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- PDB-7yib: Crystal structure of wild-type Cap4 SAVED domain-containing recep... -

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Basic information

Entry
Database: PDB / ID: 7yib
TitleCrystal structure of wild-type Cap4 SAVED domain-containing receptor from Enterobacter cloacae
ComponentsCD-NTase-associated protein 4
KeywordsHYDROLASE / SAVED domain-containing protein
Function / homologySMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / nucleotide binding / DNA binding / metal ion binding / CD-NTase-associated protein 4
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.18 Å
AuthorsKo, T.-P. / Yang, C.-S. / Hou, M.-H. / Wang, Y.-C. / Chen, Y.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2311-B241-001 Taiwan
Ministry of Science and Technology (MoST, Taiwan)111-2311-B-039-001-MY3 Taiwan
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Specific recognition of cyclic oligonucleotides by Cap4 for phage infection.
Authors: Chang, J.J. / You, B.J. / Tien, N. / Wang, Y.C. / Yang, C.S. / Hou, M.H. / Chen, Y.
History
DepositionJul 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD-NTase-associated protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6392
Polymers56,6031
Non-polymers351
Water6,720373
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area22330 Å2
Unit cell
Length a, b, c (Å)150.958, 70.947, 56.468
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-501-

CL

21A-932-

HOH

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Components

#1: Protein CD-NTase-associated protein 4 / Cap4 / Endodeoxyribonuclease Cap4


Mass: 56603.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: cap4, P853_02261 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DUD5, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 0.2 M sodium chloride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.979, 0.979, 0.954
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2021
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9541
ReflectionResolution: 2.18→30 Å / Num. obs: 60956 / % possible obs: 99.6 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 43.13
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 5.95 / Num. unique obs: 3126 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.17.1_3660phasing
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.18→26.44 Å / SU ML: 0.1796 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2279
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1998 3064 5.03 %
Rwork0.1656 57892 -
obs0.1673 60956 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.57 Å2
Refinement stepCycle: LAST / Resolution: 2.18→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3941 0 0 373 4314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00234027
X-RAY DIFFRACTIONf_angle_d0.56565458
X-RAY DIFFRACTIONf_chiral_restr0.0439595
X-RAY DIFFRACTIONf_plane_restr0.0034725
X-RAY DIFFRACTIONf_dihedral_angle_d17.87991489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.210.2421240.21552394X-RAY DIFFRACTION89.48
2.21-2.250.28371350.21232527X-RAY DIFFRACTION96.24
2.25-2.280.22241410.20282628X-RAY DIFFRACTION99.25
2.29-2.330.23011340.2012657X-RAY DIFFRACTION99.86
2.33-2.370.25931380.18652625X-RAY DIFFRACTION100
2.37-2.420.21031400.18142666X-RAY DIFFRACTION100
2.42-2.470.23881430.18612664X-RAY DIFFRACTION100
2.47-2.530.21221390.1812641X-RAY DIFFRACTION100
2.53-2.590.22461460.18832671X-RAY DIFFRACTION99.93
2.59-2.660.20651410.19362624X-RAY DIFFRACTION100
2.66-2.740.24941450.19362650X-RAY DIFFRACTION100
2.74-2.830.23151380.19822698X-RAY DIFFRACTION99.96
2.83-2.930.25511410.18862619X-RAY DIFFRACTION100
2.93-3.050.2141380.18512639X-RAY DIFFRACTION100
3.05-3.190.2391370.18632660X-RAY DIFFRACTION100
3.19-3.350.19091430.17042660X-RAY DIFFRACTION100
3.35-3.560.1971410.162645X-RAY DIFFRACTION99.86
3.56-3.840.17391380.15252643X-RAY DIFFRACTION99.93
3.84-4.220.22331400.13722635X-RAY DIFFRACTION100
4.22-4.830.13841390.12062654X-RAY DIFFRACTION99.79
4.83-6.070.17381420.15872675X-RAY DIFFRACTION99.86
6.08-26.440.17761410.16452617X-RAY DIFFRACTION99.07
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)
11.96798731511-1.163662660050.9151704660931.77694568636-0.9151160115210.9493073453420.08663943616580.04615610648150.00973928139995-0.110814677391-0.0486900198885-0.06605051319650.07207322776950.0310978116730.0002244774307170.255754656410.01750501526250.06238732134350.2695495853890.03538070085990.2884367139561.060156477516.096190539215.1277972329
21.09301225969-0.114564525467-0.3492493935520.375475340409-0.478236317420.3819809672390.005266831885840.09064881540340.372947479334-0.0670179764233-0.122114427421-0.01690758821840.02448346242620.00739945658775-0.05625713809780.3692263182710.02851393656160.01824493527890.3653459440050.08610471567010.34815627046649.520895911132.08886819097.07579731986
33.178625991360.55673366669-0.5841590476621.114063958730.3761501552431.1281715683-0.0783001974468-0.01130099086580.0872343822545-0.0574751055339-0.06168210936960.1924181137980.164761657234-0.0235469647107-3.36823039496E-50.3354766510860.02660334443950.00161454644080.284858538389-0.0483830911540.27989984998624.553625522921.764530090418.4950868801
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 192 )
2X-RAY DIFFRACTION2chain 'A' and (resid 193 through 287 )
3X-RAY DIFFRACTION3chain 'A' and (resid 288 through 499 )

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