 3.4 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 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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
C: Chaperone protein ClpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1276
Polymers106,8453
Non-polymers1,2823
Water00
1
A: Chaperone protein ClpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0422
Polymers35,6151
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)36,0422
Polymers35,6151
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chaperone protein ClpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0422
Polymers35,6151
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.146, 116.814, 68.945
Angle α, β, γ (deg.)90.000, 119.520, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
33C
14A
24B
34C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A542 - 636
2113B542 - 636
3113C542 - 636
1123A757 - 852
2123B757 - 852
3123C757 - 852
1133A853 - 901
2133B853 - 901
3133C853 - 901
1143A651 - 756
2143B651 - 756
3143C651 - 756

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Chaperone protein ClpB


Mass: 35615.008 Da / Num. of mol.: 3 / Fragment: UNP residues 544-852 / Mutation: E668A, I683M, L706M, L770M
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
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 294 K / Method: hanging drop / pH: 8
Details: ammonium acetate, PEG 3350, pH 8.0, 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
ReflectionResolution: 3.4→60 Å / Num. obs: 12853

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→41.85 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 1 / SU B: 77.89 / SU ML: 0.584 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.711 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 647 5 %RANDOM
Rwork0.2331 ---
obs0.2345 12853 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 217.93 Å2 / Biso mean: 107.8985 Å2 / Biso min: 53.25 Å2
Baniso -1Baniso -2Baniso -3
1--4.84 Å20 Å2-2.28 Å2
2--4.19 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 3.4→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7446 0 81 0 7527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227659
X-RAY DIFFRACTIONr_angle_refined_deg1.1912.00110353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.445930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11922.623366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.163151392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9791596
X-RAY DIFFRACTIONr_chiral_restr0.0760.21161
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215754
X-RAY DIFFRACTIONr_mcbond_it0.5591.54641
X-RAY DIFFRACTIONr_mcangle_it1.22527491
X-RAY DIFFRACTIONr_scbond_it2.02533018
X-RAY DIFFRACTIONr_scangle_it3.6194.52862
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A380TIGHT POSITIONAL0.020.05
12B380TIGHT POSITIONAL0.020.05
13C380TIGHT POSITIONAL0.020.05
11A366LOOSE POSITIONAL0.035
12B366LOOSE POSITIONAL0.035
13C366LOOSE POSITIONAL0.035
11A380TIGHT THERMAL0.030.5
12B380TIGHT THERMAL0.030.5
13C380TIGHT THERMAL0.030.5
11A366LOOSE THERMAL0.0410
12B366LOOSE THERMAL0.0310
13C366LOOSE THERMAL0.0310
21A384TIGHT POSITIONAL0.030.05
22B384TIGHT POSITIONAL0.030.05
23C384TIGHT POSITIONAL0.030.05
21A376LOOSE POSITIONAL0.035
22B376LOOSE POSITIONAL0.035
23C376LOOSE POSITIONAL0.035
21A384TIGHT THERMAL0.030.5
22B384TIGHT THERMAL0.040.5
23C384TIGHT THERMAL0.030.5
21A376LOOSE THERMAL0.0410
22B376LOOSE THERMAL0.0510
23C376LOOSE THERMAL0.0310
31A27LOOSE POSITIONAL0.275
32B27LOOSE POSITIONAL0.445
33C27LOOSE POSITIONAL0.245
31A27LOOSE THERMAL4.7110
32B27LOOSE THERMAL5.0410
33C27LOOSE THERMAL2.4410
41A424TIGHT POSITIONAL0.020.05
42B424TIGHT POSITIONAL0.020.05
43C424TIGHT POSITIONAL0.020.05
41A456LOOSE POSITIONAL0.025
42B456LOOSE POSITIONAL0.025
43C456LOOSE POSITIONAL0.025
41A424TIGHT THERMAL0.030.5
42B424TIGHT THERMAL0.030.5
43C424TIGHT THERMAL0.030.5
41A456LOOSE THERMAL0.0310
42B456LOOSE THERMAL0.0410
43C456LOOSE THERMAL0.0310
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 46 -
Rwork0.27 876 -
all-922 -
obs--98.19 %
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)
19.31013.29312.25127.34381.14834.8816-0.11780.238-0.4539-0.40020.5115-0.34550.27230.1915-0.39370.2054-0.2101-0.08240.36460.1480.1578-2.5834-15.3249-9.8058
26.814-2.54316.38743.1104-1.92768.39450.5877-0.4526-0.4147-0.0026-0.30780.4310.2881-1.0316-0.27990.2952-0.27160.0460.6038-0.0820.2428-25.41-14.3595-29.3305
36.56240.4226-0.30697.07332.91696.4909-0.1899-0.5431-0.02650.69640.1941-0.29850.2507-0.0185-0.00410.33980.0510.0070.0606-0.00740.0213-8.52074.4515-37.8988
44.1850.4808-2.53.9305-4.295712.6906-0.41570.79420.1138-0.2209-0.0666-0.21820.7697-0.11910.48230.0967-0.08440.05460.2201-0.04430.1555-4.08064.1182-67.689
59.43282.8310.03916.8328-2.09376.8501-0.26270.38460.2591-0.63720.3817-0.2810.3842-0.1514-0.11890.1212-0.00250.04170.04970.01450.3354-10.4213-34.6432-61.3931
615.5081-5.7583-4.93084.55581.74082.7218-0.1698-1.1189-0.70480.07370.26570.4160.0041-0.0534-0.09590.1779-0.1857-0.06950.50940.2530.2169-38.5906-32.6426-50.7455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A542 - 744
2X-RAY DIFFRACTION2A745 - 852
3X-RAY DIFFRACTION3B542 - 744
4X-RAY DIFFRACTION4B745 - 852
5X-RAY DIFFRACTION5C542 - 744
6X-RAY DIFFRACTION6C745 - 852

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