PDB-4wec: Crystal structure of a Short chain dehydrogenase from Mycobacteri...

ID or keywords:

Entry

Database: PDB / ID: 4wec

Title

Crystal structure of a Short chain dehydrogenase from Mycobacterium smegmatis

Components

Short chain dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / Mycobacerium smegmatis / Short chain dehydrogenase / reductase SDR / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Collaborative Crystallography

Function / homology

Function and homology information

nucleotide binding
Similarity search - Function

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of a Short chain dehydrogenase from Mycobacterium smegmatis
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Sankaran, B. / Dranow, D.M. / Lorimer, D. / Edwards, T.E.

History

Deposition	Sep 9, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 8, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 29, 2014	Group: Database references
Revision 1.2	Nov 22, 2017	Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / software / struct_keywords Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3	Sep 27, 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 / pdbx_struct_conn_angle / refine_hist / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4wec.cif.gz	413.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4wec.ent.gz	335.4 KB	Display	PDB format
PDBx/mmJSON format	4wec.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4wec_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	4wec_full_validation.pdf.gz	1.8 MB	Display
Data in XML	4wec_validation.xml.gz	51 KB	Display
Data in CIF	4wec_validation.cif.gz	73.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/we/4wec ftp://data.pdbj.org/pub/pdb/validation_reports/we/4wec	HTTPS FTP

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Related structure data

Related structure data	1iy8S S: Starting model for refinement
Similar structure data	3gvc-2 6zzs-2 3pk0-2 3gvc-1 3tox-3 3rih-d 6gtu-1 2bgl-1 1yde-3 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
Other databases	TargetTrack: SSGCID-MysmA.00391.b

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Short chain dehydrogenase

B: Short chain dehydrogenase

C: Short chain dehydrogenase

D: Short chain dehydrogenase

hetero molecules

120 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

2

A: Short chain dehydrogenase

D: Short chain dehydrogenase

hetero molecules

B: Short chain dehydrogenase

C: Short chain dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.900, 96.640, 81.540
Angle α, β, γ (deg.)	90.000, 101.940, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR Mass: 29171.895 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2598, MSMEI_2536 / Plasmid: MysmA.00391.b.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QVJ7

#1: Protein

Short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR

Mass: 29171.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2598, MSMEI_2536 / Plasmid: MysmA.00391.b.A1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QVJ7

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Non-polymers , 5 types, 1079 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1063 / 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: 2.57 Å³/Da / Density % sol: 52 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: EmeraldBio JCSG+ screen E9: 1.6 M Magnesium sulfate, 0.1 M MES pH 6.5; MysmA.00391.b.A1.PS00660 at 21.3mg/ml; cryo: 25% ethylene glycol; tray 236637e9, puck vsr8-15

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.9774 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2012

Radiation

Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9774 Å / Relative weight: 1

Reflection

Resolution: 1.55→50 Å / Num. obs: 147821 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / B_iso Wilson estimate: 14.23 Å² / R_merge F obs: 0.108 / R_merge(I) obs: 0.051 / R_rim(I) all: 0.06 / Χ²: 0.986 / Net I/σ(I): 17.16 / Num. measured all: 546099

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.55-1.59		3.7	0.624	0.488	2.98	39679	11173	10777	0.571	96.5
1.59-1.63			0.536	0.414	3.5	38974	10931	10561	0.484	96.6
1.63-1.68			0.437	0.348	4.13	37961	10563	10233	0.406	96.9
1.68-1.73			0.393	0.309	4.59	37153	10265	9972	0.361	97.1
1.73-1.79			0.312	0.244	5.75	36107	9933	9663	0.285	97.3
1.79-1.85			0.23	0.183	7.55	35141	9663	9413	0.214	97.4
1.85-1.92			0.185	0.152	9.13	33826	9277	9060	0.177	97.7
1.92-2			0.14	0.118	11.4	32550	8945	8750	0.138	97.8
2-2.09			0.102	0.092	14.26	31500	8639	8450	0.107	97.8
2.09-2.19			0.076	0.071	17.79	29703	8158	7998	0.083	98
2.19-2.31			0.064	0.06	20.49	28417	7830	7676	0.07	98
2.31-2.45			0.052	0.052	23.26	26762	7392	7261	0.061	98.2
2.45-2.62			0.043	0.045	26.63	25063	6938	6832	0.052	98.5
2.62-2.83			0.034	0.037	30.63	23261	6491	6393	0.044	98.5
2.83-3.1			0.027	0.031	35.58	21271	5961	5883	0.037	98.7
3.1-3.47			0.023	0.028	40.25	18732	5412	5329	0.033	98.5
3.47-4			0.017	0.023	47.88	17385	4775	4734	0.026	99.1
4-4.9			0.015	0.02	51.55	14959	4048	4022	0.024	99.4
4.9-6.93			0.014	0.02	49.81	11695	3163	3146	0.023	99.5
	6.93		0.012	0.017	53.22	5960	1760	1668	0.02	94.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PHENIX	3.15	refinement
Coot		model building
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1iy8, modified with CCP4 program CHAINSAW

1iy8

Resolution: 1.55→41.33 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.78 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1961	7429	5.03 %	Random
R_work	0.1652	140343	-	-
obs	0.1667	147772	97.72 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 91.84 Å² / B_iso mean: 23.5417 Å² / B_iso min: 8.37 Å²

Refinement step

Cycle: final / Resolution: 1.55→41.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7408	0	206	1063	8677
B_iso mean	-	-	29.57	33.38	-
Num. residues	-	-	-	-	1023

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7873
X-RAY DIFFRACTION	f_angle_d	1.07	10734
X-RAY DIFFRACTION	f_chiral_restr	0.04	1281
X-RAY DIFFRACTION	f_plane_restr	0.005	1400
X-RAY DIFFRACTION	f_dihedral_angle_d	14.154	2821

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.55-1.5676	0.2652	236	0.2421	4698	4934	96
1.5676-1.5861	0.2785	220	0.2274	4570	4790	97
1.5861-1.6054	0.2494	237	0.2243	4663	4900	97
1.6054-1.6257	0.2878	229	0.219	4574	4803	97
1.6257-1.6471	0.239	223	0.22	4655	4878	97
1.6471-1.6697	0.2416	237	0.2037	4634	4871	97
1.6697-1.6935	0.2419	243	0.201	4631	4874	97
1.6935-1.7188	0.2324	284	0.1934	4589	4873	97
1.7188-1.7457	0.2322	261	0.1914	4604	4865	97
1.7457-1.7743	0.2135	223	0.1834	4689	4912	97
1.7743-1.8049	0.196	262	0.1804	4623	4885	97
1.8049-1.8377	0.2393	256	0.1817	4616	4872	98
1.8377-1.8731	0.2225	270	0.1755	4656	4926	98
1.8731-1.9113	0.1872	264	0.1721	4653	4917	98
1.9113-1.9528	0.2083	256	0.1742	4661	4917	98
1.9528-1.9983	0.2136	226	0.1676	4676	4902	98
1.9983-2.0482	0.2003	243	0.1696	4698	4941	98
2.0482-2.1036	0.1976	268	0.1638	4645	4913	98
2.1036-2.1655	0.2039	240	0.1573	4703	4943	98
2.1655-2.2354	0.1791	260	0.1569	4681	4941	98
2.2354-2.3153	0.1877	204	0.1582	4721	4925	98
2.3153-2.408	0.193	279	0.1621	4685	4964	98
2.408-2.5176	0.2028	232	0.1717	4726	4958	98
2.5176-2.6503	0.2159	262	0.16	4703	4965	98
2.6503-2.8163	0.1904	263	0.1633	4732	4995	99
2.8163-3.0337	0.1909	259	0.1662	4700	4959	99
3.0337-3.3389	0.1879	267	0.1565	4734	5001	99
3.3389-3.8217	0.1834	232	0.1511	4799	5031	99
3.8217-4.8138	0.1583	242	0.1347	4810	5052	99
4.8138-41.3443	0.1599	251	0.1514	4814	5065	98

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	1.4079	0.5188	-0.587	1.4528	-0.1837	1.5293	-0.0094	-0.0212	-0.0103	0.0159	0.0529	0.1373	0.0329	-0.0338	-0.045	0.1453	-0.0148	0.0363	0.1017	0.0291	0.1053	-8.5989	-30.1595	37.9518
2	0.7813	-0.1572	-0.1445	1.5486	-0.1858	0.7658	0.0105	0.0603	0.0333	-0.071	0.0463	0.1158	-0.0017	-0.0699	-0.0628	0.1022	-0.0188	0.0135	0.1019	-0.0014	0.0856	-2.9894	-14.7708	29.9252
3	1.6017	-0.7698	-0.2421	0.3693	0.1198	0.0334	0.0067	0.4991	0.0838	-0.5949	-0.0562	1.0391	0.0408	-0.9037	0.315	0.3567	-0.0817	-0.1995	0.586	0.0532	0.4678	-17.2549	-24.8873	12.8424
4	0.4622	0.188	-0.1778	1.509	0.0326	1.5458	-0.0916	0.1526	-0.0176	-0.2661	0.1084	0.1778	-0.0048	-0.2298	-0.0072	0.1434	-0.0236	-0.0123	0.1318	-0.0016	0.1036	-1.4166	-25.9794	16.3127
5	1.591	-0.4515	-0.922	0.9348	0.518	1.3875	0.1435	0.061	0.2878	-0.2293	0.0235	-0.214	-0.2387	-0.0224	-0.1573	0.2369	0.0248	0.1023	0.1106	0.0045	0.1921	3.5941	15.2094	20.7744
6	0.9198	-0.3054	-0.5375	1.9365	0.0275	1.272	0.0881	-0.0404	0.0919	0.0534	0.0283	-0.1558	-0.0756	0.0529	-0.0902	0.1142	-0.0081	0.0217	0.0781	-0.0218	0.094	3.9134	-1.4832	26.4731
7	1.5641	-0.0389	0.1618	1.7744	-0.4222	0.8867	0.0752	-0.0994	0.0828	0.0545	0.0172	-0.3912	-0.1415	0.0401	-0.0871	0.1412	-0.003	0.0322	0.1171	-0.0429	0.1954	18.4687	-3.3967	21.0101
8	0.953	-0.6774	-0.3689	1.2839	0.1387	1.5423	-0.1256	0.0327	-0.1533	-0.1411	0.0524	-0.2626	0.2659	0.133	0.0873	0.2199	0.0076	0.0778	0.1072	-0.0211	0.221	17.5747	-47.0485	16.2905
9	1.0616	-0.2041	0.2444	2.1567	0.3009	0.7359	0.1026	0.2094	-0.0803	-0.4751	0.0622	0.0015	0.1971	-0.0155	-0.0071	0.3624	-0.0218	0.0327	0.1234	-0.0372	0.1946	14.129	-46.2941	5.2686
10	1.0614	0.0452	-0.1056	1.657	-0.2739	1.1993	-0.0479	0.0193	0.0227	-0.2937	0.0101	-0.404	0.1073	0.1006	-0.0097	0.1943	-0.0097	0.0826	0.1071	-0.0251	0.2067	21.3391	-29.2815	9.133
11	2.4657	0.1743	-0.2577	2.5542	0.0996	1.4337	-0.0557	-0.2319	-0.1006	0.1044	0.0908	-0.4543	0.2093	0.2487	-0.0973	0.1253	0.0283	0.0028	0.1193	-0.0314	0.1808	18.2419	-31.7761	20.3237
12	0.702	0.0877	-0.333	1.6102	0.0377	1.1033	-0.0522	-0.0665	0.0023	0.0723	0.0775	-0.3306	0.0735	0.1754	-0.0165	0.097	0.0158	-0.0031	0.1012	-0.0207	0.1457	15.8217	-26.9692	26.286
13	2.214	-0.0735	-0.9513	1.002	-0.2078	1.4609	0.0125	0.2345	0.094	-0.5386	-0.0599	-0.4622	-0.1731	-0.064	-0.1118	0.3004	-0.0319	0.2411	0.1687	0.0134	0.3729	29.2581	-1.6079	-3.7204
14	1.2221	0.4903	-0.2776	2.0413	-0.135	0.8609	-0.1367	0.132	-0.0325	-0.5784	0.0308	-0.3161	0.1539	-0.0342	0.0628	0.3288	-0.019	0.1325	0.1628	-0.0093	0.2698	25.3621	-19.9742	-1.1639
15	3.0976	1.7467	0.4445	3.244	0.2414	1.5364	-0.0679	0.1028	0.1943	-0.3684	0.0288	-0.003	0.1289	-0.1258	-0.0211	0.2185	-0.0025	0.0723	0.1366	-0.0036	0.1827	16.5228	-14.2081	4.5426
16	1.5617	0.2045	-0.0441	2.3245	0.2258	1.9193	-0.0516	0.16	0.0557	-0.4023	0.0533	-0.2515	0.0434	-0.1054	0.0061	0.1933	-0.0292	0.1004	0.125	-0.0082	0.1672	18.3779	-12.6459	4.4436
17	1.2841	-0.2024	-0.3662	1.5493	-0.3901	0.6273	0.0063	0.2469	-0.0011	-0.4694	0.0869	-0.0988	0.0334	-0.1492	-0.1077	0.2766	-0.0217	0.051	0.1724	-0.0095	0.124	8.1444	-7.1189	4.3458

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 87 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 88 through 186 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 187 through 201 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 202 through 257 )	A
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 4 through 87 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 88 through 201 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 202 through 257 )	B
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 5 through 64 )	C
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 65 through 87 )	C
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 88 through 173 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 174 through 201 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 202 through 257 )	C
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 0 through 87 )	D
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 88 through 132 )	D
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 133 through 153 )	D
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 154 through 201 )	D
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 202 through 257 )	D

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