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- PDB-2bka: CC3(TIP30)Crystal Structure -

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Basic information

Entry
Database: PDB / ID: 2bka
TitleCC3(TIP30)Crystal Structure
ComponentsTAT-INTERACTING PROTEIN TIP30
KeywordsTRANSCRIPTION / CC3 / TIP30 / NADPH / PEG600
Function / homology
Function and homology information


import into nucleus / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / positive regulation of programmed cell death / regulation of angiogenesis / nuclear envelope / angiogenesis / protein autophosphorylation / transcription coactivator activity / cell differentiation / oxidoreductase activity ...import into nucleus / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / positive regulation of programmed cell death / regulation of angiogenesis / nuclear envelope / angiogenesis / protein autophosphorylation / transcription coactivator activity / cell differentiation / oxidoreductase activity / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / apoptotic process / positive regulation of transcription by RNA polymerase II / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Oxidoreductase HTATIP2 / Oxidoreductase HTATIP2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsEl Omari, K. / Bird, L.E. / Nichols, C.E. / Ren, J. / Stammers, D.K.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of Cc3 (Tip30): Implications for its Role as a Tumor Suppressor
Authors: El Omari, K. / Bird, L.E. / Nichols, C.E. / Ren, J. / Stammers, D.K.
History
DepositionFeb 14, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2005Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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

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Assembly

Deposited unit
A: TAT-INTERACTING PROTEIN TIP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5837
Polymers27,0911
Non-polymers1,4926
Water6,071337
1
A: TAT-INTERACTING PROTEIN TIP30
hetero molecules

A: TAT-INTERACTING PROTEIN TIP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,16614
Polymers54,1822
Non-polymers2,98412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)68.140, 68.140, 119.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-901-

PE8

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TAT-INTERACTING PROTEIN TIP30 / CC3


Mass: 27091.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET45B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60520, UniProt: Q9BUP3*PLUS

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Non-polymers , 5 types, 343 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE RESIDUE CONFLCIT DESCRIBED IN THE SEQADV RECORDS BELOW IS A NATURAL VARIANT SEEN IN OTHER CC3 ...THE RESIDUE CONFLCIT DESCRIBED IN THE SEQADV RECORDS BELOW IS A NATURAL VARIANT SEEN IN OTHER CC3 SEQUENCES, WHERE THE ARGININE AT POSITION 182 IS REPLACED BY A TRYPTOPHAN. FOR EXAMPLE: GB ENTRY NP006401

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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: 3 Å3/Da / Density % sol: 59 %
Description: MAD DATA WERE COLLECTED FROM A SEMET CRYSTAL AT ESRF BM14
Crystal growpH: 8.4
Details: 1.8M AMMONIUM SULPHATE 0.1M TRIS AT PH 8.4 8% PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 665406 / % possible obs: 100 % / Observed criterion σ(I): -1.5 / Redundancy: 18.5 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 33
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 15.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 6.5 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.58 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1602878.35 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: RESIDUAL, MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1780 5 %RANDOM
Rwork0.166 ---
obs0.166 35941 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.3465 Å2 / ksol: 0.376992 e/Å3
Displacement parametersBiso mean: 20.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.43 Å20 Å2
2---0.22 Å20 Å2
3---0.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 95 337 2258
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.384
X-RAY DIFFRACTIONc_mcangle_it3.216
X-RAY DIFFRACTIONc_scbond_it4.515
X-RAY DIFFRACTIONc_scangle_it6.5610
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.222 174 4.9 %
Rwork0.181 3368 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP

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