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- PDB-7c50: Crystal structure of a Simpl-like protein from Campylobacter jeju... -

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Basic information

Entry
Database: PDB / ID: 7c50
TitleCrystal structure of a Simpl-like protein from Campylobacter jejuni (selenomethionine-incorporated protein)
ComponentsSIMPL domain-containing protein
KeywordsUNKNOWN FUNCTION / Campylobacter jejuni / Simpl-like protein
Function / homologyUncharacterised conserved protein UCP029033, periplasmic protein / Interleukin-1 receptor-associated kinase 1-binding protein 1/DUF541 / : / Protein of unknown function (DUF541) / DNA damage response / SIMPL domain-containing protein
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsOh, H.B. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural analysis of a Simpl-like protein from Campylobacter jejuni.
Authors: Oh, H.B. / Yoon, S.I.
History
DepositionMay 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIMPL domain-containing protein


Theoretical massNumber of molelcules
Total (without water)24,5491
Polymers24,5491
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.675, 82.675, 202.043
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-368-

HOH

21A-369-

HOH

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Components

#1: Protein SIMPL domain-containing protein / Simpl-like protein


Mass: 24548.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: EAS83_04275, EID16_09040 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Z9IF87
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: polyethylene glycol 8000, calcium acetate, imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.93→30 Å / Num. obs: 20244 / % possible obs: 99.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 41.1
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1001 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.93→29.21 Å / SU ML: 0.2411 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2496 1021 5.04 %
Rwork0.2185 19221 -
obs0.2201 20242 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.51 Å2
Refinement stepCycle: LAST / Resolution: 1.93→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 0 71 1568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01271515
X-RAY DIFFRACTIONf_angle_d1.15322053
X-RAY DIFFRACTIONf_chiral_restr0.0731244
X-RAY DIFFRACTIONf_plane_restr0.0074265
X-RAY DIFFRACTIONf_dihedral_angle_d16.5558935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-2.030.30411490.23912678X-RAY DIFFRACTION99.79
2.03-2.160.34291400.25442746X-RAY DIFFRACTION99.97
2.16-2.330.28841350.24622725X-RAY DIFFRACTION99.93
2.33-2.560.2871400.24162759X-RAY DIFFRACTION99.9
2.56-2.930.27841560.24082746X-RAY DIFFRACTION99.97
2.93-3.690.24711380.21092774X-RAY DIFFRACTION99.83
3.69-29.210.21121630.19832793X-RAY DIFFRACTION97.08
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)
11.039438775760.165867847191-3.345959756244.508928400822.620166848012.15726865736-0.291603574663-0.3746087074790.1219662815020.421676833104-0.4842329971960.1811959401620.09654601123870.5107179886220.6872547896730.243499016063-0.03059256012690.006195870244620.536749155233-0.07575095145560.28050936238228.4838436114-4.0870820870957.3133308915
25.984612768114.969751674084.642983925156.550584475384.539471908166.38553950872-0.216018200793-0.01206942583880.108550445055-0.3784390286310.1117698427730.982610075506-0.285138065-0.02592913837720.1477601126990.271426834826-0.0378696465722-0.1244964601460.232094523950.08709493342230.4532973245611.4901506683-27.064032847419.4868232793
36.883512400645.728231601251.845008296462.676289903983.727831669812.95728524272-0.6343390229730.445890082956-0.13742645614-1.178936703130.5098834332510.26689217031-0.4542941270940.1600488378340.1007317734130.411214374711-0.127332428973-0.1670135315790.32726319230.1234389874230.46803884480212.7784702737-29.36808647989.99138244644
46.086700891532.025701344792.43407698896.953064669261.570231937922.95926555150.0813098935491-0.19087282207-0.427471758220.0693843629952-0.1355691093680.211998225189-0.2435290153260.4811174206030.05381768046150.242516583747-0.0358403545042-0.06142922966210.3140161073030.07245232446150.31128116581917.1750602999-30.197917908317.9971805286
50.4048590228870.130126331046-1.161052123484.097444899243.699113505427.97195226547-0.233947308379-0.0428972075186-0.404631437758-0.5026511880540.351411396183-0.573570443034-1.53649371374-2.34863452565-0.1172094372030.5602670303890.0951152497548-0.09819566130990.8748589574810.06224593148671.27414152083-10.0196847897-38.126147277913.6297071114
63.346215042042.124798007541.577041371684.206195565632.593324475563.819971108-0.3891664215650.2600291626510.469404340022-0.3886541943370.07915641596290.936550123107-0.7431924323910.13247961080.3061643172850.33703115857-0.0431475146632-0.08926347326650.2851175272660.07236104735740.39198501374515.2968168231-20.30075137321.5093348248
74.234748675283.013822823830.7957655965657.954448706265.195473039267.49122200034-0.012637128307-0.5887125422330.3431872091640.01033650979210.451793838142-0.428184650102-0.2327945483891.4516053199-0.4825853251010.243222296619-0.03571227944190.03109234041990.810039132526-0.09286628621180.29367901688634.1751711863-9.2162050537150.1930835416
85.958713690134.722946968754.144465825526.091816434463.396973967576.67900989989-0.1266878760350.16915220904-0.002833423569660.333954919670.464942216386-0.8476061448110.419738949181.00924473204-0.6187384581870.4500264733990.159035461341-0.02928998539560.845317977958-0.07975702385640.47661289124832.2956213613-8.2738745191764.200709418
92.5601180950.166829128596-0.7894890924674.429310336763.773763518385.833607383590.01844807570860.0238717639610.470623984347-0.891079745693-0.1194528926670.95256799982-1.11504634053-1.122604068310.2579736265750.4587823932960.0713548550652-0.1590752334630.4457994938650.009809632775670.40811164787520.4579777791-9.4424348960137.4141745154
102.252448458920.7692544710310.1327450003425.088314964714.609705297452.096462971210.220399448831-0.695705660673-0.07393120253070.4081109938880.5941165084260.01396556333510.4564426890040.866986167376-0.2336920549080.2070135051570.0443998393050.008762107039390.719377080969-0.05733710957810.21100213599628.1068372383-7.8058491889953.5523363212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 102 )
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 117 )
6X-RAY DIFFRACTION6chain 'A' and (resid 118 through 164 )
7X-RAY DIFFRACTION7chain 'A' and (resid 165 through 185 )
8X-RAY DIFFRACTION8chain 'A' and (resid 186 through 203 )
9X-RAY DIFFRACTION9chain 'A' and (resid 204 through 217 )
10X-RAY DIFFRACTION10chain 'A' and (resid 218 through 230 )

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