PDB-3qwf: Crystal structure of the 17beta-hydroxysteroid dehydrogenase from...

ID or keywords:

Entry

Database: PDB / ID: 3qwf

Title

Crystal structure of the 17beta-hydroxysteroid dehydrogenase from Cochliobolus lunatus

Components

17beta-hydroxysteroid dehydrogenase

Keywords

OXIDOREDUCTASE / HYDROXYSTEROID DEHYDROGENASE / SHORT CHAIN DEHYDROGENASE/REDUCTASE / SDR STEROID / FUNGI / COCHLIOBOLUS LUNATUS / Rossmann Fold / Cytosol

Function / homology

Function and homology information

oxidoreductase activity, acting on CH-OH group of donors / nucleotide binding
Similarity search - Function

Biological species

Cochliobolus lunatus (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.88 Å

Authors

Cassetta, A. / Lamba, D. / Krastanova, I. / Stojan, J. / Lanisnik-Rizner, T. / Kristan, K. / Brunskole, M.

Citation

Journal: Biochem.J. / Year: 2012
Title: Structural Studies on a Fungal 17Beta-Hydroxysteroid Dehydrogenase
Authors: Cassetta, A. / Krastanova, I. / Kristan, K. / Brunskole Svegelj, M. / Lamba, D. / Lanisnik Rizner, T. / Stojan, J.

History

Deposition	Feb 28, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 18, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3qwf.cif.gz	814.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3qwf.ent.gz	681.5 KB	Display	PDB format
PDBx/mmJSON format	3qwf.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3qwf_validation.pdf.gz	3.3 MB	Display	wwPDB validaton report
Full document	3qwf_full_validation.pdf.gz	3.3 MB	Display
Data in XML	3qwf_validation.xml.gz	89.4 KB	Display
Data in CIF	3qwf_validation.cif.gz	123.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qw/3qwf ftp://data.pdbj.org/pub/pdb/validation_reports/qw/3qwf	HTTPS FTP

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Related structure data

Related structure data	3qwiC 3is3S 3itd 3qwh S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4fj1-1 3qwh-2 4fiz-1 4fj1-2 4fj0-2 3csd-d 3itd-1 4fj0-1 3qwi-2 3qwh-1 3ri3-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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

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: 17beta-hydroxysteroid dehydrogenase

B: 17beta-hydroxysteroid dehydrogenase

C: 17beta-hydroxysteroid dehydrogenase

D: 17beta-hydroxysteroid dehydrogenase

E: 17beta-hydroxysteroid dehydrogenase

F: 17beta-hydroxysteroid dehydrogenase

G: 17beta-hydroxysteroid dehydrogenase

H: 17beta-hydroxysteroid dehydrogenase

hetero molecules

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

1

A: 17beta-hydroxysteroid dehydrogenase

B: 17beta-hydroxysteroid dehydrogenase

hetero molecules

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

2

C: 17beta-hydroxysteroid dehydrogenase

D: 17beta-hydroxysteroid dehydrogenase

hetero molecules

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

3

E: 17beta-hydroxysteroid dehydrogenase

F: 17beta-hydroxysteroid dehydrogenase

hetero molecules

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

4

G: 17beta-hydroxysteroid dehydrogenase

H: 17beta-hydroxysteroid dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.520, 67.830, 138.890
Angle α, β, γ (deg.)	84.20, 85.31, 66.57
Int Tables number	1
Space group name H-M	P1

#1: Protein	17beta-hydroxysteroid dehydrogenase Mass: 28936.545 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cochliobolus lunatus (fungus) / Strain: M118 / Gene: 17HSDcl / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): JM107 References: UniProt: O93874, 17beta-estradiol 17-dehydrogenase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1314 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.41 %
Crystal grow	Method: vapor diffusion, hanging drop / pH: 8 Details: 20% (W/V) PEG 6000, 25% (V/V) GLYCEROL, 0.1M TRIS, 5MM NADPH SODIUM SALT, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 / Wavelength: 0.939 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2008 / Details: RH COATED, SILICON TOROIDAL FOCUSING MIRROR
Radiation	Monochromator: SI (111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.939 Å / Relative weight: 1
Reflection	Resolution: 1.88→53.4 Å / Num. all: 170185 / Num. obs: 170185 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / R_merge(I) obs: 0.056 / R_sym value: 0.056 / Net I/σ(I): 10.1
Reflection shell	Resolution: 1.88→1.98 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.526 / Mean I/σ(I) obs: 1.6 / R_sym value: 0.526 / % possible all: 94.9

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Processing

Software

Name	Version	Classification
DNA		data collection
MOLREP		phasing
REFMAC	5.5.0094	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3IS3

3is3

Resolution: 1.88→37.45 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.958 / SU B: 7.318 / SU ML: 0.096 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19438	8540	5 %	RANDOM
R_work	0.16514	-	-	-
obs	0.16663	161632	95.95 %	-
all	-	170171	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 34.2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.15 Å²	-0.07 Å²	0.01 Å²
2-	-	0.02 Å²	-0.01 Å²
3-	-	-	-0.11 Å²

Refine analyze

Luzzati coordinate error obs: 0.284 Å

Refinement step

Cycle: LAST / Resolution: 1.88→37.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15768	0	444	1314	17526

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	16546
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.133	1.968	22466
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.608	5	2080
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.034	23.678	696
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.386	15	2592
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.967	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	2528
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	12392
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.389	1.5	10280
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.701	2	16472
X-RAY DIFFRACTION	r_scbond_it	1.17	3	6266
X-RAY DIFFRACTION	r_scangle_it	1.841	4.5	5994
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.88→1.929 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.353	570	-
R_work	0.314	11774	-
obs	-	-	93.76 %

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	2.1539	-0.4882	0.4445	1.4064	-0.1051	1.8326	0.0444	-0.2817	0.0337	0.0921	0.0298	-0.2084	0.1265	0.2783	-0.0742	0.0915	-0.0143	-0.0405	0.1416	-0.0207	0.1452	1.1278	0.4662	-1.521
2	1.9956	-0.0948	0.7141	1.2117	-0.0692	2.075	-0.1059	-0.3435	0.2966	0.0882	-0.0075	0.0452	-0.2334	-0.2942	0.1133	0.1031	0.0123	-0.0078	0.0905	-0.0876	0.1939	-20.4158	20.6787	-9.4822
3	1.6416	-0.1723	0.7815	1.6053	0.285	2.2479	0.0393	0.5282	0.1147	-0.3242	-0.0555	-0.1659	-0.0615	0.3109	0.0162	0.1728	-0.0117	0.0362	0.1834	0.0329	0.1205	-15.3576	10.5779	-39.1094
4	1.9553	-0.0155	1.29	1.3276	-0.1056	2.1778	0.4295	0.3098	-0.5947	-0.1397	-0.035	0.0591	0.7498	0.2065	-0.3945	0.373	0.0839	-0.1448	0.0676	-0.126	0.3176	-9.7944	-16.482	-26.3076
5	1.4463	-0.3831	-0.4166	1.4359	0.2751	1.8361	0.102	0.2402	0.2512	-0.1524	-0.074	-0.0808	-0.3199	-0.0254	-0.028	0.2014	-0.0054	0.0066	0.2053	0.0932	0.1618	-34.7283	23.0637	42.7451
6	1.5105	-0.4607	-0.1875	1.3067	-0.0456	1.8435	-0.13	-0.2694	-0.0987	0.1738	0.0746	0.1693	0.0145	-0.1955	0.0554	0.1447	0.0016	0.0511	0.2426	0.0356	0.1193	-40.169	10.0638	71.3266
7	1.6737	-0.7953	-0.4812	1.3484	0.2913	2.1323	-0.0344	0.3943	-0.2711	-0.122	-0.1443	0.2695	0.1976	-0.2602	0.1786	0.164	-0.064	-0.0023	0.2663	-0.0435	0.1657	-29.9849	-5.8334	33.3943
8	1.5657	-0.6361	-0.4846	0.9351	0.699	1.9974	-0.2348	-0.2819	-0.1953	0.1987	0.1124	-0.036	0.3439	0.3619	0.1224	0.2266	0.0565	0.0552	0.2303	0.1071	0.1703	-18.9526	-10.3248	62.8917

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	C	10 - 270
2	X-RAY DIFFRACTION	1	C	273
3	X-RAY DIFFRACTION	1	C	274 - 1307
4	X-RAY DIFFRACTION	2	A	10 - 270
5	X-RAY DIFFRACTION	2	A	273
6	X-RAY DIFFRACTION	2	A	274 - 1307
7	X-RAY DIFFRACTION	3	B	10 - 270
8	X-RAY DIFFRACTION	3	B	272
9	X-RAY DIFFRACTION	3	B	274 - 1311
10	X-RAY DIFFRACTION	4	D	10 - 270
11	X-RAY DIFFRACTION	4	D	272
12	X-RAY DIFFRACTION	4	D	274 - 1308
13	X-RAY DIFFRACTION	5	E	10 - 270
14	X-RAY DIFFRACTION	5	E	272
15	X-RAY DIFFRACTION	5	E	273 - 1300
16	X-RAY DIFFRACTION	6	F	10 - 270
17	X-RAY DIFFRACTION	6	F	272
18	X-RAY DIFFRACTION	6	F	273 - 1309
19	X-RAY DIFFRACTION	7	G	10 - 270
20	X-RAY DIFFRACTION	7	G	272
21	X-RAY DIFFRACTION	8	H	10 - 270
22	X-RAY DIFFRACTION	8	H	272
23	X-RAY DIFFRACTION	8	H	273 - 1286

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