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- PDB-3nrt: The crystal structure of putative ryanodine receptor from Bactero... -

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Basic information

Entry
Database: PDB / ID: 3nrt
TitleThe crystal structure of putative ryanodine receptor from Bacteroides thetaiotaomicron VPI-5482
ComponentsPutative ryanodine receptor
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics (MCSG)
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
Actin; Chain A, domain 4 / Actin; Chain A, domain 4 - #10 / Ryanodine receptor Ryr / RyR domain / Other non-globular / : / Special
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.54 Å
AuthorsWu, R. / Zhang, R. / James, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: he crystal strucutre of putative ryanodine receptor from Bacteroides thetaiotaomicron VPI-5482
Authors: Ruiying, W. / Rongguang, Z. / James, A. / Andrzej, J. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 9, 2020Group: Advisory / Derived calculations / Structure summary
Category: pdbx_unobs_or_zero_occ_atoms / struct ...pdbx_unobs_or_zero_occ_atoms / struct / struct_conn / struct_site
Item: _struct.title / _struct_conn.pdbx_leaving_atom_flag ..._struct.title / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 27, 2023Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)74,86114
Polymers74,1926
Non-polymers6698
Water1,53185
1
A: Putative ryanodine receptor
B: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0316
Polymers24,7312
Non-polymers3014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-38 kcal/mol
Surface area11340 Å2
MethodPISA
2
C: Putative ryanodine receptor
D: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9154
Polymers24,7312
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-29 kcal/mol
Surface area11860 Å2
MethodPISA
3
E: Putative ryanodine receptor
F: Putative ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9154
Polymers24,7312
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-28 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.642, 89.272, 74.697
Angle α, β, γ (deg.)90.00, 110.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative ryanodine receptor


Mass: 12365.373 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_2247 / Plasmid: PDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8A5J2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 400, 0.2M MgCl, , pH 6.5, 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: 0.9792 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 8, 2009 / Details: mirrors
RadiationMonochromator: Si 111, channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 14
Reflection shellResolution: 2.54→2.59 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.17 / Num. unique all: 1618 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.54→32.48 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 3128 5.07 %RANDOM
Rwork0.198 ---
obs0.2006 61648 96.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.551 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7553 Å20 Å2-3.2424 Å2
2--7.889 Å20 Å2
3----5.1337 Å2
Refinement stepCycle: LAST / Resolution: 2.54→32.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 43 85 4866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094875
X-RAY DIFFRACTIONf_angle_d1.1296570
X-RAY DIFFRACTIONf_dihedral_angle_d20.1461903
X-RAY DIFFRACTIONf_chiral_restr0.072693
X-RAY DIFFRACTIONf_plane_restr0.005852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4772-2.56570.30172890.25935046X-RAY DIFFRACTION84
2.5657-2.66840.30312910.23846007X-RAY DIFFRACTION98
2.6684-2.78980.31812710.24756034X-RAY DIFFRACTION99
2.7898-2.93680.2943480.24415923X-RAY DIFFRACTION99
2.9368-3.12070.27433180.19976108X-RAY DIFFRACTION99
3.1207-3.36140.26492980.19235984X-RAY DIFFRACTION99
3.3614-3.69920.2363370.17846033X-RAY DIFFRACTION99
3.6992-4.23350.23123320.16535927X-RAY DIFFRACTION98
4.2335-5.330.20573250.16025785X-RAY DIFFRACTION95
5.33-32.48290.21713190.19775673X-RAY DIFFRACTION94
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)
11.3204-0.4423-0.06190.3631-0.05371.20980.0088-0.15050.04970.0293-0.0157-0.05640.04380.04780.00740.1193-0.0022-0.01020.11070.03240.2001-3.9914-1.702733.3547
21.4484-0.1037-0.23260.1264-0.21461.5533-0.03350.17510.024-0.073-0.0078-0.0015-0.0198-0.15220.0460.19680.02760.01910.13390.00130.1241-8.3802-4.316926.4335
31.2777-0.03790.23140.5394-0.98161.8138-0.03650.1308-0.1461-0.07230.108-0.06410.3428-0.1453-0.05950.278-0.05260.02880.1872-0.05470.1498-8.5263-12.21261.8866
40.81320.4187-0.23990.6711-0.81442.23780.0549-0.2118-0.2386-0.1451-0.14030.0150.12520.16320.04620.14-0.0001-0.01550.20950.02540.1809-10.7014-11.1334-6.0981
51.7526-0.6531.06180.2776-0.55011.4461-0.1617-0.05820.36490.00510.0922-0.1282-0.13590.15990.10010.09-0.05-0.03020.125-0.05790.250519.12476.260542.1792
62.3791-0.51170.50250.30310.23151.07210.07850.20840.15540.0877-0.1278-0.1244-0.2278-0.07620.04350.1551-0.0025-0.00350.17770.0220.132825.69034.940647.1691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A resid 7:100
2X-RAY DIFFRACTION2chain B resid 7:100
3X-RAY DIFFRACTION3chain C resid 7:100
4X-RAY DIFFRACTION4chain D resid 7:100
5X-RAY DIFFRACTION5chain E resid 7:100
6X-RAY DIFFRACTION6chain F resid 7:100

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