[English] 日本語
Yorodumi
- PDB-6ug5: Closed Dimer of Y77A Mutant Putative Ryanodine Receptor from Bact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ug5
TitleClosed Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron VPI-5482
ComponentsPutative ryanodine receptor
KeywordsMETAL TRANSPORT / Alpha Fold / PSI-BIOLOGY / MCSG / Structural Genomics / Midwest Center for Structural Genomics
Function / homology
Function and homology information


ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / calcium channel complex / sarcolemma / Z disc / metal ion binding
Similarity search - Function
Ryanodine receptor Ryr / RyR domain / :
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.357 Å
AuthorsWu, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Closed Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron VPI-5482
Authors: Wu, R. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionSep 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative ryanodine receptor
C: Putative ryanodine receptor
E: Putative ryanodine receptor
G: Putative ryanodine receptor
I: Putative ryanodine receptor
K: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,05214
Polymers71,3156
Non-polymers7378
Water1,27971
1
A: Putative ryanodine receptor
C: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1406
Polymers23,7722
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-30 kcal/mol
Surface area11380 Å2
MethodPISA
2
E: Putative ryanodine receptor
I: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9564
Polymers23,7722
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-33 kcal/mol
Surface area11620 Å2
MethodPISA
3
G: Putative ryanodine receptor
K: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9564
Polymers23,7722
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-32 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.012, 87.421, 74.041
Angle α, β, γ (deg.)90.000, 110.560, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Putative ryanodine receptor


Mass: 11885.885 Da / Num. of mol.: 6 / Mutation: Y77A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2247 / Plasmid: pMCSG50 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8A5J2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.5M sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.357→50 Å / Num. obs: 36401 / % possible obs: 99.4 % / Redundancy: 5 % / Biso Wilson estimate: 29.05 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.042 / Rrim(I) all: 0.095 / Χ2: 0.884 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.36-2.43.70.5117110.7120.2960.5930.9893.3
2.4-2.4440.57417500.7180.3250.6630.97297
2.44-2.494.50.4918410.7990.2590.5560.96398.9
2.49-2.544.80.52218040.8130.2670.5880.96399.9
2.54-2.65.10.48818220.830.2410.5460.956100
2.6-2.665.20.42718310.8730.2070.4750.942100
2.66-2.725.30.37918200.8910.1810.420.9499.9
2.72-2.85.30.35817900.9070.1710.3970.93699.9
2.8-2.885.30.28918180.9440.1390.3210.94100
2.88-2.975.30.21418370.9640.1030.2380.897100
2.97-3.085.30.15818240.9780.0760.1760.86799.9
3.08-3.25.30.13618180.9830.0650.1510.892100
3.2-3.355.30.10118330.9890.0480.1120.867100
3.35-3.535.30.07618320.9920.0370.0850.8599.9
3.53-3.755.30.05818100.9940.0280.0650.815100
3.75-4.035.30.04918370.9950.0230.0550.80199.9
4.03-4.445.30.04318370.9950.0210.0480.832100
4.44-5.085.20.04418310.9940.0210.0490.966100
5.08-6.45.20.04218650.9940.020.0460.75599.9
6.4-5050.03818900.9960.0180.0420.63299.8

-
Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.357→36.974 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.97
RfactorNum. reflection% reflection
Rfree0.2241 1712 4.99 %
Rwork0.174 --
obs0.1765 34321 93.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.97 Å2 / Biso mean: 40.52 Å2 / Biso min: 11.1 Å2
Refinement stepCycle: final / Resolution: 2.357→36.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4574 0 48 71 4693
Biso mean--52.65 31.76 -
Num. residues----561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084707
X-RAY DIFFRACTIONf_angle_d1.1166333
X-RAY DIFFRACTIONf_chiral_restr0.071684
X-RAY DIFFRACTIONf_plane_restr0.005827
X-RAY DIFFRACTIONf_dihedral_angle_d15.5121881
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3574-2.42670.22781020.1928200469
2.4267-2.5050.25081170.1934225679
2.505-2.59460.24481120.1875250986
2.5946-2.69840.26341370.1989266693
2.6984-2.82120.25581370.208286199
2.8212-2.96990.26331560.20052906100
2.9699-3.15580.24021490.18692864100
3.1558-3.39930.25261730.19152882100
3.3993-3.74110.24411550.17272892100
3.7411-4.28180.19341630.14532891100
4.2818-5.39190.19121580.14662915100
5.3919-36.9740.19161530.16792963100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.6952.953-1.18962.1753-0.31341.70070.2155-0.0382-1.13390.4918-0.0443-0.34610.38410.0792-0.0280.2194-0.0308-0.02950.17820.04150.279811.7822-16.6297-6.8199
24.6683-1.6191-0.58861.82870.10051.97930.1277-0.2873-0.0072-0.0056-0.15370.0872-0.17990.06060.11710.1629-0.03-0.04510.0978-0.02580.20112.01794.6101-2.1137
34.1468-1.34890.88711.25780.1151.41740.0009-0.421-0.15940.2941-0.05620.57360.2484-0.5520.04240.1882-0.00260.05250.345-0.03630.3705-2.09315.69146.451
43.1566-0.29410.26633.06723.69318.7914-0.143-0.2422-0.14620.1156-0.23430.320.3225-0.35940.30790.1834-0.0244-0.05310.11550.04440.232913.701-5.4519-1.3569
56.99166.25931.98518.2721.97123.6052-0.00560.352-0.0945-0.6073-0.2975-0.7303-0.13390.50330.08880.24180.11590.04110.23640.03050.309522.8483-5.2074-15.4408
62.4584-0.6272-1.32432.45650.77692.20430.1920.03340.3365-0.5269-0.05790.1082-1.05960.1237-0.29420.31250.0477-0.02420.2317-0.02410.219510.391111.1092-8.7128
72.77230.6248-1.9352.1449-2.09964.5520.00510.0198-0.27420.1161-0.2038-0.1142-0.0165-0.23080.08930.2268-0.0208-0.03320.0872-0.00590.15455.9825-10.2659-9.6533
80.7839-0.3043-0.67790.93190.3034.0451-0.0028-0.51450.1550.40070.0430.4213-0.7044-0.4664-0.0290.4057-0.04550.12730.4005-0.03160.2736-7.9242-11.12672.3904
97.5127-1.8443-0.10493.1284-0.0364.2073-0.01740.6006-0.2741-0.41310.07410.50960.5652-0.35590.00030.2538-0.06830.01070.23890.00840.2669-4.1715-10.8115-12.2199
107.81451.61860.88731.36910.49281.44840.2535-0.19670.2440.3863-0.23840.08570.1378-0.1908-0.04120.26120.0079-0.00430.1289-0.01170.16866.28920.0136-12.248
113.1067-0.75830.6457.56465.8477.40190.33680.36710.1118-0.3783-0.3637-0.72260.13180.52160.03490.3202-0.02670.04330.240.12030.27622.5063-0.3023-15.9692
122.4063-2.77511.05553.366-1.2260.4629-0.42880.2039-0.995-0.527-0.3113-1.5569-0.4221-0.1580.3980.3422-0.02320.06050.52030.00930.654156.58226.07431.1948
134.52354.7987-0.95995.266-1.56952.02190.11890.7008-1.1471-0.24190.2628-0.65040.34860.28630.05830.19890.0207-0.01770.2768-0.07510.305639.2044-7.95452.7639
142.37841.07760.56375.72511.2953.6831-0.0722-0.25980.29740.27550.0670.0855-0.3707-0.2503-0.02310.17210.0199-0.01330.1624-0.01990.226426.03476.911510.6342
152.14540.85261.3040.94931.27943.46510.22640.24660.34190.58310.0113-0.9541-0.70961.33650.20110.7865-0.3250.10640.5157-0.15210.944135.497623.714710.0413
163.2887-1.4609-2.51970.9766-0.11176.53240.09810.03730.58710.0971-0.10520.7682-1.2012-0.0969-0.95990.3679-0.0203-0.02580.05150.01850.563824.62114.81163.8416
173.3348-2.02630.7045.2729-1.98743.4211-0.03060.2220.2561-0.24730.1115-0.1614-0.0651-0.0251-0.0280.0852-0.0151-0.01090.2128-0.01490.168232.1991.50334.2377
188.74260.05820.86642.8563-0.34242.75520.1574-0.4732-0.6560.20820.00880.55710.4767-0.47570.01680.31140.007-0.01940.2235-0.00890.356129.4629-12.161113.4167
192.1343-2.5246-2.47133.06932.27237.48910.204-0.25070.1446-1.07230.0842-0.6597-0.58310.5603-0.34880.4536-0.07840.11550.4017-0.05050.36415.8281-5.7871-49.246
204.375-0.7455-3.17322.3898-2.11935.4266-0.1464-0.22170.63860.34140.3552-0.3631-1.1830.8953-0.1050.2545-0.08-0.01090.3213-0.00970.19589.27314.614-31.8701
213.8269-0.52980.06884.6796-0.51742.5621-0.28390.2493-0.6411-0.45690.43490.32260.5573-0.0583-0.09020.3101-0.05790.02470.2278-0.00140.1932-0.8819-15.5489-29.709
221.8762-1.4951-0.91.791.65841.91830.51270.9687-0.3953-1.0388-0.09090.017-0.26920.5918-0.19580.83660.07330.16010.5291-0.21460.79344.7276-29.4191-36.8617
237.51091.5803-1.10761.119-1.64042.68180.2602-0.262-0.84650.89130.06940.12730.5486-0.03130.45540.485-0.00250.04740.06970.00130.37445.0225-20.3264-24.4414
242.9934-1.14490.58475.0004-2.59174.2848-0.1518-0.1568-0.13850.0540.1223-0.20380.20860.35650.07470.17-0.01690.01610.2185-0.01370.07747.3888-6.9849-31.6559
253.67230.066-1.34882.4431-0.56788.4398-0.1409-0.36370.92280.46040.24260.2821-0.8974-0.43730.11130.42770.0208-0.01350.2394-0.00560.3054-2.22986.7223-32.3057
263.5305-1.17560.3598.0518-3.15393.9899-0.226-0.82280.56430.89810.77460.2882-0.9735-0.6314-0.35150.34240.07150.0380.3638-0.08230.300124.29218.196219.4268
272.28180.892-1.13423.5274-0.95824.86430.02180.37440.11360.13520.2527-0.3575-0.06240.0705-0.12690.0833-0.0134-0.0150.311-0.00430.177342.6422-0.746110.2547
284.8416-1.97120.88834.2278-1.09124.6143-0.90950.91971.5384-0.69960.4878-0.1618-1.0251-0.7680.21250.5657-0.0621-0.04690.59580.16050.694647.279215.00030.2507
297.49642.3637-0.92462.3463-0.6822.35360.12620.09840.40980.31390.0369-0.0937-0.25750.1307-0.04870.16390.0017-0.03230.136-0.00240.189639.37824.408515.8776
306.7016-2.92122.96885.3842-1.00394.56660.2921-0.2324-0.70980.5062-0.10010.09950.8315-0.5671-0.17960.2867-0.1223-0.04020.29480.05260.255226.5039-9.849916.647
312.3659-1.8348-0.49986.8051-1.50422.6976-0.2731-0.4348-0.7507-0.10660.72230.74760.4975-0.9928-0.26970.2923-0.1044-0.03840.32470.06030.3616-10.0104-12.4467-30.0387
322.20880.03080.08682.75911.21243.154-0.1686-0.3307-0.398-0.24210.3743-0.24360.47150.4876-0.18240.27890.02880.01840.31960.00340.20579.0556-10.1873-43.7814
333.61491.17692.94084.4377-1.0297.52990.1867-0.3566-1.01870.38580.8016-0.63730.90580.2233-0.20020.47760.16010.01540.4452-0.10750.542215.8224-18.9849-45.2971
343.674-0.8388-2.25031.92581.34436.0664-0.17420.2635-0.2826-0.21650.01780.0910.2002-0.06750.09780.1909-0.0248-0.00460.15380.01320.1203-1.3408-9.8262-42.1877
353.6367-0.26250.94393.5065-3.81678.393-0.2452-0.53280.5859-0.0311-0.12630.3079-0.8846-0.69910.05640.31460.1029-0.06560.307-0.06080.237-6.34.3462-30.5806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 21 )A7 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 45 )A22 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 71 )A46 - 71
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 90 )A72 - 90
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 99 )A91 - 99
6X-RAY DIFFRACTION6chain 'C' and (resid 7 through 21 )C7 - 21
7X-RAY DIFFRACTION7chain 'C' and (resid 22 through 46 )C22 - 46
8X-RAY DIFFRACTION8chain 'C' and (resid 47 through 66 )C47 - 66
9X-RAY DIFFRACTION9chain 'C' and (resid 67 through 71 )C67 - 71
10X-RAY DIFFRACTION10chain 'C' and (resid 72 through 90 )C72 - 90
11X-RAY DIFFRACTION11chain 'C' and (resid 91 through 99 )C91 - 99
12X-RAY DIFFRACTION12chain 'E' and (resid 5 through 9 )E5 - 9
13X-RAY DIFFRACTION13chain 'E' and (resid 10 through 21 )E10 - 21
14X-RAY DIFFRACTION14chain 'E' and (resid 22 through 45 )E22 - 45
15X-RAY DIFFRACTION15chain 'E' and (resid 46 through 65 )E46 - 65
16X-RAY DIFFRACTION16chain 'E' and (resid 66 through 71 )E66 - 71
17X-RAY DIFFRACTION17chain 'E' and (resid 72 through 90 )E72 - 90
18X-RAY DIFFRACTION18chain 'E' and (resid 91 through 99 )E91 - 99
19X-RAY DIFFRACTION19chain 'G' and (resid 5 through 14 )G5 - 14
20X-RAY DIFFRACTION20chain 'G' and (resid 15 through 21 )G15 - 21
21X-RAY DIFFRACTION21chain 'G' and (resid 22 through 50 )G22 - 50
22X-RAY DIFFRACTION22chain 'G' and (resid 51 through 65 )G51 - 65
23X-RAY DIFFRACTION23chain 'G' and (resid 66 through 71 )G66 - 71
24X-RAY DIFFRACTION24chain 'G' and (resid 72 through 90 )G72 - 90
25X-RAY DIFFRACTION25chain 'G' and (resid 91 through 99 )G91 - 99
26X-RAY DIFFRACTION26chain 'I' and (resid 7 through 21 )I7 - 21
27X-RAY DIFFRACTION27chain 'I' and (resid 22 through 45 )I22 - 45
28X-RAY DIFFRACTION28chain 'I' and (resid 46 through 65 )I46 - 65
29X-RAY DIFFRACTION29chain 'I' and (resid 66 through 90 )I66 - 90
30X-RAY DIFFRACTION30chain 'I' and (resid 91 through 99 )I91 - 99
31X-RAY DIFFRACTION31chain 'K' and (resid 8 through 21 )K8 - 21
32X-RAY DIFFRACTION32chain 'K' and (resid 22 through 56 )K22 - 56
33X-RAY DIFFRACTION33chain 'K' and (resid 57 through 66 )K57 - 66
34X-RAY DIFFRACTION34chain 'K' and (resid 67 through 90 )K67 - 90
35X-RAY DIFFRACTION35chain 'K' and (resid 91 through 99 )K91 - 99

+
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://pdbjlvh1.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