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- PDB-7kwm: CtBP1 (28-375) L182F/V185T - AMP -

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Basic information

Entry
Database: PDB / ID: 7kwm
TitleCtBP1 (28-375) L182F/V185T - AMP
ComponentsC-terminal-binding protein 1
KeywordsTRANSCRIPTION / C-terminal Binding Protein / Co-transcriptional factor / D-isomer specific 2-hydroxyacid dehydrogenase
Function / homology
Function and homology information


Signaling by TCF7L2 mutants / Repression of WNT target genes / 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 / lncRNA binding / white fat cell differentiation / synaptic vesicle endocytosis / Notch signaling pathway ...Signaling by TCF7L2 mutants / Repression of WNT target genes / 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 / lncRNA binding / white fat cell differentiation / synaptic vesicle endocytosis / Notch signaling pathway / transcription repressor complex / SUMOylation of transcription cofactors / viral genome replication / transcription corepressor binding / transcription coregulator binding / Deactivation of the beta-catenin transactivating complex / GABA-ergic synapse / NAD binding / transcription corepressor activity / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / protein phosphorylation / regulation of cell cycle / protein domain specific binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
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 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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 domain superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / C-terminal-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRoyer, W.E. / Del Campo, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM119014 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: NAD(H) phosphates mediate tetramer assembly of human C-terminal binding protein (CtBP).
Authors: Nichols, J.C. / Schiffer, C.A. / Royer Jr., W.E.
History
DepositionDec 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,9293
Polymers38,5421
Non-polymers3872
Water1,982110
1
A: C-terminal-binding protein 1
hetero molecules

A: C-terminal-binding protein 1
hetero molecules

A: C-terminal-binding protein 1
hetero molecules

A: C-terminal-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,71712
Polymers154,1674
Non-polymers1,5498
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_564x,x-y+1,-z-1/31
Unit cell
Length a, b, c (Å)89.262, 89.262, 163.658
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-590-

HOH

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Components

#1: Protein C-terminal-binding protein 1 / CtBP1


Mass: 38541.844 Da / Num. of mol.: 1 / Fragment: UNP residues 28-356 / Mutation: L182F, V185T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTBP1, CTBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q13363
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 140 mM calcium chloride, 4% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 10, 2020 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→30.16 Å / Num. obs: 17800 / % possible obs: 99.4 % / Redundancy: 7.4 % / Biso Wilson estimate: 41.86 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.108 / Net I/σ(I): 17.65
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 1723 / CC1/2: 0.22

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Processing

Software
NameVersionClassification
CrysalisPro1.15.2_3472data collection
PHENIX1.15.2_3472refinement
Cootmodel building
PHASERphasing
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6V89

6v89


Resolution: 2.3→30.16 Å / SU ML: 0.3069 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3505
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2601 884 4.98 %
Rwork0.2105 16850 -
obs0.213 17734 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 1 110 2655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372605
X-RAY DIFFRACTIONf_angle_d0.67863541
X-RAY DIFFRACTIONf_chiral_restr0.0419411
X-RAY DIFFRACTIONf_plane_restr0.004464
X-RAY DIFFRACTIONf_dihedral_angle_d9.31732122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.34851390.28262680X-RAY DIFFRACTION98.12
2.44-2.630.29721450.26572770X-RAY DIFFRACTION99.93
2.63-2.90.33211460.25672761X-RAY DIFFRACTION100
2.9-3.320.2751470.23122800X-RAY DIFFRACTION99.93
3.32-4.180.2381490.19192832X-RAY DIFFRACTION99.63
4.18-30.160.22561580.17893007X-RAY DIFFRACTION99.25
Refinement TLS params.Method: refined / Origin x: 2.86964836314 Å / Origin y: 32.7417958547 Å / Origin z: -26.3962133346 Å
111213212223313233
T0.200090850309 Å2-0.0519368828102 Å2-0.00846526329129 Å2-0.363146552874 Å2-0.0376050424708 Å2--0.296854862371 Å2
L0.527330567062 °2-0.375060883822 °20.188478738852 °2-0.692738216021 °2-0.291416660685 °2--0.904534952777 °2
S0.0289911130796 Å °0.0570334795651 Å °0.0200414958479 Å °-0.0509083073062 Å °-0.0114578820196 Å °-0.154382200264 Å °0.054389229429 Å °0.227386833744 Å °-0.0172623519219 Å °
Refinement TLS groupSelection details: all

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