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- PDB-4lcj: CtBP2 in complex with substrate MTOB -

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Basic information

Entry
Database: PDB / ID: 4lcj
TitleCtBP2 in complex with substrate MTOB
ComponentsC-terminal-binding protein 2
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE SUBSTRATE / Rossmann Fold / Transcriptional Corepressor / D-isomer 2-hydroxyacid dehydrogenase / OXIDOREDUCTASE-OXIDOREDUCTASE SUBSTRATE complex
Function / homology
Function and homology information


positive regulation of retinoic acid receptor signaling pathway / Signaling by TCF7L2 mutants / Repression of WNT target genes / Sensory processing of sound by inner hair cells of the cochlea / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / white fat cell differentiation / transcription repressor complex / viral genome replication / transcription coregulator binding / transcription corepressor binding ...positive regulation of retinoic acid receptor signaling pathway / Signaling by TCF7L2 mutants / Repression of WNT target genes / Sensory processing of sound by inner hair cells of the cochlea / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / white fat cell differentiation / transcription repressor complex / viral genome replication / transcription coregulator binding / transcription corepressor binding / NAD binding / transcription corepressor activity / DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / synapse / regulation of transcription by RNA polymerase II / protein-containing complex binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
C-terminal binding protein / : / 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 ...C-terminal binding protein / : / 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
4-(METHYLSULFANYL)-2-OXOBUTANOIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / C-terminal-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.86 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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

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Assembly

Deposited unit
A: C-terminal-binding protein 2
B: C-terminal-binding protein 2
C: C-terminal-binding protein 2
D: C-terminal-binding protein 2
E: C-terminal-binding protein 2
F: C-terminal-binding protein 2
G: C-terminal-binding protein 2
H: C-terminal-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,65124
Polymers308,1598
Non-polymers6,49316
Water3,693205
1
A: C-terminal-binding protein 2
B: C-terminal-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6636
Polymers77,0402
Non-polymers1,6234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-46 kcal/mol
Surface area24410 Å2
MethodPISA
2
C: C-terminal-binding protein 2
D: C-terminal-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6636
Polymers77,0402
Non-polymers1,6234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-44 kcal/mol
Surface area24290 Å2
MethodPISA
3
E: C-terminal-binding protein 2
F: C-terminal-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6636
Polymers77,0402
Non-polymers1,6234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-46 kcal/mol
Surface area24340 Å2
MethodPISA
4
G: C-terminal-binding protein 2
H: C-terminal-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6636
Polymers77,0402
Non-polymers1,6234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-46 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.151, 140.605, 135.126
Angle α, β, γ (deg.)90.000, 97.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
C-terminal-binding protein 2 / CtBP2


Mass: 38519.828 Da / Num. of mol.: 8 / Fragment: UNP residues 31-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTBP2 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RIL / References: UniProt: P56545
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / 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.: 8 / Source method: obtained synthetically / Formula: C5H8O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200 mM potassium nitrate, 15-20% PEG 3350, 100 mM bis tris propane, pH 7.0, 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: Jun 30, 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: 4.1 % / Av σ(I) over netI: 13.24 / Number: 298092 / Rmerge(I) obs: 0.093 / Χ2: 1 / D res high: 2.86 Å / D res low: 50 Å / Num. obs: 73374 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.165098.610.0520.9964
4.896.1699.910.0710.9964
4.274.8999.910.0730.9944.1
3.884.2799.910.0861.0024.1
3.63.8899.910.1040.9924.1
3.393.699.710.1250.9974.1
3.223.3999.610.1671.0054.1
3.083.229910.2331.0064.1
2.963.0898.710.3130.9994.1
2.862.9698.810.3891.0034
ReflectionResolution: 2.86→50 Å / Num. all: 73837 / Num. obs: 73374 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.093 / Χ2: 0.999 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.86-2.9640.38972631.003198.8
2.96-3.084.10.31372530.999198.7
3.08-3.224.10.23372761.006199
3.22-3.394.10.16773191.005199.6
3.39-3.64.10.12573550.997199.7
3.6-3.884.10.10473390.992199.9
3.88-4.274.10.08673681.002199.9
4.27-4.894.10.07373770.994199.9
4.89-6.1640.07174290.996199.9
6.16-5040.05273950.996198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.86 Å32.3 Å
Translation2.86 Å32.3 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.1phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→32.303 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.36 / σ(F): 1.34 / Phase error: 28.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 3692 5.04 %Random
Rwork0.2139 ---
obs0.2158 73303 99.2 %-
all-73327 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.94 Å2 / Biso mean: 52.6922 Å2 / Biso min: 29.8 Å2
Refinement stepCycle: LAST / Resolution: 2.86→32.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19394 0 424 205 20023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00920200
X-RAY DIFFRACTIONf_angle_d1.21927553
X-RAY DIFFRACTIONf_chiral_restr0.0573243
X-RAY DIFFRACTIONf_plane_restr0.0073581
X-RAY DIFFRACTIONf_dihedral_angle_d17.3417111
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.86-2.89410.33191210.31212545266693
2.8941-2.93370.32451280.292648277699
2.9337-2.97560.34261370.28192666280399
2.9756-3.020.3291480.28452651279999
3.02-3.06710.281520.28132655280799
3.0671-3.11740.29591530.26482608276199
3.1174-3.17110.38141240.26782681280599
3.1711-3.22870.28981170.26982681279899
3.2287-3.29080.35031490.26792673282299
3.2908-3.35790.28941340.243126712805100
3.3579-3.43080.31841430.242227232866100
3.4308-3.51050.2791510.232126352786100
3.5105-3.59820.28531460.236327082854100
3.5982-3.69530.24021460.220626662812100
3.6953-3.80390.30041260.215327092835100
3.8039-3.92650.25381600.213826892849100
3.9265-4.06660.21051630.196626552818100
4.0666-4.22910.22831450.19526992844100
4.2291-4.42110.23581330.187126802813100
4.4211-4.65350.20731570.175326892846100
4.6535-4.94410.21181290.176126982827100
4.9441-5.32430.22191640.179126882852100
5.3243-5.85720.23941380.203427322870100
5.8572-6.69820.22961460.217127222868100
6.6982-8.41430.20611360.181727262862100
8.4143-32.30460.20581460.18462713285998

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