PDB-6h0m: 17beta-hydroxysteroid dehydrogenase type 14 mutant K158A in compl...

Basic information

• Entry: Database: PDB / ID: 6h0m
• Title: 17beta-hydroxysteroid dehydrogenase type 14 mutant K158A in complex with Nicotinamide Adenine Dinucleotide
• Components: 17-beta-hydroxysteroid dehydrogenase 14
• Keywords: OXIDOREDUCTASE / mutant hsd cofactor nad complex

Function / homology

Function:

Estrogen biosynthesis / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)] activity / steroid catabolic process / identical protein binding / cytosol

Domain/homology:

Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Component:

beta-D-glucopyranose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 17-beta-hydroxysteroid dehydrogenase 14

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
• Authors: Badran, M. / Klebe, G. / Heine, A. / Marchais-Oberwinkler, S.
• Citation: Journal: To Be Published; Title: 17beta-hydroxysteroid dehydrogenase type 14 mutant K158A in complex with Nicotinamide Adenine Dinucleotide; Authors: Badran, M. / Klebe, G. / Heine, A. / Merabet, A. / Bertoletti, N. / Marchais-Oberwinkler, S.

History

Deposition	Jul 10, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 31, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Assembly

Deposited unit

A: 17-beta-hydroxysteroid dehydrogenase 14

hetero molecules

Summary:

• 29.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	29,216	5
Polymers	28,271	1
Non-polymers	945	4
Water	3,801	211

1

A: 17-beta-hydroxysteroid dehydrogenase 14

hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14

hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14

hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14

hetero molecules

Summary:

• defined by author&software
• Evidence: mass spectrometry
• 117 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	116,864	20
Polymers	113,085	4
Non-polymers	3,779	16
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_565	-x,-y+1,z	1
crystal symmetry operation	5_555	-x,y,-z	1
crystal symmetry operation	6_565	x,-y+1,-z	1

Calculated values:

Buried area	23050 Å2
ΔGint	-193 kcal/mol
Surface area	33130 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	91.590, 91.590, 131.112
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	97
Space group name H-M	I422

Components on special symmetry positions

ID	Model	Components
1	1	A-458- HOH
2	1	A-541- HOH
3	1	A-601- HOH
4	1	A-611- HOH

Components

Protein / Sugars , 2 types, 2 molecules A

#1: Protein

A 17-beta-hydroxysteroid dehydrogenase 14 / 17-beta-HSD 14 / 17-beta-hydroxysteroid dehydrogenase DHRS10 / Dehydrogenase/reductase SDR family member 10 / Retinal short-chain dehydrogenase/reductase retSDR3 / Short chain dehydrogenase/reductase family 47C member 1

Details:

Mass: 28271.295 Da / Num. of mol.: 1 / Mutation: K158A
Source method: isolated from a genetically manipulated source
Details: mutation K158A / Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

#5: Sugar

A-304 ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose

Details:

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

Identifier:

Identifier	Type	Program
DGlcpb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
b-D-glucopyranose	COMMON NAME	GMML 1.0
b-D-Glcp	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
Glc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

Non-polymers , 4 types, 214 molecules

#2: Chemical

A-301 ChemComp-NA / SODIUM ION

Details:

Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

#3: Chemical

A-302 ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide

Details:

Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM

#4: Chemical

A-303 ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide

Details:

Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM

#6: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.43 ų/Da / Density % sol: 49.47 %
• Crystal grow: Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: PEG 6000 20% W/V HEPES 0.1 M DMSO 5% / PH range: 6.5 - 7.5

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2018
• Radiation: Monochromator: x-ray / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9184 Å / Relative weight: 1
• Reflection: Resolution: 1.25→50 Å / Num. obs: 76893 / % possible obs: 99.9 % / Redundancy: 10.1 % / CC_1/2: 1 / R_rim(I) all: 0.047 / R_sym value: 0.045 / Χ²: 0.97 / Net I/σ(I): 27.1
• Reflection shell: Resolution: 1.25→1.33 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 4.1 / Num. unique obs: 12249 / CC_1/2: 0.921 / R_rim(I) all: 0.547 / R_sym value: 0.495 / Χ²: 59.77 / % possible all: 99.7

Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ICM

5icm

Resolution: 1.25→46.072 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 10.93

	Rfactor	Num. reflection	% reflection
Rfree	0.1472	3845	5 %
Rwork	0.1264	-	-
obs	0.1274	76889	99.93 %

• Solvent computation: Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.25→46.072 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1856	0	61	211	2128

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2039
X-RAY DIFFRACTION	f_angle_d	1.015	2801
X-RAY DIFFRACTION	f_dihedral_angle_d	23.305	756
X-RAY DIFFRACTION	f_chiral_restr	0.078	329
X-RAY DIFFRACTION	f_plane_restr	0.006	390

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
1.2495-1.2653	0.1509	140	0.1493	2653	X-RAY DIFFRACTION	99
1.2653-1.282	0.1739	140	0.1391	2663	X-RAY DIFFRACTION	100
1.282-1.2995	0.1796	140	0.1329	2673	X-RAY DIFFRACTION	100
1.2995-1.3181	0.1617	140	0.1344	2647	X-RAY DIFFRACTION	100
1.3181-1.3378	0.1555	142	0.1247	2694	X-RAY DIFFRACTION	100
1.3378-1.3587	0.1539	141	0.1265	2693	X-RAY DIFFRACTION	100
1.3587-1.3809	0.1401	141	0.1101	2667	X-RAY DIFFRACTION	100
1.3809-1.4048	0.138	140	0.1078	2663	X-RAY DIFFRACTION	100
1.4048-1.4303	0.142	141	0.1076	2683	X-RAY DIFFRACTION	100
1.4303-1.4578	0.1316	141	0.103	2684	X-RAY DIFFRACTION	100
1.4578-1.4876	0.1273	141	0.1008	2678	X-RAY DIFFRACTION	100
1.4876-1.5199	0.1225	141	0.0946	2677	X-RAY DIFFRACTION	100
1.5199-1.5553	0.1144	142	0.0952	2696	X-RAY DIFFRACTION	100
1.5553-1.5942	0.115	141	0.0931	2679	X-RAY DIFFRACTION	100
1.5942-1.6373	0.1266	143	0.0981	2710	X-RAY DIFFRACTION	100
1.6373-1.6855	0.1227	141	0.0973	2682	X-RAY DIFFRACTION	100
1.6855-1.7399	0.1231	142	0.1007	2702	X-RAY DIFFRACTION	100
1.7399-1.8021	0.1397	142	0.1026	2704	X-RAY DIFFRACTION	100
1.8021-1.8742	0.119	142	0.1078	2692	X-RAY DIFFRACTION	100
1.8742-1.9595	0.1286	143	0.1146	2717	X-RAY DIFFRACTION	100
1.9595-2.0628	0.1461	142	0.1188	2707	X-RAY DIFFRACTION	100
2.0628-2.1921	0.1242	144	0.1167	2728	X-RAY DIFFRACTION	100
2.1921-2.3613	0.1487	144	0.1209	2737	X-RAY DIFFRACTION	100
2.3613-2.5989	0.1387	144	0.1246	2728	X-RAY DIFFRACTION	100
2.5989-2.9749	0.1276	145	0.1385	2769	X-RAY DIFFRACTION	100
2.9749-3.7478	0.1686	147	0.1451	2780	X-RAY DIFFRACTION	100
3.7478-46.1038	0.1925	155	0.16	2938	X-RAY DIFFRACTION	100