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- PDB-6v89: Human CtBP1 (28-375) in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 6v89
TitleHuman CtBP1 (28-375) in complex with AMP
ComponentsC-terminal-binding protein 1
KeywordsTRANSCRIPTION / co-transcriptional factor
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 / synaptic vesicle endocytosis / white fat cell differentiation / GABA-ergic synapse / transcription repressor complex ...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 / synaptic vesicle endocytosis / white fat cell differentiation / GABA-ergic synapse / transcription repressor complex / viral genome replication / SUMOylation of transcription cofactors / transcription corepressor binding / Deactivation of the beta-catenin transactivating complex / transcription coregulator binding / transcription corepressor activity / NAD binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / regulation of cell cycle / protein domain specific binding / negative regulation of cell population proliferation / protein phosphorylation / 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 / 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 dehydrogenase, NAD-binding domain conserved site 1 / 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, 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: 2.45 Å
AuthorsRoyer, W.E.
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 10, 2019Deposition 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 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)40,9955
Polymers40,5371
Non-polymers4584
Water2,738152
1
A: C-terminal-binding protein 1
hetero molecules

A: C-terminal-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,99110
Polymers81,0742
Non-polymers9168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/31
Buried area7990 Å2
ΔGint-93 kcal/mol
Surface area25330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.944, 88.944, 163.720
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-702-

HOH

21A-721-

HOH

31A-724-

HOH

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Components

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


Mass: 40537.094 Da / Num. of mol.: 1 / Fragment: UNP residues 28-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTBP1, CTBP / Production host: Escherichia coli (E. coli)
References: UniProt: Q13363, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 80-200 mM calcium chloride, 2-6% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 13982 / % possible obs: 94.4 % / Redundancy: 7.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Χ2: 1.029 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.45-2.492.50.5975020.82169.6
2.49-2.543.10.515270.885174.1
2.54-2.593.60.4525850.915180.9
2.59-2.644.20.4465850.966183.1
2.64-2.74.70.3996610.885189.6
2.7-2.765.30.4036721.012195
2.76-2.8360.3667141.067199.4
2.83-2.97.30.3087321.0761100
2.9-2.999.30.2637301.0611100
2.99-3.0910.10.2177311.0881100
3.09-3.210.10.1987201.0861100
3.2-3.32100.1557351.123199.9
3.32-3.489.90.1547291.035199.9
3.48-3.669.20.1427411.046199.6
3.66-3.899.60.1157460.9531100
3.89-4.199.30.087290.924198.2
4.19-4.619.80.0587500.962199.7
4.61-5.289.90.0517660.997199.5
5.28-6.659.90.0577801.038199.1
6.65-509.10.0518471.118196.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXv1.15refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CDF

6cdf


Resolution: 2.45→36.14 Å / SU ML: 0.3851 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0665
RfactorNum. reflection% reflection
Rfree0.2735 684 5.01 %
Rwork0.231 --
obs0.2331 13660 92.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.61 Å2
Refinement stepCycle: LAST / Resolution: 2.45→36.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 3 152 2675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00152607
X-RAY DIFFRACTIONf_angle_d0.46613557
X-RAY DIFFRACTIONf_chiral_restr0.0386420
X-RAY DIFFRACTIONf_plane_restr0.0028466
X-RAY DIFFRACTIONf_dihedral_angle_d7.2322112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.640.3821090.30112089X-RAY DIFFRACTION76.96
2.64-2.90.39461390.29482630X-RAY DIFFRACTION95.85
2.9-3.320.26241430.26682707X-RAY DIFFRACTION97.84
3.32-4.190.29371370.24122603X-RAY DIFFRACTION92.85
4.19-36.140.22261560.18622947X-RAY DIFFRACTION98.23
Refinement TLS params.Method: refined / Origin x: 3.05071588489 Å / Origin y: 32.2686866215 Å / Origin z: -26.4542509842 Å
111213212223313233
T0.258308378944 Å20.00104098436132 Å20.0081805136392 Å2-0.374310797814 Å2-0.0291432444319 Å2--0.309275745006 Å2
L0.64098498103 °2-0.315202506923 °20.419424344211 °2-0.643404938653 °2-0.338789894612 °2--1.05593222147 °2
S0.0408198156541 Å °0.0844693461787 Å °-0.0248623222203 Å °-0.0743569374526 Å °-0.0195301393165 Å °-0.136284190455 Å °0.0815805863342 Å °0.272259191396 Å °0.0052582372212 Å °
Refinement TLS groupSelection details: all

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