PDB-2wzt: Crystal structure of a mycobacterium aldo-keto reductase in its a...

ID or keywords:

Entry

Database: PDB / ID: 2wzt

Title

Crystal structure of a mycobacterium aldo-keto reductase in its apo and liganded form

Components

ALDO-KETO REDUCTASE

Keywords

OXIDOREDUCTASE

Function / homology

Function and homology information

: / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Similarity search - Function

Biological species

MYCOBACTERIUM SMEGMATIS (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Scoble, J. / McAlister, A.D. / Fulton, Z. / Troy, S. / Byres, E. / Vivian, J.P. / Brammananth, R. / Wilce, M.C.J. / Le Nours, J. / Zaker-Tabrizi, L. ...

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure and Comparative Functional Analyses of a Mycobacterium Aldo-Keto Reductase.
Authors: Scoble, J. / Mcalister, A.D. / Fulton, Z. / Troy, S. / Byres, E. / Vivian, J.P. / Brammananth, R. / Wilce, M.C.J. / Le Nours, J. / Zaker-Tabrizi, L. / Coppel, R.L. / Crellin, P.K. / Rossjohn, J. / Beddoe, T.

History

Deposition	Dec 3, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 16, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jul 12, 2017	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2wzt.cif.gz	120.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2wzt.ent.gz	93.8 KB	Display	PDB format
PDBx/mmJSON format	2wzt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2wzt_validation.pdf.gz	431.5 KB	Display	wwPDB validaton report
Full document	2wzt_full_validation.pdf.gz	436.4 KB	Display
Data in XML	2wzt_validation.xml.gz	24.4 KB	Display
Data in CIF	2wzt_validation.cif.gz	36.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wz/2wzt ftp://data.pdbj.org/pub/pdb/validation_reports/wz/2wzt	HTTPS FTP

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Related structure data

Related structure data	2wzmC 1vbjS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1g0i-d 1k3d-d 4gxq-3 1h80-2 4wv3-1 3roo-2 4wj5-2 1axw-d 3o3b-1 6at2-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#92 - Aug 2007 Anabolic Steroids similarity (7)

Deposited unit

A: ALDO-KETO REDUCTASE

B: ALDO-KETO REDUCTASE

59.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	43.543, 103.677, 112.051
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 11 - 268 / Label seq-ID: 11 - 268

Dom-ID	Auth asym-ID	Label asym-ID
1	B	B
2	A	A

NCS oper: (Code: given
Matrix: (0.8724, -0.003268, 0.4889), (-0.001227, -1, -0.004495), (0.4889, 0.003321, -0.8723)
Vector: -13.77, 28.64, 52.78)

#1: Protein	ALDO-KETO REDUCTASE / UNCHARACTERIZED OXIDOREDUCTASE MSMEG_2407 Mass: 29973.307 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QV09, EC: 1.1.1.218
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

ALDO-KETO REDUCTASE / UNCHARACTERIZED OXIDOREDUCTASE MSMEG_2407

Mass: 29973.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / Plasmid: PDEST17 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QV09, EC: 1.1.1.218

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.2 Å³/Da / Density % sol: 44.1 % / Description: NONE
Crystal grow	pH: 5.1 / Details: 20% PEG 0.2M CACL2 0.1M NA CACODYLATE PH 5.1

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
Detector	Type: RIGAKE / Detector: IMAGE PLATE / Date: Oct 1, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.9→26.3 Å / Num. obs: 40896 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / R_merge(I) obs: 0.07 / Net I/σ(I): 9.3
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VBJ

1vbj

Resolution: 1.9→50 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.933 / SU B: 5.398 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20941	2047	5 %	RANDOM
R_work	0.16796	-	-	-
obs	0.17005	38786	99.95 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 14.078 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.01 Å²	0 Å²	0 Å²
2-	-	-1.16 Å²	0 Å²
3-	-	-	2.17 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3847	0	0	440	4287

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	3991
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.348	1.965	5475
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.68	5	542
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.134	24.767	172
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.607	15	611
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.665	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	654
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3062
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	2112
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.295	0.2	2840
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.14	0.2	373
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.182	0.2	4
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.202	0.2	46
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.115	0.2	23
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.231	0.2	1
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.389	3	2599
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.024	5	4172
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.392	7	1440
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.635	10	1290
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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 / Number: 1907 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	B	medium positional	0.28	0.5
2	A	medium positional	0.28	0.5
1	B	medium thermal	0.98	2
2	A	medium thermal	0.98	2

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.32	151	-
R_work	0.227	2793	-
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	2.0966	0.0105	1.192	2.364	0.0437	1.7955	0.1083	0.0064	-0.1726	-0.0994	0.0387	-0.056	0.2309	-0.0078	-0.147	0.0247	0.0137	0.0304	0.0495	0.0003	0.0366	14.022	13.208	10.902
2	2.4538	-1.2367	0.4304	9.9742	7.0737	10.2538	-0.0944	-0.3299	-0.0423	0.5405	0.2244	-0.3803	0.1548	0.2794	-0.13	0.0397	0.0239	0.0003	0.1508	0.0494	0.0645	25.983	14.593	22.873
3	1.048	-0.6944	0.0565	1.6576	-0.3739	0.3776	-0.0131	0.0265	0.0295	0.0103	0.0008	-0.1129	-0.0792	0.0877	0.0122	0.021	-0.0107	-0.0047	0.07	-0.004	0.0326	19.565	24.952	15.374
4	0.7687	-0.362	0.5398	1.8835	-0.3129	0.7024	-0.014	-0.0493	0.09	0.0706	0.0306	0.0147	-0.141	0.043	-0.0166	0.0413	-0.0002	0.0041	0.0397	0.0004	-0.002	10.852	29.496	13.531
5	2.5282	-0.1286	-0.7272	0.2526	0.1275	1.8553	-0.0106	0.1289	0.2204	-0.1599	0.0422	0.0338	-0.008	0.0556	-0.0316	0.0399	-0.0096	0.0026	0.066	0.0163	0.0071	11.972	27.207	7.05
6	0.4397	-0.2143	0.2574	2.0258	-1.0891	1.5101	0.0297	0.0402	-0.0099	-0.018	0.0302	0.2248	0.0168	-0.0309	-0.06	0.0072	0.0037	0.0066	0.0385	-0.0055	0.018	0.448	18.12	14.795
7	2.2152	1.014	0.0794	4.8853	3.9352	4.2963	-0.0689	-0.1766	-0.0663	0.0967	0.0059	-0.0169	0.2137	0.0065	0.063	0.1016	0.0051	-0.009	0.0612	0.0354	0.0306	6.094	-2.208	29.88
8	2.2974	-1.5613	0.1953	4.5145	-2.9399	3.3545	0.009	-0.0592	0.0147	0.1278	-0.155	-0.2727	0.001	0.2489	0.1459	0.0289	-0.006	0.0143	0.0331	0.0045	0.0074	11.005	3.72	20.726
9	5.2587	2.5796	2.835	8.9716	-2.4769	3.4694	-0.1947	-0.0219	-0.3351	-0.1258	-0.3394	-0.7778	0.125	0.4475	0.5341	0.0392	0.0388	0.0783	0.0952	0.0803	0.1853	17.844	0.915	19.485
10	2.8392	-0.7778	-0.731	6.7384	1.1603	3.9556	0.0438	0.0344	-0.1296	-0.0212	-0.028	0.4045	0.2909	-0.3256	-0.0158	0.0738	-0.0244	-0.0282	0.0382	0.0116	0.0694	-0.988	-1.928	20.464
11	3.0541	-0.1779	-1.1054	1.1462	-0.1316	2.0147	0.0071	-0.0804	0.102	0.11	-0.0388	-0.0893	-0.1571	0.1628	0.0318	0.0876	-0.0366	-0.0253	0.0775	-0.003	0.0124	8.981	13.179	47.543
12	1.275	0.4756	0.0536	2.2704	-0.6462	1.0356	0.0365	-0.1187	0.1005	0.1829	-0.0309	-0.2253	-0.1532	0.216	-0.0055	0.0545	-0.0251	-0.0265	0.105	-0.0086	0.0552	14.184	9.594	49.364
13	2.8723	1.9887	0.6437	1.9543	0.6341	1.5854	-0.0228	-0.1116	-0.09	0.0253	-0.0075	-0.1502	0.007	0.0968	0.0303	0.0564	0.0231	0.0026	0.0588	0.0103	0.0105	7.727	-5.391	48.815
14	1.0705	-0.2612	-1.0018	1.7043	-0.8819	1.7108	-0.1105	0.0627	-0.0687	-0.1132	0.1535	0.0555	0.0813	0.2389	-0.043	0.0347	-0.0034	0.0094	0.0248	0.0249	0.0083	1.513	0.271	44.27
15	3.7415	2.2445	4.0759	2.4752	3.977	7.6647	0.0413	-0.1839	-0.0918	0.1074	-0.0164	0.0844	0.0926	-0.1595	-0.0249	0.0265	-0.0092	0.0239	0.0289	0.0181	0.0388	-3.184	-3.496	50.25
16	3.1807	0.275	1.0817	2.8781	0.5819	4.3352	0.018	-0.0031	-0.2043	-0.0325	0.0141	0.3123	-0.0209	-0.375	-0.0321	0.022	0.0042	0.0001	0.0268	0.0048	0.0318	-7.49	2.122	44.97
17	1.149	1.1062	-0.6896	1.6975	-1.0282	1.8004	0.0061	-0.0865	0.0996	-0.0055	0.0334	0.1707	-0.0172	-0.0961	-0.0394	0.0367	0.0095	0.0085	0.0353	-0.0072	0.0282	-3.741	13.981	39.216
18	0.6246	-1.3011	-0.6403	3.0914	0.5358	2.3321	0.1079	0.1169	0.1776	-0.1167	0.0018	-0.199	-0.4013	-0.0763	-0.1097	0.0532	-0.0185	0.0343	0.0598	0.0057	0.0755	6.037	31.693	30.888
19	2.002	1.005	-0.2553	6.2527	-1.476	2.9241	-0.0706	-0.0908	-0.068	0.1195	-0.0871	-0.5108	-0.071	0.24	0.1577	0.068	-0.0006	0.0014	0.0473	-0.0126	0.0089	6.022	23.747	40.141
20	1.5567	-1.6548	0.3147	2.9983	-1.0781	3.6753	-0.0333	0.0342	0.2704	0.2006	-0.0571	-0.1951	-0.3306	0.1169	0.0904	0.0832	-0.0395	0.0273	0.0225	0.0062	0.0609	2.748	29.255	39.288

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 32
2	X-RAY DIFFRACTION	2	A	33 - 49
3	X-RAY DIFFRACTION	3	A	50 - 101
4	X-RAY DIFFRACTION	4	A	102 - 133
5	X-RAY DIFFRACTION	5	A	134 - 148
6	X-RAY DIFFRACTION	6	A	149 - 200
7	X-RAY DIFFRACTION	7	A	201 - 215
8	X-RAY DIFFRACTION	8	A	216 - 242
9	X-RAY DIFFRACTION	9	A	243 - 254
10	X-RAY DIFFRACTION	10	A	255 - 269
11	X-RAY DIFFRACTION	11	B	11 - 39
12	X-RAY DIFFRACTION	12	B	40 - 86
13	X-RAY DIFFRACTION	13	B	87 - 107
14	X-RAY DIFFRACTION	14	B	108 - 124
15	X-RAY DIFFRACTION	15	B	125 - 139
16	X-RAY DIFFRACTION	16	B	140 - 162
17	X-RAY DIFFRACTION	17	B	163 - 201
18	X-RAY DIFFRACTION	18	B	202 - 217
19	X-RAY DIFFRACTION	19	B	218 - 242
20	X-RAY DIFFRACTION	20	B	243 - 268

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