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- PDB-7yia: Crystal structure of K74A mutant of Cap4 SAVED domain-containing ... -

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Basic information

Entry
Database: PDB / ID: 7yia
TitleCrystal structure of K74A mutant of 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 / CD-NTase-associated protein 4
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.428 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 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,2882
Polymers56,2641
Non-polymers241
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area21820 Å2
Unit cell
Length a, b, c (Å)56.901, 70.212, 150.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 56263.773 Da / Num. of mol.: 1 / Mutation: K74A
Source method: isolated from a genetically manipulated source
Details: The first Gly residue is generated by the expression vector. The second Met should be assigned as +1 position.
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris propane pH 6.5, 0.2 M sodium acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.42→30 Å / Num. obs: 23087 / % possible obs: 98.1 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.7
Reflection shellResolution: 2.42→2.51 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2312 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YIB

7yib


Resolution: 2.428→29.895 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.369 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.553 / ESU R Free: 0.255
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2192 1033 4.964 %
Rwork0.2019 19775 -
all0.203 --
obs-20808 88.308 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.116 Å2
Baniso -1Baniso -2Baniso -3
1-0.639 Å20 Å2-0 Å2
2---0.602 Å20 Å2
3----0.037 Å2
Refinement stepCycle: LAST / Resolution: 2.428→29.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 1 135 4051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134001
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173706
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.6445421
X-RAY DIFFRACTIONr_angle_other_deg1.2261.5798521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2985490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78521.867241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64715667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4761534
X-RAY DIFFRACTIONr_chiral_restr0.060.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02977
X-RAY DIFFRACTIONr_nbd_refined0.2050.2820
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.23525
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21924
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21883
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2119
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0510.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.217
X-RAY DIFFRACTIONr_nbd_other0.2550.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.120.210
X-RAY DIFFRACTIONr_mcbond_it4.1014.2021966
X-RAY DIFFRACTIONr_mcbond_other4.1024.2021965
X-RAY DIFFRACTIONr_mcangle_it6.4036.2892454
X-RAY DIFFRACTIONr_mcangle_other6.4016.2892455
X-RAY DIFFRACTIONr_scbond_it4.0724.5672035
X-RAY DIFFRACTIONr_scbond_other4.0714.5672035
X-RAY DIFFRACTIONr_scangle_it6.3666.692967
X-RAY DIFFRACTIONr_scangle_other6.3666.692967
X-RAY DIFFRACTIONr_lrange_it9.13747.5864353
X-RAY DIFFRACTIONr_lrange_other9.1447.5774346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.428-2.4910.236470.248901X-RAY DIFFRACTION55.8633
2.491-2.5580.258540.2321013X-RAY DIFFRACTION64.3935
2.558-2.6320.26490.2261105X-RAY DIFFRACTION72.125
2.632-2.7120.318590.2471226X-RAY DIFFRACTION80.6654
2.712-2.8010.235530.2321309X-RAY DIFFRACTION90.4382
2.801-2.8980.215770.2061344X-RAY DIFFRACTION96.4698
2.898-3.0060.236790.2041354X-RAY DIFFRACTION99.8606
3.006-3.1280.297590.2251312X-RAY DIFFRACTION100
3.128-3.2650.265780.2121247X-RAY DIFFRACTION100
3.265-3.4230.224550.2131202X-RAY DIFFRACTION99.9205
3.423-3.6050.208540.2241179X-RAY DIFFRACTION99.8381
3.605-3.820.3420.242766X-RAY DIFFRACTION70.6912
3.82-4.0790.219560.186981X-RAY DIFFRACTION95.0504
4.079-4.3990.182510.159968X-RAY DIFFRACTION99.902
4.399-4.8090.141480.132882X-RAY DIFFRACTION99.7854
4.809-5.3590.143500.147812X-RAY DIFFRACTION99.4233
5.359-6.1560.311440.205719X-RAY DIFFRACTION100
6.156-7.4610.23370.209632X-RAY DIFFRACTION99.8507
7.461-10.240.143220.19520X-RAY DIFFRACTION99.0859
10.24-29.8950.17190.255301X-RAY DIFFRACTION89.8876

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