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- PDB-3rd2: NIP45 SUMO-like Domain 2 -

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Basic information

Entry
Database: PDB / ID: 3rd2
TitleNIP45 SUMO-like Domain 2
ComponentsNFATC2-interacting protein
KeywordsTRANSCRIPTION / SUMO-like domain 2 / protein:protein interaction / Ubc9
Function / homology
Function and homology information


protein sumoylation / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
: / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
NFATC2-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsPerry, J.J.P. / Arvai, A.S. / Tainer, J.A.
CitationJournal: Mol.Cell.Biol. / Year: 2011
Title: DNA repair and global sumoylation are regulated by distinct Ubc9 noncovalent complexes.
Authors: Prudden, J. / Perry, J.J. / Nie, M. / Vashisht, A.A. / Arvai, A.S. / Hitomi, C. / Guenther, G. / Wohlschlegel, J.A. / Tainer, J.A. / Boddy, M.N.
History
DepositionMar 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Sep 13, 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: NFATC2-interacting protein


Theoretical massNumber of molelcules
Total (without water)9,3671
Polymers9,3671
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.521, 32.446, 32.925
Angle α, β, γ (deg.)90.000, 96.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NFATC2-interacting protein / 45 kDa NF-AT-interacting protein / 45 kDa NFAT-interacting protein / Nuclear factor of activated T- ...45 kDa NF-AT-interacting protein / 45 kDa NFAT-interacting protein / Nuclear factor of activated T-cells / cytoplasmic 2-interacting protein


Mass: 9366.596 Da / Num. of mol.: 1 / Fragment: SUMO-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFATC2IP, NIP45 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NCF5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.84 Å3/Da / Density % sol: 33.23 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 1.7 M ammonium 118 sulfate, 100 mM Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.13 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 9145 / Num. obs: 8880 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 40.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GOE

3goe


Resolution: 1.6→32.703 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 431 4.86 %Random
Rwork0.1696 ---
obs0.1716 8866 96.99 %-
all-9141 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.784 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 50.2 Å2 / Biso mean: 18.9507 Å2 / Biso min: 7.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.3223 Å20 Å2-0.0361 Å2
2---0.0471 Å2-0 Å2
3---0.3694 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms652 0 0 108 760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005674
X-RAY DIFFRACTIONf_angle_d1.023906
X-RAY DIFFRACTIONf_chiral_restr0.07595
X-RAY DIFFRACTIONf_plane_restr0.003118
X-RAY DIFFRACTIONf_dihedral_angle_d13.207255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.83250.25981510.18652630278192
1.8325-2.30870.20811370.158728833020100
2.3087-32.71010.20061430.16812922306599

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