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- PDB-3ga0: CtBP1/BARS Gly172->Glu mutant structure: impairing NAD(H) binding... -

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Basic information

Entry
Database: PDB / ID: 3ga0
TitleCtBP1/BARS Gly172->Glu mutant structure: impairing NAD(H) binding and dimerization
ComponentsC-terminal-binding protein 1
KeywordsOXIDOREDUCTASE / TRANSCRIPTION CO-REPRESSION / ACYLTRANSFERASE / BREFELDIN A / NAD / GOLGI MEMBRANE / ACYL-COA / ADP-ribosylation / Cytoplasm / Nucleus / Phosphoprotein / Ubl conjugation
Function / homology
Function and homology information


SUMOylation of transcription cofactors / Repression of WNT target genes / presynapse to nucleus signaling pathway / Deactivation of the beta-catenin transactivating complex / extrinsic component of presynaptic endocytic zone membrane / synaptic vesicle clustering / presynaptic active zone cytoplasmic component / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / acyltransferase activity ...SUMOylation of transcription cofactors / Repression of WNT target genes / presynapse to nucleus signaling pathway / Deactivation of the beta-catenin transactivating complex / extrinsic component of presynaptic endocytic zone membrane / synaptic vesicle clustering / presynaptic active zone cytoplasmic component / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / acyltransferase activity / synaptic vesicle endocytosis / white fat cell differentiation / GABA-ergic synapse / transcription repressor complex / transcription corepressor binding / transcription coregulator binding / PDZ domain binding / transcription corepressor activity / NAD binding / presynapse / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / membrane fusion / transcription coactivator activity / regulation of cell cycle / neuron projection / protein domain specific binding / negative regulation of DNA-templated transcription / glutamatergic synapse / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / identical protein binding / nucleus / cytoplasm
Similarity search - Function
C-terminal binding protein / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain ...C-terminal binding protein / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD 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
FORMIC ACID / C-terminal-binding protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsNardini, M. / Valente, C. / Ricagno, S. / Luini, A. / Corda, D. / Bolognesi, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: CtBP1/BARS Gly172-->Glu mutant structure: impairing NAD(H)-binding and dimerization
Authors: Nardini, M. / Valente, C. / Ricagno, S. / Luini, A. / Corda, D. / Bolognesi, M.
History
DepositionFeb 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-terminal-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6733
Polymers39,5811
Non-polymers922
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: C-terminal-binding protein 1
hetero molecules

A: C-terminal-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3466
Polymers79,1622
Non-polymers1844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area6540 Å2
ΔGint-25.1 kcal/mol
Surface area28670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.197, 89.197, 160.259
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein C-terminal-binding protein 1 / CtBP1 / C-terminal-binding protein 3 / CtBP3 / 50 kDa BFA-dependent ADP-ribosylation substrate / BARS-50


Mass: 39581.195 Da / Num. of mol.: 1 / Fragment: UNP residues 1-350 / Mutation: G172E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ctbp1, Bars, Ctbp3 / Plasmid: PET11D-HIS / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)plyss
References: UniProt: Q9Z2F5, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 1.8-2.1M Ammonium formate, 1.0M Hepes (pH7.5), cross-seeding technique, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3
DetectorDetector: CCD / Date: Dec 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.4→29.8 Å / Num. obs: 5615 / % possible obs: 99.5 % / Redundancy: 4.4 %
Reflection shellResolution: 3.4→3.5 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HKU

1hku


Resolution: 3.4→29.75 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.85 / SU B: 40.232 / SU ML: 0.667 / Cross valid method: THROUGHOUT / ESU R: 0.665 / ESU R Free: 0.846 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.33367 560 10 %RANDOM
Rwork0.26248 ---
obs0.26974 5053 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.689 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20.92 Å20 Å2
2--1.83 Å20 Å2
3----2.75 Å2
Refinement stepCycle: LAST / Resolution: 3.4→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 0 7 2616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONo_angle_deg1.142
LS refinement shellResolution: 3.401→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 38 -
Rwork0.288 355 -
obs--100 %

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