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- PDB-4n05: The crystal structure of R43A mutant putative ryanodine receptor ... -

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Basic information

Entry
Database: PDB / ID: 4n05
TitleThe crystal structure of R43A mutant putative ryanodine receptor from Bacteroides Thetaiotaomicron VPI-5482
ComponentsPutative ryanodine receptor
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / PSI-BIOLOGY / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / PUTATIVE RYANODINE RECEPTOR / ALPHA FOLD
Function / homology
Function and homology information


calcium ion transport / metal ion binding
Similarity search - Function
Actin; Chain A, domain 4 / Actin; Chain A, domain 4 - #10 / Other non-globular / Ryanodine receptor Ryr / RyR domain / : / Special
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.605 Å
AuthorsWu, R. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The crystal structure of R43A mutant putative ryanodine receptor from Bacteroides Thetaiotaomicron VPI-5482
Authors: Wu, R. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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
B: Putative ryanodine receptor
A: 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)74,13611
Polymers73,6766
Non-polymers4605
Water1,71195
1
B: Putative ryanodine receptor
A: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8355
Polymers24,5592
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-30 kcal/mol
Surface area11590 Å2
MethodPISA
2
C: Putative ryanodine receptor
D: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6513
Polymers24,5592
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-31 kcal/mol
Surface area11440 Å2
MethodPISA
3
E: Putative ryanodine receptor
F: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6513
Polymers24,5592
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-31 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.362, 88.673, 74.370
Angle α, β, γ (deg.)90.00, 111.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative ryanodine receptor


Mass: 12279.257 Da / Num. of mol.: 6 / Mutation: R43A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_2247 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: Q8A5J2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 1.5M NA CITRATE, 0.1M BISTRIS 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2012 / Details: MIRRORS
RadiationMonochromator: SI111, CHANNEL / Protocol: MOLECULAR REPLACEMENT / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 26789 / Num. obs: 26789 / % possible obs: 97.2 % / Redundancy: 3.7 % / Rsym value: 0.102 / Net I/σ(I): 11.9
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4 / Rsym value: 0.454 / % possible all: 96.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.605→42.12 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 26.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 1325 4.97 %
Rwork0.1843 --
obs0.1875 26676 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.605→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4617 0 30 95 4742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084753
X-RAY DIFFRACTIONf_angle_d1.0456418
X-RAY DIFFRACTIONf_dihedral_angle_d16.1561861
X-RAY DIFFRACTIONf_chiral_restr0.072681
X-RAY DIFFRACTIONf_plane_restr0.005834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6049-2.70920.28981280.22062647X-RAY DIFFRACTION91
2.7092-2.83240.33311630.23222808X-RAY DIFFRACTION98
2.8324-2.98170.27671530.2162885X-RAY DIFFRACTION98
2.9817-3.16850.27361540.20422806X-RAY DIFFRACTION98
3.1685-3.4130.29671440.18222923X-RAY DIFFRACTION98
3.413-3.75630.22041610.17552821X-RAY DIFFRACTION98
3.7563-4.29940.24851400.15422853X-RAY DIFFRACTION97
4.2994-5.4150.22271490.16042793X-RAY DIFFRACTION95
5.415-42.12520.22681330.20042815X-RAY DIFFRACTION93
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)
10.09230.02990.09720.18140.05190.03980.18330.2883-0.0307-0.3924-0.19890.2621-0.6911-0.135-0.00010.44930.0013-0.00910.4296-0.02880.3929-2.901713.83125.9646
20.37610.12460.31670.1838-0.03020.32120.0962-0.0719-0.0770.0242-0.13890.0326-0.01320.01090.00010.40090.00260.03890.36520.03390.3007-11.8086-7.62628.8402
30.1342-0.00660.1020.1705-0.05770.0655-0.11070.0588-0.00010.0570.14020.2119-0.1397-0.4584-00.426-0.08870.02550.4887-0.01480.3655-19.344-8.697631.4055
40.11940.0222-0.09130.1312-0.21430.33360.13160.4980.59160.3301-0.19160.0977-0.0624-0.6033-0.00130.37980.0263-0.02440.25930.02340.3242-5.96123.353222.8827
50.004-0.04430.00470.04850.02730.035-0.17530.23910.03610.4432-0.0118-0.0022-0.089-0.0767-0.00030.3972-0.0184-0.02030.52330.02660.430610.18210.263317.0646
6-0.00430.0660.0240.1527-0.0441-0.02530.1104-0.1634-0.5964-0.0147-0.1385-0.18570.12480.141700.4205-0.01170.00260.5264-0.00950.4147-1.4389-13.922928.1207
70.0625-0.06430.15350.24930.08370.45570.2234-0.09550.0614-0.0986-0.2039-0.008-0.1454-0.007300.24590.0395-0.00390.2652-0.02420.3801-4.80488.064833.7705
80.0453-0.0562-0.00420.11860.0482-0.00010.1756-0.3958-0.02610.58140.2570.01540.2105-0.49750.00010.3803-0.02190.02450.5719-0.04050.454-18.52657.494641.8757
90.2418-0.21350.09120.14-0.25020.2836-0.0661-0.18240.03470.00980.01840.17470.20810.010700.3129-0.0008-0.05120.3592-0.00330.3583-0.442-0.948534.6981
100.034-0.06950.02010.2341-0.08050.0360.12360.11380.1409-0.5188-0.6652-0.26240.2810.8835-0.01810.3832-0.00020.04530.63540.10270.516411.571-0.210619.1366
110.0448-0.14280.2093-0.1673-0.06770.88860.02980.0411-0.02560.01750.1701-0.08280.3082-0.0568-0.00010.4266-0.05560.01610.39510.01180.2581-8.9432-5.44331.3964
120.1199-0.1981-0.02260.13930.08480.0944-0.13860.0072-0.6042-0.45440.5511-0.04550.21710.22380.21621.3781-0.31710.5920.2032-0.68970.7456-9.0292-26.794-1.1162
130.39540.27170.27230.15870.21580.231-0.04980.027-0.05880.26160.00320.010.04610.37880.00010.45160.00010.05070.4363-0.01210.3193-6.0416-6.63243.8975
140.70860.01020.68460.00310.00410.6751-0.1325-0.68530.58790.06160.0053-0.1706-0.4634-0.3068-0.01540.52610.0173-0.020.2932-0.05920.257-16.77249.63734.6152
150.1016-0.056-0.18220.04780.11130.20750.02280.1387-0.363-0.67710.42290.37770.4486-0.684800.554-0.0118-0.0530.54650.01740.5117-23.1279-9.88084.6309
160.2890.3803-0.06250.74810.03580.33070.1105-0.1962-0.1114-0.5881-0.23610.01290.11430.2624-0.02150.36080.06430.08160.58640.04360.337-4.2061-6.9222-9.1758
17-0.00330.00260.01830.05630.05220.0310.10210.17550.04450.05080.41930.2196-0.00630.2663-00.55660.24010.18350.5974-0.01380.74072.7478-16.3957-10.3778
180.30740.21020.14530.13780.16190.07730.15360.1629-0.2377-0.1275-0.0690.0887-0.1009-0.10590.00020.37150.0145-0.00620.28290.01580.3037-14.7085-6.9736-6.227
192.7763-0.38730.5781.4623-1.33831.2088-0.2965-0.49460.56080.28650.2840.6391-1.2253-0.2373-0.20210.61530.1018-0.14970.2668-0.08330.406-19.097610.32251.7773
200.201-0.12430.09660.0241-0.17780.09120.09820.4629-0.3167-0.01420.104-0.05090.12260.29640.00840.2726-0.05810.00920.62120.010.510129.4346-2.806737.2872
210.7477-0.22580.15680.31540.11591.53290.0098-0.250.39980.21660.7347-0.6956-0.0042-0.17620.33510.22330.09330.06770.2888-0.21690.573514.271513.192845.8463
220.0036-0.004-0.00590.00320.00290.0116-0.21890.0973-0.498-0.2622-0.2463-0.2352-0.1127-0.1052-0.00071.1777-0.12160.17440.8309-0.18962.156625.105827.476940.2185
230.29220.122-0.03370.0639-0.06660.02490.09840.12780.0742-0.00480.5146-0.224-0.15080.14090.14560.4737-0.21370.33240.0575-0.54841.927720.843225.744144.3727
240.34220.1086-0.33920.27640.18950.540.07250.15690.3505-0.3806-0.0589-0.09080.214-0.0474-0.00010.32250.0246-0.04360.49950.01570.46318.04956.524938.9114
250.06270.08890.22920.12540.29620.7514-0.0591-0.0664-0.55110.3230.0567-0.00171.0229-0.57470.01840.4562-0.1024-0.03250.42070.09310.515913.4421-9.664148.9133
260.0413-0.0406-0.06940.02020.03050.02720.0069-0.66050.7216-0.02080.41610.2628-0.04170.2688-0.00040.65040.0661-0.07040.469-0.03660.58739.540713.625653.3918
270.01550.03820.00150.1149-0.0420.0405-0.1681-0.4733-0.30680.27740.20120.13380.0419-0.6808-00.3743-0.0395-0.07530.5331-0.01510.279421.6051-2.867557.481
280.06430.0111-0.02930.01910.01750.00790.40560.1565-0.43920.1127-0.287-0.22-0.05720.5443-0.00040.2912-0.00230.00180.60370.02450.363230.52121.744446.0791
290.18760.1688-0.42310.1361-0.36811.0549-0.20920.3537-0.0121-0.5212-0.0752-0.43110.11370.1159-0.25080.34540.06950.39021.43380.77140.170531.68988.610732.5887
300.00230.0131-0.01360.00350.00830.0034-0.6929-0.08310.7413-0.0670.2171-0.35060.3119-0.00330.00020.8046-0.15240.09990.96350.09831.208134.937420.533234.6696
310.13460.09480.08470.05610.05840.0816-0.0772-0.0014-0.0931-0.0819-0.00190.1142-0.09730.0072-0.00530.86440.08460.64820.51911.0140.92934.408315.786738.2527
32-0.0007-0.0098-0.01620.01350.0080.04170.27130.31530.57390.2896-0.006-0.228-0.0490.67530.00030.498-0.09280.03810.69580.03770.570335.791310.393448.3305
330.0450.00810.02240.08610.08730.04580.653-0.082-0.20230.2653-0.10040.3857-0.5340.2806-0.00030.37830.02710.01220.40190.03070.373724.99397.765651.586
340.4388-0.01350.08980.0378-0.13710.6531-0.1517-0.03010.2795-0.11940.3924-0.1391-0.30050.2740.03920.290.00230.01390.169-0.05140.330514.27972.629950.2192
350.0097-0.0016-0.01430.0102-0.01740.0170.1051-0.1321-0.24520.03040.3538-0.1724-0.0211-0.3112-0.00060.3103-0.0450.02570.6566-0.10320.50638.8567-1.359550.659
360.02220.0025-0.0020.03890.01290.01260.0649-0.0385-0.2242-0.2228-0.3755-0.29330.27320.02690.00060.6271-0.0629-0.2820.3792-0.00590.689717.3714-12.256952.5707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 7 through 21 )
2X-RAY DIFFRACTION2chain 'B' and (resid 22 through 56 )
3X-RAY DIFFRACTION3chain 'B' and (resid 57 through 71 )
4X-RAY DIFFRACTION4chain 'B' and (resid 72 through 92 )
5X-RAY DIFFRACTION5chain 'B' and (resid 93 through 99 )
6X-RAY DIFFRACTION6chain 'A' and (resid 7 through 21 )
7X-RAY DIFFRACTION7chain 'A' and (resid 22 through 51 )
8X-RAY DIFFRACTION8chain 'A' and (resid 52 through 66 )
9X-RAY DIFFRACTION9chain 'A' and (resid 67 through 91 )
10X-RAY DIFFRACTION10chain 'A' and (resid 92 through 100 )
11X-RAY DIFFRACTION11chain 'C' and (resid 7 through 46 )
12X-RAY DIFFRACTION12chain 'C' and (resid 47 through 66 )
13X-RAY DIFFRACTION13chain 'C' and (resid 67 through 91 )
14X-RAY DIFFRACTION14chain 'C' and (resid 92 through 100 )
15X-RAY DIFFRACTION15chain 'D' and (resid 8 through 21 )
16X-RAY DIFFRACTION16chain 'D' and (resid 22 through 56 )
17X-RAY DIFFRACTION17chain 'D' and (resid 57 through 66 )
18X-RAY DIFFRACTION18chain 'D' and (resid 67 through 92 )
19X-RAY DIFFRACTION19chain 'D' and (resid 93 through 100 )
20X-RAY DIFFRACTION20chain 'E' and (resid 7 through 21 )
21X-RAY DIFFRACTION21chain 'E' and (resid 22 through 51 )
22X-RAY DIFFRACTION22chain 'E' and (resid 52 through 56 )
23X-RAY DIFFRACTION23chain 'E' and (resid 57 through 66 )
24X-RAY DIFFRACTION24chain 'E' and (resid 67 through 91 )
25X-RAY DIFFRACTION25chain 'E' and (resid 92 through 100 )
26X-RAY DIFFRACTION26chain 'F' and (resid 8 through 17 )
27X-RAY DIFFRACTION27chain 'F' and (resid 18 through 27 )
28X-RAY DIFFRACTION28chain 'F' and (resid 28 through 37 )
29X-RAY DIFFRACTION29chain 'F' and (resid 38 through 48 )
30X-RAY DIFFRACTION30chain 'F' and (resid 49 through 59 )
31X-RAY DIFFRACTION31chain 'F' and (resid 60 through 64 )
32X-RAY DIFFRACTION32chain 'F' and (resid 65 through 74 )
33X-RAY DIFFRACTION33chain 'F' and (resid 75 through 84 )
34X-RAY DIFFRACTION34chain 'F' and (resid 85 through 89 )
35X-RAY DIFFRACTION35chain 'F' and (resid 90 through 94 )
36X-RAY DIFFRACTION36chain 'F' and (resid 95 through 100 )

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