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- PDB-3a4r: The crystal structure of SUMO-like domain 2 in Nip45 -

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Basic information

Entry
Database: PDB / ID: 3a4r
TitleThe crystal structure of SUMO-like domain 2 in Nip45
ComponentsNFATC2-interacting protein
KeywordsTRANSCRIPTION / ubiquitin fold / Coiled coil / Cytoplasm / Methylation / Nucleus
Function / homology
Function and homology information


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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1 Å
AuthorsSekiyama, N. / Arita, K. / Ikeda, Y. / Ariyoshi, M. / Tochio, H. / Saitoh, H. / Shirakawa, M.
CitationJournal: Proteins / Year: 2009
Title: Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45
Authors: Sekiyama, N. / Arita, K. / Ikeda, Y. / Hashiguchi, K. / Ariyoshi, M. / Tochio, H. / Saitoh, H. / Shirakawa, M.
History
DepositionJul 14, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NFATC2-interacting protein
B: NFATC2-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5765
Polymers17,3562
Non-polymers2203
Water4,954275
1
A: NFATC2-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7402
Polymers8,6781
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NFATC2-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8363
Polymers8,6781
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.953, 35.373, 68.943
Angle α, β, γ (deg.)90.00, 97.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NFATC2-interacting protein / Nip45 / Nuclear factor of activated T-cells / cytoplasmic 2-interacting protein / 45 kDa NF-AT- ...Nip45 / Nuclear factor of activated T-cells / cytoplasmic 2-interacting protein / 45 kDa NF-AT-interacting protein / 45 kDa NFAT-interacting protein


Mass: 8677.913 Da / Num. of mol.: 2 / Fragment: SLD2, Ubiquitin-like domain, residues 339-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nip45 / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O09130
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS COORDINATES IN ALL CHAINS USE NON-SEQUENTIAL RESIDUE NUMBERING TO CLARIFY THE EXPRESSION TAGS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3.5M ammonium sulfate, 0.1M TrisHCl, 1% 2-methyl-2,4-pentanediol (MPD), pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONPhoton Factory AR-NW12A20.97919, 0.97931, 0.96408
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDNov 12, 2008
ADSC QUANTUM 2102CCDNov 12, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979191
30.979311
40.964081
ReflectionResolution: 1→50 Å / Num. obs: 62499 / % possible obs: 89.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 7.7 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 17.3
Reflection shellResolution: 1→1.04 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.413 / % possible all: 81.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1→19.811 Å / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.898 / SU ML: 0.06 / σ(F): 1.36 / Phase error: 16.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1836 3132 5.06 %
Rwork0.158 58749 -
obs0.1593 61881 88.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.575 Å2 / ksol: 0.403 e/Å3
Displacement parametersBiso max: 54.23 Å2 / Biso mean: 10.863 Å2 / Biso min: 0.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å20.297 Å2
2---0.458 Å2-0 Å2
3---0.317 Å2
Refinement stepCycle: LAST / Resolution: 1→19.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 13 275 2711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082464
X-RAY DIFFRACTIONf_angle_d1.114448
X-RAY DIFFRACTIONf_dihedral_angle_d14.313628
X-RAY DIFFRACTIONf_chiral_restr0.09183
X-RAY DIFFRACTIONf_plane_restr0.007374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9996-1.01520.27331100.23192225X-RAY DIFFRACTION74
1.0152-1.03190.21831140.1882529X-RAY DIFFRACTION84
1.0319-1.04960.21321350.16592534X-RAY DIFFRACTION85
1.0496-1.06870.18591360.14762549X-RAY DIFFRACTION85
1.0687-1.08930.16581470.13442614X-RAY DIFFRACTION86
1.0893-1.11150.1511340.13032566X-RAY DIFFRACTION86
1.1115-1.13570.18621420.12642599X-RAY DIFFRACTION87
1.1357-1.16210.16551370.12322624X-RAY DIFFRACTION87
1.1621-1.19120.15631490.11992629X-RAY DIFFRACTION88
1.1912-1.22340.13971390.12252627X-RAY DIFFRACTION87
1.2234-1.25940.14551350.12022665X-RAY DIFFRACTION89
1.2594-1.30.15461620.11862669X-RAY DIFFRACTION89
1.3-1.34640.15741420.11722723X-RAY DIFFRACTION90
1.3464-1.40030.15221370.12282706X-RAY DIFFRACTION90
1.4003-1.46410.15941480.12172753X-RAY DIFFRACTION92
1.4641-1.54120.16241640.12572771X-RAY DIFFRACTION92
1.5412-1.63770.16121350.12292837X-RAY DIFFRACTION94
1.6377-1.76410.16041340.12742891X-RAY DIFFRACTION95
1.7641-1.94150.1571630.12752887X-RAY DIFFRACTION95
1.9415-2.22210.14941570.12892898X-RAY DIFFRACTION95
2.2221-2.79840.15981630.14712890X-RAY DIFFRACTION96
2.7984-19.81440.23551490.21322563X-RAY DIFFRACTION82

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