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- PDB-9umd: autoinhibited kpNLRL -

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Basic information

Entry
Database: PDB / ID: 9umd
Titleautoinhibited kpNLRL
ComponentsTetratricopeptide repeat protein
KeywordsIMMUNE SYSTEM / bacterial immune system / NLR-like
Function / homology
Function and homology information


signal transduction
Similarity search - Function
TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Tetratricopeptide-like helical domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Tetratricopeptide repeat protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.14 Å
AuthorsWang, L. / Wang, H. / Li, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Higher-order activation of a NLR-like bacterial defense system
Authors: Wang, L. / Wang, H. / Li, J.
History
DepositionApr 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetratricopeptide repeat protein
B: Tetratricopeptide repeat protein
C: Tetratricopeptide repeat protein
D: Tetratricopeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,3218
Polymers384,2924
Non-polymers2,0294
Water00
1
A: Tetratricopeptide repeat protein
D: Tetratricopeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,1604
Polymers192,1462
Non-polymers1,0142
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tetratricopeptide repeat protein
hetero molecules

C: Tetratricopeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,1604
Polymers192,1462
Non-polymers1,0142
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Unit cell
Length a, b, c (Å)77.243, 150.856, 381.728
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETASNASNAA1 - 8241 - 824
d_12ATPATPATPATPAE901
d_21METMETASNASNBB1 - 8241 - 824
d_22ATPATPATPATPBF901
d_31METMETASNASNCC1 - 8241 - 824
d_32ATPATPATPATPCG901
d_41METMETASNASNDD1 - 8241 - 824
d_42ATPATPATPATPDH901

NCS oper:
IDCodeMatrixVector
1given(-0.308022221283, 0.0142103067105, 0.951273030407), (0.0215302520749, 0.999736486569, -0.00796276756812), (-0.951135510557, 0.0180284387828, -0.308247004776)-4.21743055565, 33.6091386576, -64.6486877099
2given(0.184399979635, 0.0772471050568, -0.979810967621), (-0.0228678022247, -0.996299561324, -0.0828507557364), (-0.982585218254, 0.0376838010957, -0.181951147298)-58.8326623932, 114.93554604, -57.9392745284
3given(0.8754835893, -0.0687672070498, 0.478329965715), (-0.0286686478228, -0.995470805455, -0.0906420659423), (0.48239671796, 0.0656425679025, -0.873489816644)34.1447388398, 80.2407923976, -127.712618863

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Components

#1: Protein
Tetratricopeptide repeat protein


Mass: 96072.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: NGKP54_PROKKA_04522 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8D6T472
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM HEPES (pH 7.6) 10% PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 27, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 4.14→140.38 Å / Num. obs: 34756 / % possible obs: 99.42 % / Redundancy: 2 % / Biso Wilson estimate: 126.38 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 10
Reflection shellResolution: 4.14→4.29 Å / Rmerge(I) obs: 0.213 / Num. unique obs: 3414

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.14→140.3 Å / SU ML: 0.7623 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.1031
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3353 2000 5.77 %
Rwork0.2516 32674 -
obs0.2564 34674 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 134.42 Å2
Refinement stepCycle: LAST / Resolution: 4.14→140.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27024 0 124 0 27148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005827604
X-RAY DIFFRACTIONf_angle_d0.970937224
X-RAY DIFFRACTIONf_chiral_restr0.05434180
X-RAY DIFFRACTIONf_plane_restr0.00764752
X-RAY DIFFRACTIONf_dihedral_angle_d13.189310784
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.45540736269
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS3.10698747506
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS2.91881680627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.14-4.250.40571400.34132280X-RAY DIFFRACTION98.69
4.25-4.360.43921360.32532232X-RAY DIFFRACTION97.33
4.36-4.490.36591390.29282272X-RAY DIFFRACTION98.33
4.49-4.640.37451410.29332306X-RAY DIFFRACTION99.76
4.64-4.80.34771440.2892343X-RAY DIFFRACTION100
4.8-4.990.33771400.26362296X-RAY DIFFRACTION100
4.99-5.220.36081440.25452348X-RAY DIFFRACTION99.96
5.22-5.50.34051430.2642326X-RAY DIFFRACTION99.96
5.5-5.840.36971430.27162343X-RAY DIFFRACTION99.96
5.84-6.290.34751430.26512347X-RAY DIFFRACTION99.96
6.29-6.920.34531450.2552359X-RAY DIFFRACTION99.88
6.93-7.930.2921450.2422370X-RAY DIFFRACTION99.88
7.93-9.990.28791480.20382418X-RAY DIFFRACTION99.81
9.99-140.30.29681490.19822434X-RAY DIFFRACTION95.53

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