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- PDB-1mx3: Crystal structure of CtBP dehydrogenase core holo form -

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Basic information

Entry
Database: PDB / ID: 1mx3
TitleCrystal structure of CtBP dehydrogenase core holo form
ComponentsC-terminal binding protein 1
KeywordsTRANSCRIPTION REPRESSOR / nuclear protein / phosphorylation / Transcriptional Corepressor
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 / transcription corepressor binding / SUMOylation of transcription cofactors / 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 Rossmann-like Domain ...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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / C-terminal-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsKumar, V. / Carlson, J.E. / Ohgi, K.E. / Edwards, T.E. / Rose, D.W. / Escalante, C.R. / Aggarwal, A.K.
CitationJournal: Mol.Cell / Year: 2002
Title: Transcription Corepressor CtBP Is an NAD+-Regulated Dehydrogenase
Authors: Kumar, V. / Carlson, J.E. / Ohgi, K.E. / Edwards, T.E. / Rose, D.W. / Escalante, C.R. / Aggarwal, A.K.
History
DepositionOct 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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: C-terminal binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8633
Polymers38,1391
Non-polymers7232
Water7,476415
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)77,7266
Polymers76,2792
Non-polymers1,4474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+2/31
Buried area8330 Å2
ΔGint-43 kcal/mol
Surface area25590 Å2
MethodPISA
3
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)155,45212
Polymers152,5584
Non-polymers2,8948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
crystal symmetry operation12_565x,x-y+1,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)89.100, 89.100, 164.000
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


Mass: 38139.469 Da / Num. of mol.: 1 / Fragment: residues 28-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTBP1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) pLysS / References: UniProt: Q13363
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 48 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: sodium formate, magnesium acetate, HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1140 mMsodium formate11
270 mMmagnesium acetate11
3100 mMHEPES11pH7.0

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Data collection

Diffraction
IDCrystal-ID
11
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.14
SYNCHROTRONAPS 32-ID20.97957, 0.97941, 0.96859
Detector
IDDetector
1CCD
2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.141
20.979571
30.979411
40.968591
ReflectionResolution: 1.95→50 Å / Num. all: 52834 / Num. obs: 52854 / % possible obs: 99 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.041
Reflection
*PLUS
Num. measured all: 173537
Reflection shell
*PLUS
% possible obs: 94.1 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.253 2642 5 %
Rwork0.211 --
all-52834 -
obs-52834 99 %
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 48 415 2975
Refinement
*PLUS
Lowest resolution: 50 Å / Num. reflection obs: 50259 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.53

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