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- PDB-4lce: CtBP1 in complex with substrate MTOB -

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Basic information

Entry
Database: PDB / ID: 4lce
TitleCtBP1 in complex with substrate MTOB
ComponentsC-terminal-binding protein 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE SUBSTRATE / Rossmann Fold / Transcriptional Co-repressor / D-isomer 2-hydroxyacid dehydrogenase / OXIDOREDUCTASE-OXIDOREDUCTASE SUBSTRATE complex
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 / white fat cell differentiation / synaptic vesicle endocytosis / 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 / white fat cell differentiation / synaptic vesicle endocytosis / GABA-ergic synapse / transcription repressor complex / viral genome replication / transcription corepressor binding / SUMOylation of transcription cofactors / transcription coregulator binding / Deactivation of the beta-catenin transactivating complex / 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 phosphorylation / negative regulation of cell population proliferation / 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 / 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 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 ...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
4-(METHYLSULFANYL)-2-OXOBUTANOIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / C-terminal-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 Å
AuthorsHilbert, B.J. / Schiffer, C.A. / Royer Jr., W.E.
CitationJournal: Febs Lett. / Year: 2014
Title: Crystal structures of human CtBP in complex with substrate MTOB reveal active site features useful for inhibitor design.
Authors: Hilbert, B.J. / Grossmann, S.R. / Schiffer, C.A. / Royer, W.E.
History
DepositionJun 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Revision 1.5Feb 28, 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)38,9513
Polymers38,1391
Non-polymers8122
Water1,51384
1
A: C-terminal-binding protein 1
hetero molecules

A: C-terminal-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9026
Polymers76,2792
Non-polymers1,6234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area8160 Å2
ΔGint-43 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.970, 88.970, 161.538
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-574-

HOH

21A-579-

HOH

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Components

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


Mass: 38139.469 Da / Num. of mol.: 1 / Fragment: Dehydrogenase Domain (UNP residues 28-353)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTBP, CTBP1 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RIL
References: UniProt: Q13363, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-KMT / 4-(METHYLSULFANYL)-2-OXOBUTANOIC ACID


Mass: 148.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 250 mM magnesium chloride, 140 mM sodium formate, 100 mM hepes, 2.5 mM NAD+, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2011
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionRedundancy: 10.7 % / Av σ(I) over netI: 31.92 / Number: 167249 / Rmerge(I) obs: 0.065 / Χ2: 1 / D res high: 2.38 Å / D res low: 50 Å / Num. obs: 15565 / % possible obs: 97.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.135091.610.0391.0079.1
4.075.1391.110.0531.0069.1
3.554.0797.110.0621.0059.8
3.233.5599.310.0691.00410.8
33.2399.810.0840.99811.2
2.82310010.1110.99811.3
2.682.8299.910.1551.00211.5
2.562.6810010.2091.00711.5
2.472.5699.910.2651.00711.5
2.382.4799.910.391.00811.6
ReflectionResolution: 2.38→50 Å / Num. all: 15930 / Num. obs: 15565 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rmerge(I) obs: 0.065 / Χ2: 1.004 / Net I/σ(I): 16.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.38-2.4711.60.3915411.008199.9
2.47-2.5611.50.26515511.007199.9
2.56-2.6811.50.20915451.0071100
2.68-2.8211.50.15515471.002199.9
2.82-311.30.11115680.9981100
3-3.2311.20.08415670.998199.8
3.23-3.5510.80.06915761.004199.3
3.55-4.079.80.06215631.005197.1
4.07-5.139.10.05314811.006191.1
5.13-509.10.03916261.007191.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.9 Å
Translation2.5 Å29.9 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMAC5.7.0025refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→29.92 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 8.305 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.394 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 769 5 %RANDOM
Rwork0.2004 ---
obs0.2023 15420 97.02 %-
all-15893 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 104.18 Å2 / Biso mean: 55.5441 Å2 / Biso min: 25.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.38→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 53 84 2587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192608
X-RAY DIFFRACTIONr_bond_other_d0.0010.022436
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9993561
X-RAY DIFFRACTIONr_angle_other_deg0.76135566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55223.784111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47515400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5681520
X-RAY DIFFRACTIONr_chiral_restr0.0710.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
LS refinement shellResolution: 2.38→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 47 -
Rwork0.312 1074 -
all-1121 -
obs--99.12 %

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