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- PDB-3rus: Crystal structure of Cpn-rls in complex with ADP from Methanococc... -

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Basic information

Entry
Database: PDB / ID: 3rus
TitleCrystal structure of Cpn-rls in complex with ADP from Methanococcus maripaludis
ComponentsChaperonin
KeywordsCHAPERONE / double-ring / protein folding machinery / group II chaperonin / ATP binding
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Thermosome, archaeal / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site ...GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Thermosome, archaeal / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chaperonin
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.338 Å
AuthorsPereira, J.H. / Ralston, C.Y. / Douglas, N.R. / Kumar, R. / McAndrew, R.P. / Knee, K.M. / King, J.A. / Frydman, J. / Adams, P.D.
CitationJournal: Embo J. / Year: 2012
Title: Mechanism of nucleotide sensing in group II chaperonins.
Authors: Pereira, J.H. / Ralston, C.Y. / Douglas, N.R. / Kumar, R. / Lopez, T. / McAndrew, R.P. / Knee, K.M. / King, J.A. / Frydman, J. / Adams, P.D.
History
DepositionMay 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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.ptnr1_label_seq_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: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,03520
Polymers232,4604
Non-polymers2,57516
Water9,944552
1
A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
hetero molecules

A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
hetero molecules

A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
hetero molecules

A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)940,14080
Polymers929,84216
Non-polymers10,29864
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area131120 Å2
ΔGint-1174 kcal/mol
Surface area274380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.564, 185.585, 185.494
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-554-

HOH

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Components

#1: Protein
Chaperonin / / Cpn


Mass: 58115.105 Da / Num. of mol.: 4 / Mutation: T327A,N328A,K330A,D331A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q877G8
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 20% PEG3350, 0.2 M lithium sulfate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2010
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.338→50 Å / Num. all: 117349 / Num. obs: 117127 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KFB

3kfb


Resolution: 2.338→49.037 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 5480 4.99 %
Rwork0.1735 --
obs0.1759 109711 93.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.765 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.512 Å20 Å2-0 Å2
2--3.527 Å2-0 Å2
3----2.015 Å2
Refinement stepCycle: LAST / Resolution: 2.338→49.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15436 0 152 552 16140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815680
X-RAY DIFFRACTIONf_angle_d1.06820960
X-RAY DIFFRACTIONf_dihedral_angle_d14.8985956
X-RAY DIFFRACTIONf_chiral_restr0.0722556
X-RAY DIFFRACTIONf_plane_restr0.0042712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3383-2.36490.28861410.2482967X-RAY DIFFRACTION80
2.3649-2.39270.28851730.2353066X-RAY DIFFRACTION84
2.3927-2.42190.29821560.23033160X-RAY DIFFRACTION85
2.4219-2.45260.31441380.22233215X-RAY DIFFRACTION86
2.4526-2.48480.27311770.21643178X-RAY DIFFRACTION86
2.4848-2.51890.25081620.22373176X-RAY DIFFRACTION87
2.5189-2.55490.29911640.22153229X-RAY DIFFRACTION88
2.5549-2.5930.28811690.22173275X-RAY DIFFRACTION89
2.593-2.63350.24981530.22253279X-RAY DIFFRACTION89
2.6335-2.67670.29151920.21133356X-RAY DIFFRACTION91
2.6767-2.72280.27652040.21293317X-RAY DIFFRACTION91
2.7228-2.77230.28031710.20833434X-RAY DIFFRACTION93
2.7723-2.82570.27521920.20933406X-RAY DIFFRACTION93
2.8257-2.88330.25861720.20543468X-RAY DIFFRACTION94
2.8833-2.9460.2531870.21393498X-RAY DIFFRACTION94
2.946-3.01450.26381700.22153521X-RAY DIFFRACTION94
3.0145-3.08990.29261940.2233554X-RAY DIFFRACTION96
3.0899-3.17340.28372010.21593550X-RAY DIFFRACTION97
3.1734-3.26680.27962030.20473614X-RAY DIFFRACTION98
3.2668-3.37220.24751710.19083675X-RAY DIFFRACTION98
3.3722-3.49270.25151900.18233655X-RAY DIFFRACTION99
3.4927-3.63250.25341820.17313663X-RAY DIFFRACTION99
3.6325-3.79780.20462110.16173687X-RAY DIFFRACTION99
3.7978-3.99790.18751790.14313715X-RAY DIFFRACTION99
3.9979-4.24830.1742030.12823713X-RAY DIFFRACTION100
4.2483-4.57610.15972030.12143712X-RAY DIFFRACTION100
4.5761-5.03620.17021990.12793742X-RAY DIFFRACTION100
5.0362-5.76390.1992000.15243764X-RAY DIFFRACTION100
5.7639-7.25820.20992090.17073770X-RAY DIFFRACTION99
7.2582-49.04730.15942140.14653872X-RAY DIFFRACTION99
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)
10.7977-0.09730.17540.54310.44390.97680.1092-0.06110.04220.0192-0.0574-0.02080.00440.0673-0.03360.075-0.01080.0450.0691-0.02060.112735.0155-41.182278.5199
21.0325-0.18650.24870.2492-0.1760.68310.16520.1838-0.0004-0.1169-0.07040.04370.0337-0.21-0.01910.16140.03870.04470.2237-0.05970.12619.1754-50.877958.5003
30.0602-0.12910.04360.812-0.7420.94210.095-0.0932-0.0189-0.027-0.16450.0842-0.00110.33910.03970.21590.0556-0.02760.4202-0.00040.24373.683-35.331533.8058
40.7808-0.19010.10680.6260.14950.78690.0302-0.1381-0.03340.00950.00080.04940.06530.0663-0.02530.06710.02430.00970.1028-0.04830.1356-4.2199-53.81378.4364
50.3574-0.50650.37270.6025-0.22770.48060.22770.49690.00810.0495-0.11430.3308-0.0681-0.15610.04940.15260.0375-0.08090.3921-0.21410.1258-22.1894-49.559758.4459
60.15140.3359-0.40650.998-1.02980.91680.1946-0.18350.0373-0.1726-0.2711-0.02180.09370.57380.06450.33410.0548-0.00450.5108-0.09720.2517-22.1032-27.474533.7406
71.3636-0.47440.39780.4243-0.24361.6052-0.2301-0.2683-0.15230.19550.38410.16290.0141-0.1586-0.01970.0122-0.1037-0.0612-0.2059-0.21610.0273-40.9991-35.119878.3293
80.28470.06780.09740.34870.25011.33330.00280.04390.0257-0.0710.0133-0.0042-0.3309-0.0980.02410.2329-0.0238-0.05060.1764-0.06320.1784-50.9632-19.236258.4319
90.83190.2404-0.87370.3421-0.52171.3376-0.16410.08240.1041-0.10780.25170.01870.81330.03470.03280.58750.07520.00250.3179-0.03140.2651-35.3436-3.717333.8237
100.76530.0734-0.12620.7084-0.11270.8198-0.03220.03150.02220.10780.03540.05070.0972-0.0827-0.00730.1652-0.0112-0.03640.1141-0.02850.2254-53.93054.331778.4421
110.6040.4424-0.08520.6369-0.26721.2756-0.02760.07290.0121-0.06770.17370.0044-0.06790.0145-0.04390.2627-0.0235-0.06840.24720.01850.2284-49.624822.49758.5406
121.5324-0.4154-1.47220.17510.31481.6899-0.03750.23640.12080.0510.0603-0.06790.3825-0.27660.01450.4274-0.0458-0.00690.42860.01170.3631-27.465122.376833.89
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 4:141 or resid 400:519)
2X-RAY DIFFRACTION2chain A and (resid 362:399 or resid 142:210)
3X-RAY DIFFRACTION3chain A and resid 211:361
4X-RAY DIFFRACTION4chain B and (resid 4:141 or resid 400:519)
5X-RAY DIFFRACTION5chain B and (resid 362:399 or resid 142:210)
6X-RAY DIFFRACTION6chain B and resid 211:361
7X-RAY DIFFRACTION7chain C and (resid 4:141 or resid 400:519)
8X-RAY DIFFRACTION8chain C and (resid 362:399 or resid 142:210)
9X-RAY DIFFRACTION9chain C and resid 211:361
10X-RAY DIFFRACTION10chain D and (resid 4:141 or resid 400:519)
11X-RAY DIFFRACTION11chain D and (resid 362:399 or resid 142:210)
12X-RAY DIFFRACTION12chain D and resid 211:361

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