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- PDB-8fz9: Crystal Structure of Bacillus cereus TIR protein -

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Basic information

Entry
Database: PDB / ID: 8fz9
TitleCrystal Structure of Bacillus cereus TIR protein
ComponentsTIR
KeywordsCHAPERONE / molecular chaperone
Function / homologyCITRIC ACID
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsKhudaverdyan, N. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of Toll/interleukin-1 receptor like protein from Bacillus cereus (BcTir)
Authors: Khudaverdyan, N. / Song, J.
History
DepositionJan 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TIR
B: TIR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9704
Polymers31,5862
Non-polymers3842
Water6,738374
1
A: TIR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9852
Polymers15,7931
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TIR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9852
Polymers15,7931
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.695, 38.285, 66.822
Angle α, β, γ (deg.)102.27, 95.75, 101.91
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein TIR


Mass: 15793.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.03 M Citric Acid, 0.07 M Bis-Tris, pH 7.6, 20% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→64.55 Å / Num. obs: 27618 / % possible obs: 94.2 % / Redundancy: 3 % / CC1/2: 0.987 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.061 / Rrim(I) all: 0.108 / Net I/σ(I): 9.1 / Num. measured all: 81850
Reflection shellResolution: 1.78→1.82 Å / % possible obs: 88.3 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.541 / Num. measured all: 4421 / Num. unique obs: 1513 / CC1/2: 0.76 / Rpim(I) all: 0.378 / Rrim(I) all: 0.663 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→36.37 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 2000 7.26 %
Rwork0.1613 --
obs0.1637 27533 93.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→36.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 26 374 2496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142173
X-RAY DIFFRACTIONf_angle_d1.2832951
X-RAY DIFFRACTIONf_dihedral_angle_d19.177301
X-RAY DIFFRACTIONf_chiral_restr0.079335
X-RAY DIFFRACTIONf_plane_restr0.012374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.830.32181340.24681707X-RAY DIFFRACTION88
1.83-1.880.22371300.23181666X-RAY DIFFRACTION86
1.88-1.930.25871450.19841848X-RAY DIFFRACTION94
1.93-1.990.23991410.19811801X-RAY DIFFRACTION94
1.99-2.060.24521470.17351867X-RAY DIFFRACTION95
2.06-2.150.20831440.16151847X-RAY DIFFRACTION95
2.15-2.240.18961440.16481839X-RAY DIFFRACTION95
2.24-2.360.2081440.16171832X-RAY DIFFRACTION94
2.36-2.510.21731450.16921856X-RAY DIFFRACTION95
2.51-2.70.21571380.17261762X-RAY DIFFRACTION92
2.7-2.980.1951490.16351914X-RAY DIFFRACTION97
2.98-3.410.19271470.15131867X-RAY DIFFRACTION98
3.41-4.290.15881460.12981870X-RAY DIFFRACTION96
4.29-36.370.15351460.15371857X-RAY DIFFRACTION96
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)
11.80140.104-0.42475.1891-2.03583.7833-0.0997-0.1072-0.25280.5109-0.3066-0.3908-0.05180.14730.33220.1802-0.0233-0.00510.23530.03150.1973-0.4516-4.62567.0703
22.38670.505-0.62432.5940.53112.44680.1248-0.2821-0.02430.1017-0.0201-0.3546-0.09670.2209-0.13180.1589-0.0093-0.00240.22180.00960.20857.6081.14758.6869
30.72710.61030.80550.67290.27192.3570.05070.4065-0.2044-0.1010.04330.03880.08750.1514-0.08820.19810.01940.01390.2629-0.0060.1912-1.8652-3.2368-5.4655
40.9970.42270.80791.7286-0.89695.8899-0.0004-0.0069-0.46660.05610.1814-0.27250.5884-0.4246-0.14390.2844-0.0309-0.03020.2347-0.02980.2471-6.8618-9.7225-3.956
51.4727-0.66630.38131.8761-0.78732.96130.07490.0727-0.0389-0.0842-0.0080.20520.0471-0.2883-0.0440.1265-0.002-0.01060.18440.02070.1398-8.4397-0.03952.1128
62.01620.33810.0522.23450.09561.79690.1853-0.21920.13270.2948-0.15640.0282-0.136-0.0804-0.04010.1673-0.00110.010.17680.01090.1542-6.1836.65418.4695
73.23570.683-0.36192.0630.88191.4160.1172-0.00980.1318-0.0271-0.06310.2819-0.1598-0.16160.02910.17180.00990.01090.2369-0.00090.1946-11.04156.03859.6565
83.75760.1434-0.5582.4534-0.25181.76890.0511-0.6331-0.06240.3868-0.0044-0.16290.0540.0283-0.06790.2113-0.0482-0.01620.31170.02530.1497-0.32552.046217.7501
99.4947-1.1121-1.31962.0263-0.02078.73980.9273-0.7602-0.51270.21540.15571.4794-0.149-0.72510.55390.29090.0317-0.08820.40510.25570.5351-12.0196-7.499820.4483
102.6928-0.9348-0.59551.7077-0.28992.39080.0505-0.18770.15630.0840.0233-0.1225-0.02690.3251-0.0710.1385-0.0011-0.00630.163-0.0260.1557-6.17917.935433.4216
111.86950.3037-0.89121.87540.04631.55340.0676-0.4308-0.28850.235-0.15520.02310.54120.26740.01640.29860.026-0.01680.20710.0440.1941-16.169710.780745.0332
121.87560.1104-0.17082.18390.17682.4932-0.00660.0095-0.1112-0.01590.0128-0.1450.198-0.08890.0460.16080.0009-0.01110.1436-0.01670.1711-17.537612.347732.6487
131.0620.3219-0.19993.92720.07111.9942-0.0061-0.1674-0.20490.3277-0.05760.47760.1264-0.16210.02340.187-0.00940.00920.18490.0050.185-22.951214.302740.0939
141.8706-0.2606-0.88011.74790.57612.7670.02670.2652-0.0426-0.1584-0.10630.081-0.1003-0.19910.02630.1568-0.0081-0.00260.16470.00160.1749-17.937515.419827.6167
154.319-2.7084-0.09544.15410.26592.4270.1180.2953-0.5268-0.02730.03040.51560.4903-0.75670.02350.1239-0.0244-0.01160.27770.01530.1928-27.884512.766530.7836
162.41220.2151-1.11241.087-0.64911.5582-0.05640.19980.4468-0.07830.01790.09780.1498-0.1808-0.02490.1589-0.0023-0.01670.22660.0140.1916-19.318819.094224.844
170.2950.22830.10620.4448-0.19160.37530.33020.02840.7348-0.1450.03350.0521-0.4717-0.0857-0.13380.2234-0.00340.03430.18470.03980.2951-13.583327.053827.8063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 35 )
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 47 )
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 61 )
5X-RAY DIFFRACTION5chain 'A' and (resid 62 through 89 )
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 106 )
7X-RAY DIFFRACTION7chain 'A' and (resid 107 through 120 )
8X-RAY DIFFRACTION8chain 'A' and (resid 121 through 129 )
9X-RAY DIFFRACTION9chain 'A' and (resid 130 through 136 )
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 35 )
11X-RAY DIFFRACTION11chain 'B' and (resid 36 through 61 )
12X-RAY DIFFRACTION12chain 'B' and (resid 62 through 77 )
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 88 )
14X-RAY DIFFRACTION14chain 'B' and (resid 89 through 106 )
15X-RAY DIFFRACTION15chain 'B' and (resid 107 through 111 )
16X-RAY DIFFRACTION16chain 'B' and (resid 112 through 120 )
17X-RAY DIFFRACTION17chain 'B' and (resid 121 through 132 )

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