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- PDB-6q3v: Crystal structure of Human N4BP1 KH domains -

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Basic information

Entry
Database: PDB / ID: 6q3v
TitleCrystal structure of Human N4BP1 KH domains
ComponentsNEDD4-binding protein 1
KeywordsRNA BINDING PROTEIN / N4BP1 KH domains
Function / homology
Function and homology information


negative regulation of cytokine production / negative regulation of viral genome replication / regulation of innate immune response / RNA nuclease activity / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / ubiquitin binding / Regulation of NF-kappa B signaling / PML body / cellular response to UV ...negative regulation of cytokine production / negative regulation of viral genome replication / regulation of innate immune response / RNA nuclease activity / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / ubiquitin binding / Regulation of NF-kappa B signaling / PML body / cellular response to UV / Hydrolases; Acting on ester bonds / innate immune response / mRNA binding / nucleolus / nucleus / cytosol
Similarity search - Function
N4BP1, UBA-like domain / N4BP1, first type I KH-domain / N4BP1, second type I KH-domain / N4BP1, C-terminal UBA domain / Ribonuclease Zc3h12a-like, NYN domain / : / Zc3h12a-like Ribonuclease NYN domain
Similarity search - Domain/homology
NEDD4-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.882 Å
AuthorsGarg, A. / Heinemann, U.
CitationJournal: To Be Published
Title: Crystal structure of Human N4BP1 KH domains
Authors: Garg, A. / Heinemann, U.
History
DepositionDec 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEDD4-binding protein 1


Theoretical massNumber of molelcules
Total (without water)20,8471
Polymers20,8471
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.690, 108.690, 27.727
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

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Components

#1: Protein NEDD4-binding protein 1 / N4BP1


Mass: 20846.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: N4BP1, KIAA0615 / Production host: Escherichia coli (E. coli) / References: UniProt: O75113
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2016
RadiationMonochromator: Se / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.882→47.06 Å / Num. obs: 15568 / % possible obs: 99.69 % / Redundancy: 6.51 % / Rrim(I) all: 0.063 / Net I/σ(I): 19.78
Reflection shellResolution: 1.882→1.95 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
Cootmodel building
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.882→35.577 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.21
RfactorNum. reflection% reflection
Rfree0.231 779 5 %
Rwork0.1806 --
obs0.1831 15566 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.88 Å2 / Biso mean: 47.8727 Å2 / Biso min: 21.71 Å2
Refinement stepCycle: final / Resolution: 1.882→35.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 0 106 1540
Biso mean---50.75 -
Num. residues----188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061490
X-RAY DIFFRACTIONf_angle_d0.9512021
X-RAY DIFFRACTIONf_chiral_restr0.038232
X-RAY DIFFRACTIONf_plane_restr0.004266
X-RAY DIFFRACTIONf_dihedral_angle_d13.376561
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8823-2.00020.34571280.28052420254899
2.0002-2.15460.25321280.211524442572100
2.1546-2.37140.25531270.196724182545100
2.3714-2.71450.20951300.196324692599100
2.7145-3.41950.26851310.189224722603100
3.4195-35.58350.1981350.153325642699100
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)
16.88730.8863-0.76297.12910.75496.1533-0.04360.50760.5164-0.2219-0.0405-0.209-0.26510.27710.07850.2166-0.0006-0.08080.24650.05450.21347.050643.834621.3305
28.5315-0.09620.78541.2551-0.25891.51820.05860.1594-0.76940.150.010.13580.1376-0.1344-0.05040.29-0.00660.04290.2228-0.04280.327430.909426.130622.9914
32.3118-1.89750.31447.56140.27427.5597-0.0041-0.0571-0.03890.503-0.00580.57880.2073-0.38750.0470.239-0.01720.07520.2768-0.0340.298213.998330.469424.3617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 68 )A-1 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 135)A69 - 135
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 186 )A136 - 186

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