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- PDB-8gy8: The structure of Bax1 from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 8gy8
TitleThe structure of Bax1 from Pyrococcus furiosus
ComponentsPutative translation initiation factor (IF-2 homolog)
KeywordsDNA BINDING PROTEIN / nuclease RecJ2
Function / homologyProtein of unknown function DUF790, endonuclease-like / Protein of unknown function (DUF790) / translation initiation factor activity / Translation initiation factor (IF-2 homolog)
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å
AuthorsWang, W.W. / Liu, X.P.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170097 China
National Natural Science Foundation of China (NSFC)U1832161 China
National Natural Science Foundation of China (NSFC)41921006 China
CitationJournal: To Be Published
Title: The structure of Bax1 from Pyrococcus furiosus
Authors: Yi, G.S. / Huang, Q.Y. / Wang, W.W. / Yu, F. / Xiao, X. / Liu, X.P.
History
DepositionSep 21, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative translation initiation factor (IF-2 homolog)
B: Putative translation initiation factor (IF-2 homolog)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7443
Polymers87,6482
Non-polymers961
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-21 kcal/mol
Surface area37180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.250, 110.490, 126.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative translation initiation factor (IF-2 homolog) / Bax1


Mass: 43824.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Gene: PF1903 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZT0
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2M Ammonium Sulfate, 0.1M Tris-HCl pH 7.0, 0.2M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.94→50.05 Å / Num. obs: 85680 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 35.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Net I/σ(I): 20 / Num. measured all: 620986 / Scaling rejects: 174
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.94-1.997.41.0594612762500.6850.4171.1392.2100
8.68-50.055.90.042636410780.9950.020.04750.998.8

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Processing

Software
NameVersionClassification
Aimless0.7.9data scaling
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.94→45.59 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2176 4299 5.02 %
Rwork0.1977 81300 -
obs0.1987 85599 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.97 Å2 / Biso mean: 47.7801 Å2 / Biso min: 20.03 Å2
Refinement stepCycle: final / Resolution: 1.94→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6160 0 5 430 6595
Biso mean--33.07 49.54 -
Num. residues----750
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-1.960.3851470.360826652812100
1.96-1.990.41321250.317526612786100
1.99-2.010.30771660.283226982864100
2.01-2.030.29031290.250226752804100
2.03-2.060.28511430.243226672810100
2.06-2.090.2691340.227427002834100
2.09-2.120.23221500.21626812831100
2.12-2.150.23431240.211827052829100
2.15-2.180.24681470.205226712818100
2.18-2.220.22981440.205826762820100
2.22-2.260.23121210.21527162837100
2.26-2.30.2351650.210426672832100
2.3-2.340.19211520.205626572809100
2.34-2.390.24821500.208627042854100
2.39-2.440.22681250.208326942819100
2.44-2.50.23161370.206527292866100
2.5-2.560.25121400.212326792819100
2.56-2.630.26531490.211226952844100
2.63-2.710.23451490.207326892838100
2.71-2.80.251500.2127162866100
2.8-2.90.25491490.207526912840100
2.9-3.010.21951520.212527062858100
3.01-3.150.22371330.207827332866100
3.15-3.320.24511360.198827202856100
3.32-3.520.20911480.183627402888100
3.53-3.80.20481460.175227342880100
3.8-4.180.161280.170527572885100
4.18-4.780.15511480.151227752923100
4.78-6.020.1941420.188928112953100
6.02-45.590.21791700.20742888305899
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)
13.244-1.48013.63694.20211.42688.12090.45130.3101-0.6296-0.2976-0.0358-0.41940.26360.8125-0.48120.3110.0077-0.0290.30040.02960.393636.36460.484642.5921
27.91911.7087-2.08582.6652-0.70474.2213-0.08210.3397-0.6362-0.29-0.051-0.19510.14460.05810.10420.32960.0453-0.00390.261-0.00070.193255.15121.383852.438
33.87520.9453-3.33980.857-0.33383.77130.0949-0.32220.06170.2441-0.068-0.1361-0.11710.3173-0.00480.2732-0.0177-0.06080.28890.00090.242477.901212.124842.1582
41.9747-1.60151.07743.1065-1.68112.74720.0122-0.05410.09470.2040.019-0.0242-0.2253-0.0187-0.02470.2379-0.00580.03030.21260.01710.260735.078318.454843.1269
52.5483-0.91760.762.755-1.63863.2973-0.0412-0.18710.2370.40130.0037-0.2134-0.6513-0.01150.02750.313-0.02470.02880.25750.04240.310532.925313.794745.977
63.87640.7005-1.22658.5257-0.9254.05340.356-0.25270.4920.1712-0.09650.152-0.86150.041-0.06570.4580.06350.12180.27090.04650.330128.448642.811935.8032
71.4589-0.2833-0.04386.1015-0.03711.91030.02370.29340.1205-0.7213-0.01920.1187-0.3779-0.1972-0.03050.40840.07130.04370.30110.08820.275229.473534.369625.7571
83.30443.14520.07573.48990.5666.48270.4022-0.1676-0.32660.0984-0.07330.24270.1229-0.4697-0.21890.20410.02260.03820.21840.00890.146669.85831.457319.0383
95.9063-1.5276-2.35250.92340.60481.64370.01540.5597-0.1494-0.1495-0.04960.127-0.0545-0.28170.02410.282-0.0254-0.01760.2813-0.00720.251138.72923.242416.1301
101.19781.19210.16293.11741.42141.2959-0.0639-0.00480.2682-0.3149-0.02060.1633-0.251-0.00660.05920.19650.0395-0.00860.2219-0.00940.220871.299218.509716.7363
111.91350.5418-0.58066.1118-0.3483.4592-0.0424-0.20.35380.1574-0.0673-0.2914-0.41170.21210.10640.2909-0.0033-0.09310.2827-0.10040.457577.011937.275926.4031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 22 )A1 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 72 )A23 - 72
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 142 )A73 - 142
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 222 )A143 - 222
5X-RAY DIFFRACTION5chain 'A' and (resid 223 through 262 )A223 - 262
6X-RAY DIFFRACTION6chain 'A' and (resid 263 through 304 )A263 - 304
7X-RAY DIFFRACTION7chain 'A' and (resid 305 through 375 )A305 - 375
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 22 )B1 - 22
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 142 )B23 - 142
10X-RAY DIFFRACTION10chain 'B' and (resid 143 through 276 )B143 - 276
11X-RAY DIFFRACTION11chain 'B' and (resid 277 through 375 )B277 - 375

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