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- PDB-6ug4: Open Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacter... -

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Basic information

Entry
Database: PDB / ID: 6ug4
TitleOpen 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 / Complex Structure
Function / homologyRyanodine receptor Ryr / RyR domain / : / calcium ion transport / metal ion binding / CAFFEINE / PYRUVIC ACID / Ryanodine receptor
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.295 Å
AuthorsWu, R. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Open 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
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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)75,23531
Polymers72,0066
Non-polymers3,22925
Water2,378132
1
A: Putative ryanodine receptor
B: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,05710
Polymers24,0022
Non-polymers1,0558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-69 kcal/mol
Surface area10420 Å2
MethodPISA
2
C: Putative ryanodine receptor
D: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,04110
Polymers24,0022
Non-polymers1,0398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-43 kcal/mol
Surface area10520 Å2
MethodPISA
3
E: Putative ryanodine receptor
F: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,13711
Polymers24,0022
Non-polymers1,1359
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-28 kcal/mol
Surface area10230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.201, 84.201, 229.704
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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: PLASMID / Details (production host): PMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: Q8A5J2

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Non-polymers , 5 types, 157 molecules

#2: Chemical
ChemComp-CFF / CAFFEINE / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE


Mass: 194.191 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H10N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris Propane:NaOH pH 7.0, 2.5 M Ammonium Sulfate

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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 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 41451 / % possible obs: 96.2 % / Redundancy: 7.7 % / Biso Wilson estimate: 41.19 Å2 / Rmerge(I) obs: 0.111 / Χ2: 2.064 / Net I/σ(I): 9.8 / Num. measured all: 321203
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.2-2.2480.72520741.005198.1
2.24-2.288.10.63220741.023198
2.28-2.328.20.56620431.06197.7
2.32-2.378.10.49420501.084197.7
2.37-2.4280.47120791.078197.5
2.42-2.4880.46220701.091197.1
2.48-2.5480.34620471.176197.3
2.54-2.6180.28820491.234196.6
2.61-2.697.90.2620421.33196.6
2.69-2.777.80.24420591.374196.4
2.77-2.877.80.20120531.447196.4
2.87-2.997.60.15520561.591196.4
2.99-3.127.60.13320811.759196.5
3.12-3.297.50.10920462.018195.7
3.29-3.497.30.09120782.367195.7
3.49-3.767.20.08520562.744195.4
3.76-4.147.10.08420793.241195.3
4.14-4.746.80.07720923.498194.8
4.74-5.977.30.0821464.118195.1
5.97-508.90.08121776.677190.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575_1309refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.295→42.101 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.58
RfactorNum. reflection% reflection
Rfree0.2354 1850 4.98 %
Rwork0.1973 --
obs0.1992 37120 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.95 Å2 / Biso mean: 54.4683 Å2 / Biso min: 26.26 Å2
Refinement stepCycle: final / Resolution: 2.295→42.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 0 218 132 4986
Biso mean--57.35 55.11 -
Num. residues----563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.054994
X-RAY DIFFRACTIONf_angle_d1.4146756
X-RAY DIFFRACTIONf_chiral_restr0.06690
X-RAY DIFFRACTIONf_plane_restr0.008862
X-RAY DIFFRACTIONf_dihedral_angle_d27.9451915
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.295-2.35680.33211420.2409263297
2.3568-2.42620.23081310.2378267198
2.4262-2.50450.2791420.2446266098
2.5045-2.5940.28281480.2241266598
2.594-2.69780.30411570.2319268198
2.6978-2.82060.3011450.2298269899
2.8206-2.96920.29741440.2185269399
2.9692-3.15520.23821310.2088273399
3.1552-3.39870.21951380.1988273899
3.3987-3.74060.2131590.1763268197
3.7406-4.28140.20021390.1626273497
4.2814-5.39230.19321450.1746275697
5.3923-42.1010.24511290.204292896
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)
11.7030.56540.50760.3583-0.59121.820.1762-0.0233-0.14150.02270.00590.2872-0.1722-0.3757-0.15750.43110.00270.06260.3562-0.0250.491420.6023-6.0425-13.8464
21.3414-0.1234-0.52412.67790.87265.0002-0.0873-0.0895-0.13310.4014-0.0606-0.34150.09140.38240.21960.39240.0221-0.0580.26020.0010.356341.5999-7.7079-8.0948
33.1050.3079-0.16184.09390.6451.9010.0074-0.50650.31121.71990.2907-0.06880.26010.2803-0.26040.87690.0572-0.06720.4694-0.04930.412939.2542-1.42949.1094
44.75382.90993.48145.8877-1.27686.3372-0.2011-0.7821-0.66860.79390.0542-0.99760.83110.61840.19820.73560.1884-0.13910.5314-0.00470.3941.7269-14.09240.4902
52.5968-0.51891.18654.4045-2.50136.274-0.028-0.1499-0.08020.1937-0.04860.41570.21370.0840.05570.37440.00880.03720.2338-0.0330.292331.0794-9.6515-10.9469
66.9602-6.0624-1.06338.04742.74792.53610.73780.18670.1809-2.007-0.0079-0.454-0.41070.6648-0.5580.7124-0.03940.01010.4241-0.02970.391935.9861-5.0241-26.9892
71.6072-0.15970.31642.9181-0.02282.63120.0184-0.13690.22220.3256-0.0532-0.1011-0.0915-0.08550.06750.3646-0.0095-0.00420.2024-0.06060.27932.3867-1.5278-8.2108
82.27930.00080.12235.8732-2.8633.65990.0796-0.70150.01980.2944-0.0951-0.10860.2487-0.35290.19230.7103-0.06820.17410.623-0.04940.386424.2653-6.09226.801
92.9589-1.4159-1.51882.65641.62934.4756-0.1041-0.14280.03660.2617-0.06720.2919-0.3967-0.06680.1040.42770.0068-0.00350.24-0.01080.364834.22793.0541-8.3338
102.9285-5.00144.65159.0788-9.0079.2644-0.38331.61760.3391-1.71850.0928-0.03590.70990.28470.0470.6608-0.13860.12470.5115-0.12030.481936.9443-2.6469-26.985
112.71620.94622.23041.5224-0.28261.96480.1573-0.7450.38850.5805-0.13370.4470.0313-0.69260.02150.46310.01890.05520.4481-0.05040.446823.579426.6053-7.519
122.60930.15721.38621.54830.95123.09450.02030.33860.1226-0.38050.00550.01740.03630.0935-0.02670.44660.00760.0870.27750.02120.307832.135527.1223-28.2071
132.5246-0.1627-0.24513.19241.71912.67330.20640.7201-0.2629-0.0709-0.06510.25310.1919-0.4044-0.03670.59450.0044-0.0490.5253-0.00790.396221.267625.3447-35.7402
141.9559-0.82581.26053.3322-2.43433.9228-0.1507-0.04440.14980.14830.2190.2091-0.1855-0.1125-0.04830.3655-0.03860.0330.2632-0.06710.345827.980430.7079-17.5994
155.66565.9574-1.979.4854-1.77894.6263-0.3423-0.1361-0.750.72590.1106-1.95040.19841.16290.15060.51810.0595-0.15610.55580.07540.615443.125325.4469-8.9476
160.6665-1.70742.28794.3501-5.82787.7769-0.03221.2406-0.38-0.44350.01410.85811.22940.1529-0.58030.93180.0524-0.060.8389-0.13410.710530.785327.2229-41.9046
179.2912-2.24814.57298.3385-4.52072.01160.43211.02980.4778-0.66090.2456-0.5928-1.03291.09640.0290.69830.04540.16420.61070.10340.424740.223124.5053-30.8944
181.69750.9727-5.0290.4259-2.47332.01740.1311-0.0321-0.0308-1.2241-0.3676-0.89970.94810.77210.19060.60360.07160.09420.3346-0.02190.539243.500116.5171-20.8649
194.2868-0.78941.16852.56130.31.95830.0325-0.3231-0.04820.2927-0.16740.28630.1812-0.22440.07410.3904-0.05140.08310.2701-0.03150.34523.740620.9484-14.259
202.9916-0.06870.06084.4904-0.01341.9296-0.09220.0218-0.0057-0.5198-0.12430.673-0.0429-0.44710.06650.4235-0.0186-0.05760.4306-0.10680.575810.16526.3499-24.7427
217.08172.02330.91154.62460.52991.32180.11220.2432-0.4259-0.4526-0.0040.0580.159-0.1081-0.03540.43620.0336-0.00430.24840.01910.318828.82617.4305-21.2826
222.9597-3.5454.14264.8054-5.73916.7122-0.642-0.64130.11520.8881-0.2649-1.5489-0.2250.69940.27360.44410.05090.01080.5233-0.08690.829743.436723.1485-9.6947
233.63171.2691.67121.01650.98451.26240.38250.0144-0.3730.5139-0.3295-0.6147-0.02570.466-0.10760.5984-0.0159-0.120.46950.12530.627244.617950.4995-5.2897
243.9331.3807-3.24843.851-2.29713.38-0.0490.3219-0.3278-0.3389-0.0872-0.08510.2418-0.09950.14840.36540.0196-0.03010.266-0.04050.293937.885547.8954-25.5919
252.66140.378-0.31113.2324-0.41693.88960.10240.24070.4372-0.23150.3024-0.4113-0.19850.2062-0.24760.44950.03780.14930.42670.00330.534753.628855.4828-33.3473
263.456-0.9792-2.5646.066-3.3619.14880.24340.3062-0.1893-1.11110.20080.08810.4586-0.2998-0.24470.54260.01080.03520.3074-0.03250.520245.778542.5308-31.1033
273.7141-1.7987-2.57244.29532.96864.6933-0.1871-0.1211-0.22210.18880.0797-0.40680.20510.2530.13640.3416-0.0244-0.00270.27390.01320.361941.170246.4888-15.695
287.00686.49052.78582.33534.57476.7561-0.1007-0.2079-0.32070.2996-0.0291.12130.1489-0.83210.17870.5170.03450.00340.41440.00820.678324.913451.0393-11.7347
291.78561.0918-1.18450.6493-1.0682.8480.25440.73130.0261-0.5169-0.1605-0.0411-0.0063-0.25650.03150.68670.0648-0.06950.4976-0.0370.44533.750954.33-31.006
305.2841-0.68-0.51193.5819-0.89232.10940.0945-0.25810.1729-0.0277-0.1463-0.67870.0820.45670.0580.39450.0123-0.06420.32120.01070.32749.647253.9758-14.03
310.37790.70010.07183.1066-2.25152.4366-0.02670.10730.65010.218-0.1063-1.67050.15250.65630.08730.39420.0248-0.06610.45450.00910.516657.084955.1437-16.5185
327.743.07160.1364.60580.6591.32680.21130.32640.4748-0.1526-0.10950.186-0.0030.0475-0.08890.36280.0294-0.00960.25220.00530.268538.928158.2826-21.2491
333.0818-0.85660.78562.23488.34697.3176-0.2397-0.9166-0.38010.0537-0.35710.9438-0.4194-0.08440.46490.5752-0.0684-0.01990.5272-0.01690.49624.896253.2376-13.4981
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 65 )A46 - 65
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 71 )A66 - 71
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 91 )A72 - 91
6X-RAY DIFFRACTION6chain 'A' and (resid 92 through 100 )A92 - 100
7X-RAY DIFFRACTION7chain 'B' and (resid 7 through 51 )B7 - 51
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 66 )B52 - 66
9X-RAY DIFFRACTION9chain 'B' and (resid 67 through 91 )B67 - 91
10X-RAY DIFFRACTION10chain 'B' and (resid 92 through 100 )B92 - 100
11X-RAY DIFFRACTION11chain 'C' and (resid 8 through 21 )C8 - 21
12X-RAY DIFFRACTION12chain 'C' and (resid 22 through 50 )C22 - 50
13X-RAY DIFFRACTION13chain 'C' and (resid 51 through 71 )C51 - 71
14X-RAY DIFFRACTION14chain 'C' and (resid 72 through 91 )C72 - 91
15X-RAY DIFFRACTION15chain 'C' and (resid 92 through 100 )C92 - 100
16X-RAY DIFFRACTION16chain 'D' and (resid 6 through 10 )D6 - 10
17X-RAY DIFFRACTION17chain 'D' and (resid 11 through 15 )D11 - 15
18X-RAY DIFFRACTION18chain 'D' and (resid 16 through 21 )D16 - 21
19X-RAY DIFFRACTION19chain 'D' and (resid 22 through 46 )D22 - 46
20X-RAY DIFFRACTION20chain 'D' and (resid 47 through 66 )D47 - 66
21X-RAY DIFFRACTION21chain 'D' and (resid 67 through 91 )D67 - 91
22X-RAY DIFFRACTION22chain 'D' and (resid 92 through 100 )D92 - 100
23X-RAY DIFFRACTION23chain 'E' and (resid 7 through 21 )E7 - 21
24X-RAY DIFFRACTION24chain 'E' and (resid 22 through 44 )E22 - 44
25X-RAY DIFFRACTION25chain 'E' and (resid 45 through 64 )E45 - 64
26X-RAY DIFFRACTION26chain 'E' and (resid 65 through 71 )E65 - 71
27X-RAY DIFFRACTION27chain 'E' and (resid 72 through 91 )E72 - 91
28X-RAY DIFFRACTION28chain 'E' and (resid 92 through 100 )E92 - 100
29X-RAY DIFFRACTION29chain 'F' and (resid 7 through 21 )F7 - 21
30X-RAY DIFFRACTION30chain 'F' and (resid 22 through 56 )F22 - 56
31X-RAY DIFFRACTION31chain 'F' and (resid 57 through 71 )F57 - 71
32X-RAY DIFFRACTION32chain 'F' and (resid 72 through 91 )F72 - 91
33X-RAY DIFFRACTION33chain 'F' and (resid 92 through 99 )F92 - 99

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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

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