[English] 日本語
Yorodumi
- PDB-3ruq: Crystal structure of Cpn-WT in complex with ADP from Methanococcu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ruq
TitleCrystal structure of Cpn-WT 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: 2.798 Å
AuthorsPereira, J.H. / Ralston, C.Y. / Douglas, N.R. / Kumar, R. / McAndrew, R.P. / Knee, K.M. / 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)234,96712
Polymers233,1614
Non-polymers1,8068
Water1,04558
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)939,86848
Polymers932,64416
Non-polymers7,22432
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area127280 Å2
ΔGint-699 kcal/mol
Surface area277830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.164, 185.002, 184.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein
Chaperonin / / Cpn


Mass: 58290.262 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.61 %
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

-
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: 2.798→50 Å / Num. all: 68606 / Num. obs: 68465 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 99

-
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: 2.798→48.903 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 22.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 3207 5.05 %RANDOM
Rwork0.1713 ---
obs0.1735 63541 92.65 %-
all-63541 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.378 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4956 Å2-0 Å20 Å2
2---9.95 Å20 Å2
3---10.4456 Å2
Refinement stepCycle: LAST / Resolution: 2.798→48.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15484 0 112 58 15654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915696
X-RAY DIFFRACTIONf_angle_d1.13621152
X-RAY DIFFRACTIONf_dihedral_angle_d15.496008
X-RAY DIFFRACTIONf_chiral_restr0.2242580
X-RAY DIFFRACTIONf_plane_restr0.0032724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7981-2.83980.33321250.27092141X-RAY DIFFRACTION77
2.8398-2.88420.3461020.27162312X-RAY DIFFRACTION83
2.8842-2.93150.33531180.28212360X-RAY DIFFRACTION84
2.9315-2.9820.3021210.27482284X-RAY DIFFRACTION82
2.982-3.03630.33561300.25932381X-RAY DIFFRACTION84
3.0363-3.09460.30391340.25752395X-RAY DIFFRACTION86
3.0946-3.15780.37781360.2442461X-RAY DIFFRACTION88
3.1578-3.22650.30021410.22942528X-RAY DIFFRACTION90
3.2265-3.30150.27031400.2162615X-RAY DIFFRACTION93
3.3015-3.3840.27261350.20022587X-RAY DIFFRACTION93
3.384-3.47550.21381490.19392653X-RAY DIFFRACTION94
3.4755-3.57770.23691550.1892710X-RAY DIFFRACTION96
3.5777-3.69320.24231600.17632705X-RAY DIFFRACTION97
3.6932-3.82510.20571320.16812748X-RAY DIFFRACTION97
3.8251-3.97820.23871520.16492712X-RAY DIFFRACTION96
3.9782-4.15920.18531490.13472779X-RAY DIFFRACTION97
4.1592-4.37830.1591450.12212760X-RAY DIFFRACTION98
4.3783-4.65250.16571500.11152807X-RAY DIFFRACTION99
4.6525-5.01130.14951520.11542801X-RAY DIFFRACTION99
5.0113-5.5150.19651310.15062842X-RAY DIFFRACTION99
5.515-6.31160.2051360.17282856X-RAY DIFFRACTION99
6.3116-7.94650.16171510.14462903X-RAY DIFFRACTION100
7.9465-48.91010.17421630.16292994X-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)
10.44120.1564-0.0510.430.05920.83960.10150.0345-0.03480.0268-0.07590.05470.0337-0.016500.20310.0248-0.0030.244-0.02280.1987-116.176414.082441.1797
21.40770.7988-0.52431.98050.22130.66720.0836-0.08310.0554-0.01560.0021-0.208-0.0744-0.002-00.27190.01520.01160.2584-0.04790.3248-100.288934.187150.8875
30.5701-0.1811-0.00150.8942-1.63650.9833-0.0054-0.0565-0.0875-0.09760.05850.1318-0.01350.094500.5264-0.06460.09240.4094-0.03680.601-85.096659.293335.2175
40.2710.3646-0.1540.69810.08720.5130.098-0.0164-0.03710.0753-0.11190.0055-0.05240.0136-00.21380.00050.00060.2786-0.04830.2148-76.694314.234853.6937
50.57350.9567-0.44591.8585-0.97541.23440.0451-0.04180.1790.0541-0.0567-0.23120.0350.037600.3162-0.0380.02790.3084-0.09360.4053-58.661334.348149.4911
60.0682-0.37740.3581.1757-0.96170.92670.0443-0.0036-0.0127-00.05260.0938-0.05920.002500.3513-0.01770.04620.331-0.0260.4822-59.163759.363227.6207
70.70190.1965-0.06280.5867-0.16380.42710.0158-0.0166-0.0410.0432-0.09130.00190.00680.0027-00.2045-0.0069-0.0010.2508-0.04480.1961-39.75414.352334.9032
81.257-0.38780.63521.3182-0.45421.5377-0.0603-0.05120.1776-0.2685-0.1425-0.0671-0.09050.060900.362-0.0368-0.02790.2428-0.02960.2886-29.670434.342919.1007
90.6257-0.76540.81731.04-0.05370.56-0.11260.13920.07220.47950.00660.05690.06230.002400.67830.02780.09080.3280.06630.4429-45.477859.39823.988
100.4101-0.03630.15710.4816-0.21610.7360.02550.01210.03940.0189-0.0965-0.08620.04630.01600.2729-0.0336-0.00560.3097-0.00780.2299-26.735614.2194-4.4842
111.2411-0.36360.63031.4987-0.81970.69460.05680.11430.12830.0308-0.109-0.0034-0.15740.015100.3491-0.0328-0.02530.28190.02950.3091-31.00934.1905-22.6316
121.1223-0.8718-0.28830.74230.57680.26540.11650.14910.1370.2693-0.0346-0.28530.0506-0.124700.55540.03750.00480.4050.09840.6446-53.237559.2024-22.0621
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more