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- PDB-6uag: Closed Dimer of Y77A Mutant Putative Ryanodine Receptor from Bact... -

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Basic information

Entry
Database: PDB / ID: 6uag
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 / homologyRyanodine receptor Ryr / RyR domain / : / calcium ion transport / metal ion binding / sucrose / Ryanodine receptor
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.709 Å
AuthorsWu, R. / Jedrzejczak, 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 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative ryanodine receptor
B: Putative ryanodine receptor
C: Putative ryanodine receptor
D: Putative ryanodine receptor
E: Putative ryanodine receptor
F: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,98522
Polymers72,0066
Non-polymers2,97916
Water37821
1
A: Putative ryanodine receptor
B: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9637
Polymers24,0022
Non-polymers9615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-20 kcal/mol
Surface area11420 Å2
MethodPISA
2
C: Putative ryanodine receptor
D: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9677
Polymers24,0022
Non-polymers9655
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-41 kcal/mol
Surface area11240 Å2
MethodPISA
3
E: Putative ryanodine receptor
F: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0558
Polymers24,0022
Non-polymers1,0536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-16 kcal/mol
Surface area10750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.968, 89.391, 74.927
Angle α, β, γ (deg.)90.000, 111.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative ryanodine receptor


Mass: 12001.018 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: PMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: Q8A5J2
#2: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.28 Å3/Da / Density % sol: 62.48 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.5M sodium citrate

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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: Feb 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 24972 / % possible obs: 99 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Χ2: 0.803 / Net I/σ(I): 8.7 / Num. measured all: 77014
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.7-2.753.10.62912231.017199.6
2.75-2.83.10.55812610.982199.7
2.8-2.853.10.52212470.98199.8
2.85-2.913.10.43612671.003199.7
2.91-2.973.10.31612491.027199.7
2.97-3.043.10.28312141.07199.4
3.04-3.123.10.24512861.014199.6
3.12-3.23.10.20912140.944199.5
3.2-3.33.10.14312490.856199.3
3.3-3.43.10.11212860.864199.6
3.4-3.523.10.08212380.698199.4
3.52-3.663.10.06612380.646199.6
3.66-3.833.10.05512490.637199
3.83-4.033.10.04212650.582199.3
4.03-4.293.10.03712430.612199
4.29-4.623.10.03112360.595198
4.62-5.083.10.03212520.58198.4
5.08-5.813.10.03912580.589198.4
5.81-7.3230.03612520.527198.5
7.32-502.90.03312450.837195.2

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.709→37.657 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.63
RfactorNum. reflection% reflection
Rfree0.2636 1186 5.09 %
Rwork0.1959 --
obs0.1993 23287 92.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.06 Å2 / Biso mean: 38.832 Å2 / Biso min: 9.98 Å2
Refinement stepCycle: final / Resolution: 2.709→37.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4684 0 197 21 4902
Biso mean--59.1 26.08 -
Num. residues----568
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.709-2.83190.312770.2661155652
2.8319-2.98110.30381450.2513278893
2.9811-3.16780.33281670.2315294499
3.1678-3.41220.31781630.2235297499
3.4122-3.75530.25431560.176295399
3.7553-4.29810.23091450.1601297799
4.2981-5.41260.20471630.1582295198
5.4126-37.6570.25671700.206295897
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)
12.00946.907-4.64436.7293-4.47476.6683-1.47850.5806-0.9592-0.6110.94780.48850.7737-0.95970.48020.56720.07350.01560.6007-0.01150.3849-13.8747-20.557430.044
22.17623.3739-1.7315.9278-1.56333.140.3874-0.4026-1.18940.88710.1814-0.72840.48320.6952-0.30270.4006-0.002-0.09140.0953-0.00850.32937.8234-12.980428.9507
32.0339-4.0426-3.62695.64190.48963.96760.1846-0.47120.36560.0188-0.0008-0.0045-0.4293-0.2804-0.1660.19320.0115-0.05750.15650.00710.2009-2.09544.637732.6756
46.6652-0.04612.06795.2339-1.10626.30290.3012-0.59440.68690.0773-0.19140.80460.3245-0.7708-0.18620.21940.06290.08850.4479-0.09330.4597-21.22575.323840.9326
58.3538-3.8058-0.78586.2641-5.1359.4735-0.0673-1.04310.4770.72270.3519-0.0619-0.32720.0985-0.31150.17470.1151-0.12960.2229-0.07290.3132-7.77515.959942.1287
63.6182-3.0384-4.08289.38362.19432.0171-0.3573-0.269-0.05390.55050.08480.61230.69980.38040.27390.1625-0.0195-0.02280.18910.0290.25310.4739-5.718833.1636
72.03578.57255.09112.01662.0159.94750.04511.31270.31-0.75180.9671-1.5273-0.34061.4186-0.92360.34190.1866-0.04920.3346-0.07620.395411.23-3.20919.5494
86.7138-1.8316-6.21274.64024.12812.03070.515-0.2290.3456-0.42950.0602-0.3102-1.709-0.2601-0.58650.28730.0844-0.08250.28180.03240.3378-3.617310.637125.6001
99.40854.4369-8.60514.9101-4.42059.212-0.3289-0.2671-0.1335-0.10810.07730.09810.993-0.01740.29420.2361-0.0113-0.04610.13720.03080.177-9.6245-11.317227.8249
108.63261.7768-2.33857.71112.62326.64010.1964-0.78970.75770.5122-0.41760.6237-0.9671-1.4440.25660.36130.04140.03030.439-0.10790.2725-22.0964-10.563937.2238
119.10956.8334-2.93752.204-3.69384.1982-0.04530.54680.7074-0.16240.11780.33290.2113-0.2718-0.05810.29010.017-0.01870.1729-0.04520.2673-8.9735-2.608622.55
126.37433.23732.012.01292.97792.0192-0.09890.9155-0.6427-1.448-0.1248-0.92730.77421.74350.14610.3369-0.0644-0.10710.44030.04380.30129.6628-2.818717.3843
135.3160.1263-0.93478.06911.9683.87220.181.11140.4567-1.0009-0.0702-0.2984-1.28410.2484-0.16230.21470.0229-0.01130.34560.03290.2001-0.3404-1.1426-5.9229
143.0339-0.9914-0.63552.18271.27093.6837-0.37820.2196-0.82060.1896-0.04910.59740.9844-0.23310.4450.4973-0.12080.07380.2814-0.01360.3982-12.8711-17.44554.4503
158.7806-0.7774-3.82985.02161.08137.4196-0.58490.7396-1.6409-1.029-0.3749-0.08581.4166-0.15950.79820.9796-0.10220.30690.3895-0.17210.859-6.4581-30.4647-1.2692
163.9849-2.73381.63038.4066-8.12068.5385-0.2202-0.0541-0.1807-0.0608-0.142-0.2460.46830.24620.46720.32850.00110.03360.2041-0.06910.1707-5.6961-10.22184.5422
174.66336.0995-1.82019.8979-3.80748.57330.3178-0.60591.66950.8969-0.08441.7385-1.3828-1.384-0.24840.3030.1299-0.2110.37230.11070.2632-16.84155.56824.733
186.4991-3.71450.80195.8581-5.086.4236-0.0471-0.5033-1.69530.8140.11131.06260.563-0.5078-0.06970.5142-0.2038-0.00640.34330.01590.5911-20.8316-18.27085.1362
197.1216-1.8309-1.89094.32552.69354.54780.05890.0727-0.4662-0.30940.1319-0.32860.53460.5411-0.11760.273-0.0058-0.02020.272-0.00450.1985-3.458-13.653-11.5008
204.69660.3401-1.86152.14510.1516.36060.0582-0.28950.0364-0.0961-0.48390.0863-0.2243-0.2460.35230.15320.0226-0.07720.22420.0230.2083-17.2337-5.2373-2.6952
218.45636.9941-3.51479.2651-2.00825.72150.2722-0.304-1.6607-0.3127-0.1097-1.24630.5751.2428-0.0170.3010.03880.00780.2619-0.02780.290629.3544-4.944737.3165
225.1522.728-1.00388.32930.58923.67820.1063-0.49671.40630.2662-0.091.0881-0.73350.1585-0.0950.3020.05650.03680.2296-0.08660.463714.17758.724545.4805
232.491.9075-0.40742.2345-1.15751.81711.09120.04551.59420.37-0.1269-0.7986-1.68910.5165-0.72080.5498-0.67630.0508-0.9711-0.5921.39122.248124.715542.1626
246.7687-5.48473.2637.4627-5.3496.3064-0.08320.14220.9067-0.2250.0035-0.5143-0.3008-0.0040.08710.2254-0.0453-0.00390.18320.01420.317.75914.209438.596
252.0168-1.68481.54626.53591.60845.3627-0.7087-1.039-0.940.59870.26770.95471.6005-0.62560.03370.41970.0358-0.07250.28680.09080.25914.8319-11.474548.8178
263.88330.5086-0.09666.616-4.73597.030.144-0.35390.47330.45050.18150.4356-1.2353-0.7451-0.45840.4539-0.01050.05230.3776-0.12470.31511.70938.708454.2487
277.61875.6347-5.74077.213-3.63256.937-0.04590.18880.0739-0.273-0.2578-0.5302-0.03770.6250.24190.1152-0.0316-0.02710.2483-0.0140.290631.16333.172843.0324
283.9886-0.6994-0.02578.312-0.48268.2565-0.4445-0.02971.4271-0.4208-0.234-0.2796-1.68070.53970.61540.5769-0.2111-0.22340.43350.0520.593936.516116.987838.9158
299.43986.68443.21838.62612.47597.48560.616-1.4579-0.50660.53-0.5696-0.55970.31851.3673-0.0830.2995-0.1795-0.09560.48870.04250.305237.96795.829848.7221
301.98632.1746-1.56857.328-1.3234.78960.568-0.25470.15890.2182-0.4455-0.0074-0.3556-0.0554-0.04130.29620.0279-0.03010.1641-0.01290.168722.74574.010452.2283
319.7895-2.63138.5072.0167-6.47892.06270.1092-0.754-1.1827-0.1980.07010.08660.9086-0.9161-0.31580.2722-0.0551-0.12290.36140.00980.392513.997-10.402251.1089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 13 )A4 - 13
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 21 )A14 - 21
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 45 )A22 - 45
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 60 )A46 - 60
5X-RAY DIFFRACTION5chain 'A' and (resid 61 through 71 )A61 - 71
6X-RAY DIFFRACTION6chain 'A' and (resid 72 through 91 )A72 - 91
7X-RAY DIFFRACTION7chain 'A' and (resid 92 through 100 )A92 - 100
8X-RAY DIFFRACTION8chain 'B' and (resid 7 through 21 )B7 - 21
9X-RAY DIFFRACTION9chain 'B' and (resid 22 through 51 )B22 - 51
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 66 )B52 - 66
11X-RAY DIFFRACTION11chain 'B' and (resid 67 through 91 )B67 - 91
12X-RAY DIFFRACTION12chain 'B' and (resid 92 through 100 )B92 - 100
13X-RAY DIFFRACTION13chain 'C' and (resid 7 through 21 )C7 - 21
14X-RAY DIFFRACTION14chain 'C' and (resid 22 through 51 )C22 - 51
15X-RAY DIFFRACTION15chain 'C' and (resid 52 through 66 )C52 - 66
16X-RAY DIFFRACTION16chain 'C' and (resid 67 through 91 )C67 - 91
17X-RAY DIFFRACTION17chain 'C' and (resid 92 through 100 )C92 - 100
18X-RAY DIFFRACTION18chain 'D' and (resid 4 through 21 )D4 - 21
19X-RAY DIFFRACTION19chain 'D' and (resid 22 through 71 )D22 - 71
20X-RAY DIFFRACTION20chain 'D' and (resid 72 through 100 )D72 - 100
21X-RAY DIFFRACTION21chain 'E' and (resid 7 through 21 )E7 - 21
22X-RAY DIFFRACTION22chain 'E' and (resid 22 through 46 )E22 - 46
23X-RAY DIFFRACTION23chain 'E' and (resid 47 through 66 )E47 - 66
24X-RAY DIFFRACTION24chain 'E' and (resid 67 through 91 )E67 - 91
25X-RAY DIFFRACTION25chain 'E' and (resid 92 through 99 )E92 - 99
26X-RAY DIFFRACTION26chain 'F' and (resid 7 through 21 )F7 - 21
27X-RAY DIFFRACTION27chain 'F' and (resid 22 through 51 )F22 - 51
28X-RAY DIFFRACTION28chain 'F' and (resid 52 through 66 )F52 - 66
29X-RAY DIFFRACTION29chain 'F' and (resid 67 through 71 )F67 - 71
30X-RAY DIFFRACTION30chain 'F' and (resid 72 through 91 )F72 - 91
31X-RAY DIFFRACTION31chain 'F' and (resid 92 through 99 )F92 - 99

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