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- PDB-3ruv: Crystal structure of Cpn-rls in complex with ATP analogue from Me... -

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Basic information

Entry
Database: PDB / ID: 3ruv
TitleCrystal structure of Cpn-rls in complex with ATP analogue 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Thermosome subunit
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.242 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_auth_seq_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)235,83228
Polymers232,4604
Non-polymers3,37224
Water10,503583
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)943,330112
Polymers929,84216
Non-polymers13,48896
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area136990 Å2
ΔGint-1377 kcal/mol
Surface area274160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.019, 184.477, 184.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.94 Å3/Da / Density % sol: 58.2 %
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: 8.2.1 / 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: 2.24→50 Å / Num. all: 131253 / Num. obs: 131211 / % 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: 2.242→48.813 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 5979 5.04 %
Rwork0.1708 --
obs0.1733 118641 90.38 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.352 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8699 Å2-0 Å2-0 Å2
2---0.3239 Å2-0 Å2
3----2.546 Å2
Refinement stepCycle: LAST / Resolution: 2.242→48.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15436 0 192 583 16211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815712
X-RAY DIFFRACTIONf_angle_d1.06621192
X-RAY DIFFRACTIONf_dihedral_angle_d17.1576108
X-RAY DIFFRACTIONf_chiral_restr0.0682576
X-RAY DIFFRACTIONf_plane_restr0.0042716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2416-2.2670.36371740.27473414X-RAY DIFFRACTION82
2.267-2.29370.30731520.23383203X-RAY DIFFRACTION77
2.2937-2.32170.29181930.22083234X-RAY DIFFRACTION79
2.3217-2.35110.32461640.22193359X-RAY DIFFRACTION81
2.3511-2.3820.29891840.21673409X-RAY DIFFRACTION83
2.382-2.41460.27151930.1943438X-RAY DIFFRACTION84
2.4146-2.44910.28051780.20013530X-RAY DIFFRACTION85
2.4491-2.48570.26431720.19443536X-RAY DIFFRACTION85
2.4857-2.52450.27191900.20213527X-RAY DIFFRACTION85
2.5245-2.56590.25612000.19233584X-RAY DIFFRACTION86
2.5659-2.61020.26552070.20423512X-RAY DIFFRACTION86
2.6102-2.65760.24681740.19353543X-RAY DIFFRACTION86
2.6576-2.70870.27292000.19833639X-RAY DIFFRACTION89
2.7087-2.7640.25232110.19413666X-RAY DIFFRACTION89
2.764-2.82410.26822130.19333721X-RAY DIFFRACTION90
2.8241-2.88980.25231780.2113796X-RAY DIFFRACTION91
2.8898-2.96210.28922130.21443727X-RAY DIFFRACTION91
2.9621-3.04210.26141850.21043809X-RAY DIFFRACTION92
3.0421-3.13160.27772010.19673903X-RAY DIFFRACTION94
3.1316-3.23270.23981920.20273912X-RAY DIFFRACTION94
3.2327-3.34820.2632150.19343969X-RAY DIFFRACTION96
3.3482-3.48220.23372120.18544036X-RAY DIFFRACTION97
3.4822-3.64070.22882100.16954013X-RAY DIFFRACTION97
3.6407-3.83250.22162120.16264097X-RAY DIFFRACTION98
3.8325-4.07260.18222040.14334063X-RAY DIFFRACTION98
4.0726-4.38680.16432310.12434106X-RAY DIFFRACTION98
4.3868-4.82790.1722440.1254104X-RAY DIFFRACTION99
4.8279-5.52570.16682400.13464168X-RAY DIFFRACTION99
5.5257-6.95860.19692100.16654262X-RAY DIFFRACTION100
6.9586-48.82490.16692270.14494382X-RAY DIFFRACTION100
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)
10.61620.2633-0.03430.4134-0.14340.56520.0771-0.04020.00310.0484-0.05510.0158-0.0086-0.0286-0.01520.11380.0109-0.0240.10690.020.1196-35.033340.9884-14.2292
20.7375-0.12870.04330.1976-0.07260.16780.13610.23740.0343-0.0295-0.0993-0.03810.00670.0575-0.01880.16550.0354-0.03170.22730.05830.1722-19.206750.6293-34.1095
30.1627-0.1372-0.21920.42620.62211.02530.10860.0293-0.0146-0.0643-0.1193-0.02930.0772-0.41560.02190.2710.0349-0.0070.36860.03020.2324-3.699135.083-58.8885
40.7408-0.10560.10080.51910.01040.25050.0035-0.15290.1022-0.05890.0013-0.0285-0.0205-0.0081-0.00470.15770.0014-0.01540.18290.02120.22034.323753.6146-14.2627
50.1931-0.27740.01920.3781-0.05930.09430.21040.36660.17550.0128-0.0531-0.42780.05730.18340.05470.0915-0.05350.18640.1230.4389-0.100822.219449.3133-34.1332
60.09560.05170.10290.35710.29910.38180.1807-0.0887-0.0172-0.1528-0.1619-0.0011-0.0388-0.3591-0.00530.30840.04920.01340.40680.11580.268522.016127.1825-58.9358
70.5602-0.3823-0.18740.49390.04430.7518-0.083-0.04150.08370.04280.0888-0.0403-0.02890.0145-0.00850.0829-0.0187-0.01810.09070.02890.127741.174234.8802-14.3339
80.11430.0341-0.03640.4942-0.16510.4034-0.05930.0542-0.0046-0.11030.0389-0.0930.12550.05730.02310.2173-0.01780.0440.20220.05130.201950.976519.1563-34.1504
90.39370.12460.52630.17180.30311.0207-0.13360.1218-0.0117-0.1160.1173-0.0029-0.6449-0.1450.04760.39920.04210.02690.23710.03240.157735.26323.6653-58.9533
100.49620.17120.04450.63420.02030.2023-0.01960.034-0.040.1638-0.0229-0.10680.00670.02960.02280.1828-0.0040.01410.15550.02830.246854.0505-4.3772-14.3034
110.24410.0969-0.03130.06030.0610.1196-0.07290.0428-0.1658-0.1190.1464-0.08610.04510.01080.01810.2328-0.03540.13080.1654-0.05160.205249.6927-22.2762-34.1159
120.6879-0.08780.96610.0816-0.07221.3906-0.05870.1042-0.0616-0.03330.08880.0413-0.35440.1516-0.01380.3708-0.01050.06840.3198-0.00740.30927.4431-22.1448-58.9781
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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