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- PDB-7c51: Crystal structure of a Simpl-like protein from Campylobacter jeju... -

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Basic information

Entry
Database: PDB / ID: 7c51
TitleCrystal structure of a Simpl-like protein from Campylobacter jejuni (native protein)
ComponentsSIMPL domain-containing protein
KeywordsUNKNOWN FUNCTION / Campylobacter jejuni / Simpl-like protein
Function / homology
Function and homology information


DNA damage response
Similarity search - Function
Protein of unknown function (DUF541), domain 2 / Uncharacterised conserved protein UCP029033, periplasmic protein / Interleukin-1 receptor-associated kinase 1-binding protein 1/DUF541 / : / Protein of unknown function (DUF541) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SIMPL domain-containing protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIMPL domain-containing protein


Theoretical massNumber of molelcules
Total (without water)24,5021
Polymers24,5021
Non-polymers00
Water30617
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)82.864, 82.864, 201.284
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

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Components

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


Mass: 24501.633 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 BL21(DE3) (bacteria) / References: UniProt: A0A3Z9IF87
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
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: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.46→30 Å / Num. obs: 9885 / % possible obs: 98.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 45.59 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 35.1
Reflection shellResolution: 2.46→2.5 Å / Redundancy: 6 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 504 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C50

7c50


Resolution: 2.46→29.21 Å / SU ML: 0.2842 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.694
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2641 484 4.9 %
Rwork0.2261 9401 -
obs0.228 9885 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.4 Å2
Refinement stepCycle: LAST / Resolution: 2.46→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1470 0 0 17 1487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00381488
X-RAY DIFFRACTIONf_angle_d0.58012020
X-RAY DIFFRACTIONf_chiral_restr0.0478243
X-RAY DIFFRACTIONf_plane_restr0.0035260
X-RAY DIFFRACTIONf_dihedral_angle_d16.1146914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.820.32261730.27393093X-RAY DIFFRACTION99.66
2.82-3.550.29631770.24443098X-RAY DIFFRACTION99.33
3.55-29.210.22541340.20673210X-RAY DIFFRACTION97.72
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)
11.701015809110.68969006667-1.2711046075.481103627473.285461718823.09876556968-0.465601523897-0.179539816810.1482956411620.378464785673-0.2695531792180.06156939074080.1787711651380.3264575457580.8626812147190.2765999453370.0161307187114-0.03383456421930.644907115747-0.08727856643160.39082153056528.6022444996-3.9511895749257.1405859598
24.900442519025.504388238192.152298090827.839996269922.924479532094.13481784783-0.173944180263-0.279528120064-0.141157044744-0.2474914120390.01802162614651.19587073999-0.3373377705370.03166486660940.2889901851390.3391508791470.0138136743752-0.1222691670780.3232068773610.08907510410940.57714369845311.6367252032-27.201963862619.2518507293
35.106903540675.014327838921.038707186177.699474994782.233196050413.22022952773-0.9407374753460.6142092166590.0450364566566-1.742108197460.8083132864070.677478294488-0.4169104274580.2690118452090.0360082920540.596412834803-0.149178523859-0.2607417216190.4430529595920.1532422249350.54340232156113.0334694932-29.53428166429.74459047804
48.576199961313.862669765232.870277671526.763038047921.555012941773.439998269530.320929101935-0.137217160341-0.5837117926250.144379423412-0.2952488445010.351754170774-0.301795844150.664152781916-0.03041550399950.338675839413-0.075993482722-0.05085481791660.3749711346120.1023689622040.38095040261617.0853009071-30.356301175917.9786030758
51.24421675033-1.82807994483-2.692742150032.664356025233.902201076095.82319341482-0.07657047907340.12613538105-0.505592870368-0.998284595719-0.1278677790761.24792243403-1.19829397314-2.191097978120.5437686455480.576619238170.100303525433-0.2465112652131.083068047010.298598440641.84187319642-9.59387049408-38.447347524412.9635751998
62.531985388151.576598253421.085376621665.106609537921.326028024143.64482294249-0.3464325693120.1626302525150.440047081915-0.2950208327330.1688878028721.00502740246-0.8752431846450.3048939983830.2152354269050.46369917204-0.0576116934799-0.1091758877550.3584022300610.1086786776860.49858299608714.2513431546-20.878818677320.1096184983
73.1256623142.854112623440.5128295087047.074764011252.524480730455.53353732585-0.243493644166-0.5977843971280.228221489632-0.1600007353310.584333788234-0.432236813163-0.1638048673291.35268006004-0.4180240268630.349749907821-0.01898271897350.03531927055030.934230219922-0.1076437868890.30931893629933.7451376477-10.354099835848.1020537493
88.691660228816.027264316283.009351674258.048662976363.275574743417.3849859307-0.5909226762970.1633886999750.3808390157970.6217561900570.579487256237-0.4257743620530.3342077532961.318413983310.0412558141230.584686894460.140234115309-0.1265604978930.942679668180.02573082554390.54391102718632.5120465074-8.1930377182264.0576988917
92.625978891690.263405178029-0.07307982567195.855438061893.524041263612.729149923920.145813758572-0.1402650537630.248217635611-0.7073851243120.112592312211.14004236639-1.24194050608-0.8563998920610.1217519709110.5402719417530.0764988893835-0.1024108872210.56011798040.08635043154670.44170613479120.5392415752-9.5791106098937.3738301814
101.192944039460.836884720870.6676551998455.285227722332.9418702061.677132497510.110658756611-0.6477263131290.03621326215230.3245963275560.605932122164-0.002561771466620.1924124921151.3457912206-0.231367787530.2508618145510.01845573343240.05559707913811.13528336608-0.03633324040790.18943988283328.2723616161-7.7493479502253.428058103
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 161 )
7X-RAY DIFFRACTION7chain 'A' and (resid 162 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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