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- PDB-3fau: Crystal Structure of human small-MutS related domain -

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Basic information

Entry
Database: PDB / ID: 3fau
TitleCrystal Structure of human small-MutS related domain
ComponentsNEDD4-binding protein 2
KeywordsHYDROLASE / smr / small-MutS related domain / nicking endonuclease / Alternative splicing / ATP-binding / Coiled coil / Cytoplasm / Nucleotide-binding / Phosphoprotein / Polymorphism / Ubl conjugation
Function / homology
Function and homology information


ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / Hydrolases / DNA endonuclease activity / ubiquitin binding / endonuclease activity / ATP binding / cytosol
Similarity search - Function
Domain of unknown function DUF1771 / NEDD4-binding protein 2, CUE domain / Domain of unknown function (DUF1771) / DUF1771 / Ribosomal Protein S8; Chain: A, domain 1 - #110 / Smr domain superfamily / Smr domain / Small MutS-related domain / Smr domain / Smr domain profile. ...Domain of unknown function DUF1771 / NEDD4-binding protein 2, CUE domain / Domain of unknown function (DUF1771) / DUF1771 / Ribosomal Protein S8; Chain: A, domain 1 - #110 / Smr domain superfamily / Smr domain / Small MutS-related domain / Smr domain / Smr domain profile. / Ubiquitin system component CUE / CUE domain profile. / AAA domain / Ribosomal Protein S8; Chain: A, domain 1 / UBA-like superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NEDD4-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsKim, T.G. / Kwon, T.H. / Ryu, E.K. / Min, K. / Heo, S.-D. / Song, K.M. / Jun, W.J. / Jung, E.
CitationJournal: To be Published
Title: Strcutral Dynamincs of the Endonuclease Small-MutS Related Domains of BCL3 binding protein
Authors: Kim, T.G. / Kwon, T.H. / Ban, C. / Ku, J.K.
History
DepositionNov 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEDD4-binding protein 2
B: NEDD4-binding protein 2
C: NEDD4-binding protein 2
D: NEDD4-binding protein 2


Theoretical massNumber of molelcules
Total (without water)36,6314
Polymers36,6314
Non-polymers00
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NEDD4-binding protein 2

D: NEDD4-binding protein 2


Theoretical massNumber of molelcules
Total (without water)18,3152
Polymers18,3152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area860 Å2
ΔGint-7 kcal/mol
Surface area9680 Å2
MethodPISA
3
B: NEDD4-binding protein 2
C: NEDD4-binding protein 2


Theoretical massNumber of molelcules
Total (without water)18,3152
Polymers18,3152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-10 kcal/mol
Surface area9080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.490, 57.106, 71.356
Angle α, β, γ (deg.)90.000, 97.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NEDD4-binding protein 2 / N4BP2 / BCL-3-binding protein


Mass: 9157.736 Da / Num. of mol.: 4 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Hela cDNA / Gene: B3BP, KIAA1413, N4BP2 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86UW6, Hydrolases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 1.9 Å3/Da / Density % sol: 35.27 % / Description: The file contains Friedel pairs. / Mosaicity: 0.24 °
Crystal growTemperature: 293 K / Method: hanging drop / pH: 7
Details: 0.1M Ammonium Chloride, 0.1M Mops (pH 7.0), 40% PEG 2000mme, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 24, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 42988 / % possible obs: 97.3 % / Redundancy: 5 % / Rmerge(I) obs: 0.041 / Χ2: 1.241 / Net I/σ(I): 46.607
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.217 / Num. unique all: 3817 / Χ2: 0.692 / % possible all: 87

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementStarting model: PDB ENTRY 2D9I

2d9i


Resolution: 1.9→44.419 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.84 / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.96 / Stereochemistry target values: ML / Details: The file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1094 5.05 %RANDOM
Rwork0.187 ---
obs0.19 42970 50.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.987 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso max: 73.09 Å2 / Biso mean: 22.518 Å2 / Biso min: 6.33 Å2
Baniso -1Baniso -2Baniso -3
1--2.455 Å20 Å2-1.697 Å2
2--4.195 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 0 304 2736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092474
X-RAY DIFFRACTIONf_angle_d1.1313304
X-RAY DIFFRACTIONf_chiral_restr0.078369
X-RAY DIFFRACTIONf_plane_restr0.005411
X-RAY DIFFRACTIONf_dihedral_angle_d16.037946
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 51 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.9870.2531350.18525302665
1.987-2.0910.2461320.18125762708
2.091-2.2220.2251590.16325422701
2.222-2.3940.2681290.16625822711
2.394-2.6350.2471350.18725862721
2.635-3.0160.291310.20225802711
3.016-3.7990.2211370.17526082745
3.799-44.4310.2181360.20225452681

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