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- PDB-9mtn: Crystal structure of KwaB -

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Basic information

Entry
Database: PDB / ID: 9mtn
TitleCrystal structure of KwaB
ComponentsKiwa protein KwaB
KeywordsIMMUNE SYSTEM / KwaB dimer / anti-phage defense / Kiwa system
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: 3.92 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
Authors: Zhiying, Z. / Dinshaw, J.P.
History
DepositionJan 11, 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
B: Kiwa protein KwaB
C: Kiwa protein KwaB


Theoretical massNumber of molelcules
Total (without water)144,5904
Polymers144,5904
Non-polymers00
Water00
1
A: Kiwa protein KwaB
K: Kiwa protein KwaB


Theoretical massNumber of molelcules
Total (without water)72,2952
Polymers72,2952
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-38 kcal/mol
Surface area26530 Å2
MethodPISA
2
B: Kiwa protein KwaB
C: Kiwa protein KwaB


Theoretical massNumber of molelcules
Total (without water)72,2952
Polymers72,2952
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-31 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)283.105, 283.105, 76.312
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein
Kiwa protein KwaB


Mass: 36147.453 Da / Num. of mol.: 4
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: 4.07 Å3/Da / Density % sol: 69.78 %
Crystal growTemperature: 290 K / Method: evaporation / Details: 0.1 M Tris, pH 8.5, 5% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.88→33.28 Å / Num. obs: 20404 / % possible obs: 97.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 129.85 Å2 / CC1/2: 0.972 / Net I/σ(I): 8
Reflection shellResolution: 3.88→4.09 Å / Num. unique obs: 2586 / CC1/2: 0.303

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
AUTOMARdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.92→33.28 Å / SU ML: 0.6714 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.3934
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2746 1754 9.95 %
Rwork0.238 15867 -
obs0.2417 17621 86.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 166.78 Å2
Refinement stepCycle: LAST / Resolution: 3.92→33.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9722 0 0 0 9722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00569865
X-RAY DIFFRACTIONf_angle_d1.007213277
X-RAY DIFFRACTIONf_chiral_restr0.05821547
X-RAY DIFFRACTIONf_plane_restr0.00721676
X-RAY DIFFRACTIONf_dihedral_angle_d6.61831278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.92-4.020.4309350.4256349X-RAY DIFFRACTION24.17
4.02-4.140.3661190.34181074X-RAY DIFFRACTION76.52
4.14-4.270.3608990.3361909X-RAY DIFFRACTION64
4.27-4.430.413900.3812780X-RAY DIFFRACTION56.35
4.43-4.60.31531580.27741420X-RAY DIFFRACTION99
4.6-4.810.3181570.27211419X-RAY DIFFRACTION100
4.81-5.070.31841550.24991426X-RAY DIFFRACTION100
5.07-5.380.30491570.26471393X-RAY DIFFRACTION99.87
5.38-5.80.29931580.26071418X-RAY DIFFRACTION100
5.8-6.370.3031580.27411438X-RAY DIFFRACTION100
6.38-7.290.2961560.26691398X-RAY DIFFRACTION100
7.29-9.150.21981540.1991431X-RAY DIFFRACTION100
9.15-33.280.19741580.1481412X-RAY DIFFRACTION99.62

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