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- PDB-9nyu: Crystal structure of KwaB dimer -

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Basic information

Entry
Database: PDB / ID: 9nyu
TitleCrystal structure of KwaB dimer
ComponentsKiwa protein KwaB
KeywordsANTIVIRAL PROTEIN / Antiphage / Kiwa system / KwaB dimer
Function / homologyProtein of unknown function DUF4868 / : / Kiwa protein KwaB-like / defense response to virus / Kiwa protein KwaB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsZhiying, Z. / Dinshaw, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateP30CA008748 United States
CitationJournal: To Be Published
Title: Crystal structure of KwaB dimer
Authors: Zhiying, Z. / Dinshaw, J.P.
History
DepositionMar 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kiwa protein KwaB
K: Kiwa protein KwaB


Theoretical massNumber of molelcules
Total (without water)72,2952
Polymers72,2952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-37 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.974, 163.974, 61.124
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "K"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 1 - 315 / Label seq-ID: 1 - 315

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2KB

NCS oper: (Code: givenMatrix: (-0.855329273631, -0.464523329311, 0.229412096883), (-0.434525881302, 0.402073365285, -0.805930683997), (0.282133110693, -0.789021600119, -0.545752528529)Vector: 73. ...NCS oper: (Code: given
Matrix: (-0.855329273631, -0.464523329311, 0.229412096883), (-0.434525881302, 0.402073365285, -0.805930683997), (0.282133110693, -0.789021600119, -0.545752528529)
Vector: 73.6374093079, -11.6576579638, -62.289880422)

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Components

#1: Protein Kiwa protein KwaB


Mass: 36147.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kwaB, ECO55CA74_24530 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DW46
Has protein modificationN

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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: 3.28 Å3/Da / Density % sol: 62.51 %
Crystal growTemperature: 289 K / Method: liquid diffusion
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0; 30% v/v Jeffamine ED-2001 pH 7.0

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Data collection

DiffractionMean temperature: 289 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 31, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 3.6→30.99 Å / Num. obs: 11145 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.997 / Rpim(I) all: 0.082 / Net I/σ(I): 5.8
Reflection shellResolution: 3.6→3.79 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1115 / CC1/2: 0.403 / Rpim(I) all: 0.936

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
RAPDdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→30.99 Å / SU ML: 0.6357 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.8498
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3242 1115 10 %
Rwork0.2764 10030 -
obs0.2811 11145 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 176.73 Å2
Refinement stepCycle: LAST / Resolution: 3.6→30.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5058 0 0 0 5058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00425134
X-RAY DIFFRACTIONf_angle_d0.74326908
X-RAY DIFFRACTIONf_chiral_restr0.0475798
X-RAY DIFFRACTIONf_plane_restr0.0059876
X-RAY DIFFRACTIONf_dihedral_angle_d4.92666
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.36922902838 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.760.40451370.38031223X-RAY DIFFRACTION99.78
3.76-3.960.40251340.35731247X-RAY DIFFRACTION100
3.96-4.210.32211360.34521245X-RAY DIFFRACTION100
4.21-4.530.37891390.32261237X-RAY DIFFRACTION100
4.53-4.990.32821420.32321259X-RAY DIFFRACTION99.86
4.99-5.710.42771380.30421244X-RAY DIFFRACTION100
5.71-7.170.38351460.31681259X-RAY DIFFRACTION99.93
7.18-30.990.23781430.19281316X-RAY DIFFRACTION99.66
Refinement TLS params.Method: refined / Origin x: 53.3962680396 Å / Origin y: -55.1737221557 Å / Origin z: -2.33871769993 Å
111213212223313233
T0.660762998549 Å2-0.0687358814027 Å20.197456411388 Å2-1.17087342162 Å20.0551684889519 Å2--1.16455847276 Å2
L1.61408059616 °20.465528458649 °2-0.484451734223 °2-2.44200239296 °2-0.593381455065 °2--2.35397753715 °2
S0.076794270518 Å °-0.183667431708 Å °0.228096979438 Å °0.00400426279831 Å °0.161219715302 Å °0.355187086072 Å °-0.213663821967 Å °-0.33487544131 Å °-0.19026858838 Å °
Refinement TLS groupSelection details: all

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