PDB-2ome: Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H)

ID or keywords:

Entry

Database: PDB / ID: 2ome

Title

Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H)

Components

C-terminal-binding protein 2

Keywords

OXIDOREDUCTASE / C-TERMINAL BINDING PROTEIN / CTBP2 / DEHYDROGENASE / STRUCTURAL GENOMICS CONSORTIUM / SGC

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Pilka, E.S. / Guo, K. / Rojkova, A. / Debreczeni, J.E. / Kavanagh, K.L. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. ...

Citation

Journal: To be Published
Title: Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H)
Authors: Pilka, E.S. / Guo, K. / Rojkova, A. / Debreczeni, J.E. / Kavanagh, K.L. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Oppermann, U.

History

Deposition	Jan 22, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 6, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2ome.cif.gz	492.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2ome.ent.gz	406.8 KB	Display	PDB format
PDBx/mmJSON format	2ome.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/om/2ome ftp://data.pdbj.org/pub/pdb/validation_reports/om/2ome	HTTPS FTP

-
Related structure data

Related structure data	1hl3S 1mx3S S: Starting model for refinement
Similar structure data	6v8a-1 4u6q-1 1hku-1 3pzr-2 1qp8-d 4ebf-2 2d0i-2 1t4d-2 2dbr-3 6cdr-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1hl3S

1mx3S

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#167 - Nov 2013 SNARE Proteins similarity (1)

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

304 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: C-terminal-binding protein 2

B: C-terminal-binding protein 2

hetero molecules

defined by author&software
75.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: C-terminal-binding protein 2

D: C-terminal-binding protein 2

hetero molecules

defined by author&software
75.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: C-terminal-binding protein 2

F: C-terminal-binding protein 2

hetero molecules

defined by author&software
75.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: C-terminal-binding protein 2

H: C-terminal-binding protein 2

hetero molecules

defined by author&software
75.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.754, 141.574, 138.215
Angle α, β, γ (deg.)	90.00, 98.93, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 3 / Auth seq-ID: 34 - 362 / Label seq-ID: 6 - 334

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H

#1: Protein	C-terminal-binding protein 2 / CtBP2 Mass: 37274.477 Da / Num. of mol.: 8 / Fragment: Residues 31-364 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTBP2 / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 56.74 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M KSCN, 0.1M BIS-TRIS PROPANE, 20% PEG3350, 10% ETHYLENE GLYCOL, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99991 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 21, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99991 Å / Relative weight: 1
Reflection	Resolution: 2.77→43.31 Å / Num. obs: 84796 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / R_merge(I) obs: 0.148 / R_sym value: 0.162 / Net I/σ(I): 11.6
Reflection shell	Resolution: 2.77→2.92 Å / Redundancy: 5.9 % / R_merge(I) obs: 0.81 / Mean I/σ(I) obs: 2 / R_sym value: 0.89 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MAR345	345DTB	data collection
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries 1MX3, 1HL3

1mx3

1hl3

Resolution: 2.8→43.31 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.9 / SU B: 30.465 / SU ML: 0.3 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25736	4104	5 %	RANDOM
R_work	0.20733	-	-	-
obs	0.2098	78004	99.98 %	-
all	-	84796	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 40.724 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.63 Å²	0 Å²	-0.55 Å²
2-	-	-4.83 Å²	0 Å²
3-	-	-	3.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→43.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20223	0	352	184	20759

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.021	20977
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	13837
X-RAY DIFFRACTION	r_angle_refined_deg	1.458	1.973	28515
X-RAY DIFFRACTION	r_angle_other_deg	1.116	3	33574
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.348	5	2635
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.744	23.508	972
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.854	15	3379
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.542	15	188
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	3283
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	23591
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	4305
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	4159
X-RAY DIFFRACTION	r_nbd_other	0.195	0.2	14266
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	10078
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	11775
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	404
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.023	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.181	0.2	10
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.178	0.2	18
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.27	0.2	2
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.349	1.5	13575
X-RAY DIFFRACTION	r_mcbond_other	0.128	1.5	5390
X-RAY DIFFRACTION	r_mcangle_it	0.548	2	20924
X-RAY DIFFRACTION	r_scbond_it	1.253	3	8470
X-RAY DIFFRACTION	r_scangle_it	2.014	4.5	7591
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1930	tight positional	0.04	0.05
2	B	1930	tight positional	0.04	0.05
3	C	1930	tight positional	0.04	0.05
4	D	1930	tight positional	0.04	0.05
5	E	1930	tight positional	0.04	0.05
6	F	1930	tight positional	0.04	0.05
7	G	1930	tight positional	0.03	0.05
8	H	1930	tight positional	0.04	0.05
1	A	2050	loose positional	0.4	5
2	B	2050	loose positional	0.37	5
3	C	2050	loose positional	0.39	5
4	D	2050	loose positional	0.45	5
5	E	2050	loose positional	0.51	5
6	F	2050	loose positional	0.4	5
7	G	2050	loose positional	0.47	5
8	H	2050	loose positional	0.42	5
1	A	1930	tight thermal	0.07	0.5
2	B	1930	tight thermal	0.07	0.5
3	C	1930	tight thermal	0.08	0.5
4	D	1930	tight thermal	0.07	0.5
5	E	1930	tight thermal	0.06	0.5
6	F	1930	tight thermal	0.07	0.5
7	G	1930	tight thermal	0.06	0.5
8	H	1930	tight thermal	0.07	0.5
1	A	2050	loose thermal	1.23	10
2	B	2050	loose thermal	1.16	10
3	C	2050	loose thermal	1.11	10
4	D	2050	loose thermal	1.01	10
5	E	2050	loose thermal	1.14	10
6	F	2050	loose thermal	1.08	10
7	G	2050	loose thermal	1.05	10
8	H	2050	loose thermal	1.06	10

LS refinement shell

Resolution: 2.8→2.872 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.387	298	-
R_work	0.361	5765	-
obs	-	-	100 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.2218	0.4041	-0.1077	3.4584	-0.6024	1.6492	0.1284	0.1556	-0.3536	-0.4701	-0.1088	0.2122	0.2852	0.1155	-0.0196	-0.1701	0.0778	-0.2226	-0.1656	-0.1082	-0.0942	15.525	-3.5471	5.2843
2	1.5598	-0.5827	-0.5366	2.7668	0.5926	2.1457	0.253	0.2205	0.2951	-0.4782	-0.0566	-0.466	-0.3931	0.3094	-0.1964	-0.1784	-0.0076	0.0327	-0.058	-0.0437	-0.1626	32.1865	27.7267	6.9872
3	1.5388	0.513	0.4424	3.3065	0.564	1.4577	-0.032	-0.0899	-0.0585	0.3652	-0.1072	0.4182	-0.2301	-0.0419	0.1392	-0.1343	0.068	-0.0124	-0.2394	-0.0098	-0.2701	10.2374	38.4504	35.2989
4	1.4804	0.3421	0.257	1.8088	0.5216	1.5408	-0.0559	-0.2185	-0.354	0.2975	-0.1423	0.8519	0.1522	-0.4137	0.1982	-0.1511	-0.0073	0.1554	-0.1283	-0.0569	0.3615	-7.6206	7.5268	32.1255
5	1.6382	0.4488	0.31	2.6596	0.401	1.3104	0.0973	-0.4086	0.3956	0.8789	-0.2255	1.2529	-0.0532	-0.3991	0.1282	0.134	-0.0296	0.4479	-0.0617	-0.0873	0.4669	3.0779	-28.3094	53.5182
6	1.0443	0.5653	0.2327	3.5448	1.1432	2.1079	0.2259	-0.016	0.1313	0.282	-0.1182	0.762	0.1945	-0.1163	-0.1077	-0.1371	-0.0082	0.0471	-0.2191	0.0708	-0.0524	11.8168	-59.1611	38.2784
7	2.6275	0.8143	-0.0785	3.4489	0.3194	1.889	-0.1475	0.0704	-0.8363	0.1622	0.047	-0.8612	0.4368	0.5415	0.1004	-0.1185	0.1163	0.0934	0.0354	0.0304	0.0584	47.472	-47.9929	38.4223
8	1.3617	-0.522	0.4036	4.6161	-0.236	1.6389	-0.0117	0.011	0.1897	0.6038	-0.1399	-0.2861	-0.2328	0.2213	0.1516	0.0124	-0.0605	-0.0434	-0.1073	0.0528	-0.3224	38.3738	-16.9758	52.5326

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	33 - 362	5 - 334
2	X-RAY DIFFRACTION	2	B	B	33 - 362	5 - 334
3	X-RAY DIFFRACTION	3	C	C	33 - 362	5 - 334
4	X-RAY DIFFRACTION	4	D	D	33 - 362	5 - 334
5	X-RAY DIFFRACTION	5	E	E	33 - 362	5 - 334
6	X-RAY DIFFRACTION	6	F	F	33 - 362	5 - 334
7	X-RAY DIFFRACTION	7	G	G	33 - 362	5 - 334
8	X-RAY DIFFRACTION	8	H	H	33 - 362	5 - 334

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi