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- PDB-3ruw: Crystal structure of Cpn-rls in complex with ADP-AlFx from Methan... -

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Basic information

Entry
Database: PDB / ID: 3ruw
TitleCrystal structure of Cpn-rls in complex with ADP-AlFx 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 / metal ion binding / identical protein binding
Similarity search - Function
GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / Thermosome, archaeal / GroEL / GroEL / : / Chaperonins TCP-1 signature 1. / : ...GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / Thermosome, archaeal / GroEL / GroEL / : / 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 / ALUMINUM FLUORIDE / Thermosome subunit
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 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)235,37124
Polymers232,4604
Non-polymers2,91020
Water2,090116
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)941,48396
Polymers929,84216
Non-polymers11,64280
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area135600 Å2
ΔGint-1157 kcal/mol
Surface area275930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.552, 184.464, 185.495
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-569-

HOH

21D-560-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 136 molecules

#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


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF3
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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 315r / 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: 2.7→50 Å / Num. all: 76364 / Num. obs: 76234 / % 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: 2.702→48.972 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 23.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 3536 5.04 %
Rwork0.1724 --
obs0.1751 70203 91.97 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.661 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5372 Å2-0 Å20 Å2
2---6.5726 Å20 Å2
3---3.0354 Å2
Refinement stepCycle: LAST / Resolution: 2.702→48.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15436 0 168 116 15720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715692
X-RAY DIFFRACTIONf_angle_d0.96120972
X-RAY DIFFRACTIONf_dihedral_angle_d14.9375956
X-RAY DIFFRACTIONf_chiral_restr0.0642556
X-RAY DIFFRACTIONf_plane_restr0.0032712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7021-2.73910.36471110.27862171X-RAY DIFFRACTION76
2.7391-2.77830.34741260.26492312X-RAY DIFFRACTION81
2.7783-2.81970.37581100.2492377X-RAY DIFFRACTION82
2.8197-2.86380.31951340.24122344X-RAY DIFFRACTION82
2.8638-2.91070.30281440.2292454X-RAY DIFFRACTION86
2.9107-2.96090.30111260.23292428X-RAY DIFFRACTION84
2.9609-3.01470.31361260.23582464X-RAY DIFFRACTION86
3.0147-3.07270.30281250.21952558X-RAY DIFFRACTION88
3.0727-3.13540.28561500.22592548X-RAY DIFFRACTION89
3.1354-3.20360.29571180.22592633X-RAY DIFFRACTION91
3.2036-3.27810.24871420.2152653X-RAY DIFFRACTION93
3.2781-3.36010.28351640.20072653X-RAY DIFFRACTION93
3.3601-3.45090.2461250.19442736X-RAY DIFFRACTION94
3.4509-3.55240.24751460.19422754X-RAY DIFFRACTION95
3.5524-3.6670.23781210.18722814X-RAY DIFFRACTION96
3.667-3.7980.23921380.1732790X-RAY DIFFRACTION97
3.798-3.950.23551610.15812815X-RAY DIFFRACTION96
3.95-4.12970.19281660.13952764X-RAY DIFFRACTION97
4.1297-4.34730.17821480.12312839X-RAY DIFFRACTION98
4.3473-4.61950.16981640.11992839X-RAY DIFFRACTION98
4.6195-4.97590.15641620.12182876X-RAY DIFFRACTION98
4.9759-5.4760.21761580.15552895X-RAY DIFFRACTION99
5.476-6.2670.25431610.1872911X-RAY DIFFRACTION99
6.267-7.89040.1761520.14842964X-RAY DIFFRACTION100
7.8904-48.98040.18931580.1623075X-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)
10.96830.2796-0.08011.1385-0.10180.78590.21960.07030.08060.038-0.0734-0.0168-0.23670.0108-0.03370.04320.0708-0.03940.10430.03820.0442116.326-14.177841.2147
21.1262-0.13720.26240.0286-0.01170.1440.38140.0251-0.3177-0.0428-0.0464-0.02120.16890.0338-0.11670.12060.2045-0.2175-0.18380.3532-0.0101100.5098-34.137150.951
30.15230.17450.16240.79490.71330.5990.02690.0260.0284-0.1780.1416-0.41920.0102-0.0026-0.13960.35370.0065-0.06850.25280.00830.527984.9798-58.938535.3751
40.8821-0.11480.0560.49710.01090.45090.0571-0.08320.17910.0388-0.0579-0.01940.12450.01510.01160.11010.01380.01530.1830.0220.11376.8443-14.294853.7805
50.1177-0.02620.1630.14950.00040.20620.0671-0.0903-0.0850.0267-0.10390.07390.0561-0.0707-0.01850.2597-0.0504-0.02840.28590.1250.332758.8467-34.199549.5506
60.1237-0.2254-0.07810.5170.3360.33220.0923-0.00090.0293-0.0650.0149-0.37510.03140.0215-0.0890.3492-0.0081-0.02450.27540.05490.4959.0957-58.980827.4147
70.84340.2170.18060.97430.29010.6063-0.2999-0.15260.24950.0438-0.0047-0.0359-0.14690.00130.0783-0.0178-0.00480.0960.16030.07840.038339.9402-14.330634.9137
80.24050.1634-0.32390.2631-0.37640.8295-0.12490.0007-0.2049-0.1158-0.1358-0.04660.16210.00180.12740.2653-0.07020.05520.170.02590.237929.9899-34.197819.1518
90.5362-0.6721-0.14620.80690.20420.2024-0.20230.00570.06580.60080.0752-0.2424-0.07160.03240.07760.7210.0293-0.05080.3187-0.00730.44245.7609-58.97423.7168
100.7764-0.1852-0.04730.2867-0.10360.70560.00410.0058-0.14660.0023-0.03530.0452-0.2087-0.07010.01650.1781-0.0234-0.00670.25140.02440.152927.0887-14.2713-4.5014
111.02860.2976-0.48560.34790.04770.4142-0.06140.032-0.28730.1079-0.0929-0.05310.0873-0.04130.0840.3275-0.10070.01020.257-0.04590.303331.3698-34.1264-22.5191
121.3168-0.93390.29170.6593-0.28930.242-0.01780.0813-0.01680.366-0.00330.1378-0.0082-0.01030.02460.4850.00720.04710.31960.01110.474453.6989-58.9348-22.2532
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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