PDB-1yde: Crystal Structure of Human Retinal Short-Chain Dehydrogenase/Redu...

ID or keywords:

Entry

Database: PDB / ID: 1yde

Title

Crystal Structure of Human Retinal Short-Chain Dehydrogenase/Reductase 3

Components

Retinal dehydrogenase/reductase 3

Keywords

OXIDOREDUCTASE / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

D-threo-aldose 1-dehydrogenase / D-threo-aldose 1-dehydrogenase activity / Estrogen biosynthesis / L-fucose catabolic process / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid catabolic process / identical protein binding / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Lukacik, P. / Bunkozci, G. / Kavanagh, K. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC)

Citation

Journal: Biochem.J. / Year: 2007
Title: Structural and biochemical characterization of human orphan DHRS10 reveals a novel cytosolic enzyme with steroid dehydrogenase activity.
Authors: Lukacik, P. / Keller, B. / Bunkoczi, G. / Kavanagh, K.L. / Kavanagh, K. / Lee, W.H. / Hwa Lee, W. / Adamski, J. / Oppermann, U.

History

Deposition	Dec 23, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 18, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Mar 14, 2012	Group: Database references
Revision 1.4	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1yde.cif.gz	706.4 KB	Display	PDBx/mmCIF format
PDB format	pdb1yde.ent.gz	584 KB	Display	PDB format
PDBx/mmJSON format	1yde.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	1yde_validation.pdf.gz	498.5 KB	Display	wwPDB validaton report
Full document	1yde_full_validation.pdf.gz	538.1 KB	Display
Data in XML	1yde_validation.xml.gz	74 KB	Display
Data in CIF	1yde_validation.cif.gz	121.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yd/1yde ftp://data.pdbj.org/pub/pdb/validation_reports/yd/1yde	HTTPS FTP

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Related structure data

Similar structure data	2dtd-1 6pei-d 2dtx-1 5jsf-1 3uxy-d 1uls-2 2dte-1 4dqx-d 4xgn-1 2ag5-d 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: Retinal dehydrogenase/reductase 3

B: Retinal dehydrogenase/reductase 3

C: Retinal dehydrogenase/reductase 3

D: Retinal dehydrogenase/reductase 3

E: Retinal dehydrogenase/reductase 3

F: Retinal dehydrogenase/reductase 3

G: Retinal dehydrogenase/reductase 3

H: Retinal dehydrogenase/reductase 3

I: Retinal dehydrogenase/reductase 3

J: Retinal dehydrogenase/reductase 3

K: Retinal dehydrogenase/reductase 3

L: Retinal dehydrogenase/reductase 3

M: Retinal dehydrogenase/reductase 3

N: Retinal dehydrogenase/reductase 3

O: Retinal dehydrogenase/reductase 3

P: Retinal dehydrogenase/reductase 3

453 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Retinal dehydrogenase/reductase 3

B: Retinal dehydrogenase/reductase 3

C: Retinal dehydrogenase/reductase 3

D: Retinal dehydrogenase/reductase 3

defined by author&software
113 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Retinal dehydrogenase/reductase 3

F: Retinal dehydrogenase/reductase 3

G: Retinal dehydrogenase/reductase 3

H: Retinal dehydrogenase/reductase 3

defined by author&software
113 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

I: Retinal dehydrogenase/reductase 3

J: Retinal dehydrogenase/reductase 3

K: Retinal dehydrogenase/reductase 3

L: Retinal dehydrogenase/reductase 3

defined by author&software
113 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

M: Retinal dehydrogenase/reductase 3

N: Retinal dehydrogenase/reductase 3

O: Retinal dehydrogenase/reductase 3

P: Retinal dehydrogenase/reductase 3

defined by author&software
113 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	167.115, 98.823, 167.463
Angle α, β, γ (deg.)	90.00, 115.87, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	TYR	TYR	A	A	4 - 253	4 - 253
2	1	GLY	GLY	TYR	TYR	C	C	4 - 253	4 - 253
3	1	GLY	GLY	TYR	TYR	E	E	4 - 253	4 - 253
4	1	ARG	ARG	GLY	GLY	G	G	6 - 252	6 - 252
5	1	TYR	TYR	TYR	TYR	I	I	7 - 253	7 - 253
6	1	GLY	GLY	TYR	TYR	K	K	4 - 253	4 - 253
7	1	LYS	LYS	TYR	TYR	M	M	10 - 253	10 - 253
8	1	TYR	TYR	TYR	TYR	O	O	7 - 253	7 - 253
1	2	GLY	GLY	SER	SER	D	D	4 - 258	4 - 258
2	2	THR	THR	ALA	ALA	B	B	3 - 257	3 - 257
3	2	GLY	GLY	ARG	ARG	F	F	4 - 259	4 - 259
4	2	THR	THR	SER	SER	H	H	5 - 258	5 - 258
5	2	GLY	GLY	SER	SER	J	J	4 - 258	4 - 258
6	2	GLY	GLY	SER	SER	L	L	4 - 258	4 - 258
7	2	LYS	LYS	ALA	ALA	N	N	10 - 257	10 - 257
8	2	ARG	ARG	ARG	ARG	P	P	6 - 259	6 - 259

NCS ensembles :

ID
1
2

Details

Biological subunit is a tetramer, of which there are 4 in the ASU.

#1: Protein	Retinal dehydrogenase/reductase 3 Mass: 28329.393 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: retSDR3A-p11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BPX1
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1251 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 49.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Magnesium Acetate, MPD, cacodylate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 7, 2004
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.4→30 Å / Num. all: 176307 / Num. obs: 176307 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / B_iso Wilson estimate: 34.1 Å² / R_merge(I) obs: 0.117 / R_sym value: 0.117 / Net I/σ(I): 9.1
Reflection shell	Resolution: 2.4→2.53 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.706 / Mean I/σ(I) obs: 1.8 / Num. unique all: 17963 / R_sym value: 0.706 / % possible all: 0.648

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.911 / SU B: 17.186 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22903	3559	2 %	RANDOM
R_work	0.18067	-	-	-
all	0.18166	172629	-	-
obs	0.18166	172629	91.88 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 5.147 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.69 Å²	0 Å²	0.75 Å²
2-	-	-2.41 Å²	0 Å²
3-	-	-	1.38 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	29359	0	0	1251	30610

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	29913
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	28244
X-RAY DIFFRACTION	r_angle_refined_deg	1.505	1.979	40683
X-RAY DIFFRACTION	r_angle_other_deg	0.919	3	65404
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.808	5	3987
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.459	24.042	1153
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.884	15	4768
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.4	15	217
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	4758
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	33868
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	5709
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	6483
X-RAY DIFFRACTION	r_nbd_other	0.186	0.2	28937
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	14990
X-RAY DIFFRACTION	r_nbtor_other	0.088	0.2	18046
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	1312
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.073	0.2	3
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.154	0.2	44
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.274	0.2	222
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.227	0.2	20
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	1.413	3	20396
X-RAY DIFFRACTION	r_mcbond_other	0.346	3	8294
X-RAY DIFFRACTION	r_mcangle_it	2.116	5	31575
X-RAY DIFFRACTION	r_scbond_it	4.158	8	10825
X-RAY DIFFRACTION	r_scangle_it	5.927	11	9107
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1415	tight positional	0.06	0.05
1	2	C	1415	tight positional	0.06	0.05
1	3	E	1415	tight positional	0.06	0.05
1	4	G	1415	tight positional	0.06	0.05
1	5	I	1415	tight positional	0.05	0.05
1	6	K	1415	tight positional	0.05	0.05
1	7	M	1415	tight positional	0.03	0.05
1	8	O	1415	tight positional	0.03	0.05
2	1	D	1391	tight positional	0.05	0.05
2	2	B	1391	tight positional	0.05	0.05
2	3	F	1391	tight positional	0.04	0.05
2	4	H	1391	tight positional	0.05	0.05
2	5	J	1391	tight positional	0.05	0.05
2	6	L	1391	tight positional	0.04	0.05
2	7	N	1391	tight positional	0.03	0.05
2	8	P	1391	tight positional	0.03	0.05
1	1	A	2006	medium positional	0.48	0.5
1	2	C	2006	medium positional	0.39	0.5
1	3	E	2006	medium positional	0.45	0.5
1	4	G	2006	medium positional	0.4	0.5
1	5	I	2006	medium positional	0.42	0.5
1	6	K	2006	medium positional	0.44	0.5
1	7	M	2006	medium positional	0.47	0.5
1	8	O	2006	medium positional	0.44	0.5
2	1	D	1944	medium positional	0.34	0.5
2	2	B	1944	medium positional	0.43	0.5
2	3	F	1944	medium positional	0.5	0.5
2	4	H	1944	medium positional	0.45	0.5
2	5	J	1944	medium positional	0.42	0.5
2	6	L	1944	medium positional	0.46	0.5
2	7	N	1944	medium positional	0.46	0.5
2	8	P	1944	medium positional	0.45	0.5
1	1	A	1415	tight thermal	1.49	10
1	2	C	1415	tight thermal	1.59	10
1	3	E	1415	tight thermal	1.52	10
1	4	G	1415	tight thermal	1.67	10
1	5	I	1415	tight thermal	1.69	10
1	6	K	1415	tight thermal	1.51	10
1	7	M	1415	tight thermal	2.01	10
1	8	O	1415	tight thermal	2.18	10
2	1	D	1391	tight thermal	1.72	10
2	2	B	1391	tight thermal	2.19	10
2	3	F	1391	tight thermal	1.61	10
2	4	H	1391	tight thermal	1.83	10
2	5	J	1391	tight thermal	2.03	10
2	6	L	1391	tight thermal	1.85	10
2	7	N	1391	tight thermal	2.04	10
2	8	P	1391	tight thermal	1.91	10
1	1	A	2006	medium thermal	2.3	10
1	2	C	2006	medium thermal	2.34	10
1	3	E	2006	medium thermal	2.49	10
1	4	G	2006	medium thermal	2.2	10
1	5	I	2006	medium thermal	2.31	10
1	6	K	2006	medium thermal	2.41	10
1	7	M	2006	medium thermal	2.28	10
1	8	O	2006	medium thermal	2.7	10
2	1	D	1944	medium thermal	2.43	10
2	2	B	1944	medium thermal	2.67	10
2	3	F	1944	medium thermal	2.33	10
2	4	H	1944	medium thermal	2.2	10
2	5	J	1944	medium thermal	2.29	10
2	6	L	1944	medium thermal	2.53	10
2	7	N	1944	medium thermal	2.72	10
2	8	P	1944	medium thermal	2.65	10

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.322	113	-
R_work	0.265	5090	-
obs	-	-	37.09 %

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