PDB-1oj7: STRUCTURAL GENOMICS, UNKNOWN FUNCTION CRYSTAL STRUCTURE OF E. COL...

ID or keywords:

Entry

Database: PDB / ID: 1oj7

Title

STRUCTURAL GENOMICS, UNKNOWN FUNCTION CRYSTAL STRUCTURE OF E. COLI K-12 YQHD

Components

HYPOTHETICAL OXIDOREDUCTASE YQHD

Keywords

OXIDOREDUCTASE / HYPOTHETICAL OXIDOREDUCTASE / STRUCTURAL GENOMICS / REDUCTASE

Function / homology

Function and homology information

alcohol dehydrogenase [NAD(P)+] activity / methylglyoxal reductase (NADPH) (acetol producing) activity / butanol dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) / alcohol dehydrogenase (NADP+) activity / response to reactive oxygen species / zinc ion binding / identical protein binding / cytosol
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / OTHER / Resolution: 2 Å

Authors

Sulzenbacher, G. / Perrier, S. / Roig-Zamboni, V. / Pagot, F. / Grisel, S. / Salamoni, A. / Valencia, C. / Bignon, C. / Vincentelli, R. / Tegoni, M. / Cambillau, C.

Citation

Journal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of E.Coli Alcohol Dehydrogenase Yqhd: Evidence of a Covalently Modified Nadp Coenzyme
Authors: Sulzenbacher, G. / Alvarez, K. / Van-Den-Heuvel, R.H.H. / Versluis, C. / Spinelli, S. / Campanacci, V. / Valencia, C. / Cambillau, C. / Eklund, H. / Tegoni, M.

History

Deposition	Jul 3, 2003	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 8, 2004	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn 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 / _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_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 / _struct_conn.pdbx_dist_value / _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_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	1oj7.cif.gz	346.4 KB	Display	PDBx/mmCIF format
PDB format	pdb1oj7.ent.gz	283.7 KB	Display	PDB format
PDBx/mmJSON format	1oj7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1oj7_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	1oj7_full_validation.pdf.gz	1.3 MB	Display
Data in XML	1oj7_validation.xml.gz	71.4 KB	Display
Data in CIF	1oj7_validation.cif.gz	105.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oj/1oj7 ftp://data.pdbj.org/pub/pdb/validation_reports/oj/1oj7	HTTPS FTP

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Related structure data

Similar structure data	1vhd-d 5yvs-1 3ppc-1 6c76-d 2qjj-1 4gme-d 4k1w-2 6pz1-d 4hni-d 1p7t-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: HYPOTHETICAL OXIDOREDUCTASE YQHD

B: HYPOTHETICAL OXIDOREDUCTASE YQHD

C: HYPOTHETICAL OXIDOREDUCTASE YQHD

D: HYPOTHETICAL OXIDOREDUCTASE YQHD

hetero molecules

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

1

A: HYPOTHETICAL OXIDOREDUCTASE YQHD

D: HYPOTHETICAL OXIDOREDUCTASE YQHD

hetero molecules

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

2

B: HYPOTHETICAL OXIDOREDUCTASE YQHD

C: HYPOTHETICAL OXIDOREDUCTASE YQHD

hetero molecules

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

Unit cell

Length a, b, c (Å)	237.925, 237.925, 66.744
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	171
Space group name H-M	P6₂

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.46047, 0.09124, -0.88297), (0.76068, 0.47214, 0.44548), (0.45753, -0.87679, 0.14801)	56.95176, -61.81264, -48.72829
2	given	(0.37569, 0.08239, -0.92308), (-0.78774, -0.49629, -0.36491), (-0.48818, 0.86424, -0.12155)	67.36762, 95.38748, 114.93341
3	given	(-0.62027, 0.06768, -0.78146), (0.07061, -0.98741, -0.14156), (-0.7812, -0.14298, 0.60768)	197.64517, -66.61557, 90.04625

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Protein , 1 types, 4 molecules ABCD

#1: Protein	HYPOTHETICAL OXIDOREDUCTASE YQHD Mass: 44691.711 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q46856

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Non-polymers , 5 types, 1503 molecules

#2: Chemical	ChemComp-NZQ / 5,6-DIHYDROXY-NADP Mass: 779.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₃₂N₇O₁₉P₃
#3: Chemical	ChemComp-BO3 / BORIC ACID Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH₃O₃
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1494 / 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: 3.2 Å³/Da / Density % sol: 61.7 % Description: THE STRUCTURE WAS SOLVED BY SAD ON THE PLATINUM EDGE, BUT THE MODEL WAS REFINED AGAINST THE NATIVE DATA
Crystal grow	pH: 8.5 / Details: 0,95 M NA-CITRATE, 0.01 M NA-BORATE PH 8.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9762
Detector	Type: ADSC CCD / Detector: CCD / Date: Sep 15, 2002
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2→47 Å / Num. obs: 80905 / % possible obs: 95.3 % / Redundancy: 2.5 % / B_iso Wilson estimate: 23.32 Å² / R_merge(I) obs: 0.047 / R_sym value: 0.066 / Net I/σ(I): 9.3
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.158 / Mean I/σ(I) obs: 4.6 / R_sym value: 0.223 / % possible all: 92.7

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALA		data scaling
SOLVE		phasing
MLPHARE		phasing
REFMAC	5.1.24	refinement

Refinement

Method to determine structure: OTHER / Resolution: 2→47 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.961 / SU B: 2.795 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.164	4134	3 %	RANDOM
R_work	0.145	-	-	-
obs	0.146	134578	95 %	-

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: 12.97 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.69 Å²	0.34 Å²	0 Å²
2-	-	0.69 Å²	0 Å²
3-	-	-	-1.03 Å²

Refinement step

Cycle: LAST / Resolution: 2→47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11948	0	162	1494	13604

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.021	12707
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	11649
X-RAY DIFFRACTION	r_angle_refined_deg	1.115	1.967	17330
X-RAY DIFFRACTION	r_angle_other_deg	0.776	3	27149
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.212	5	1570
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	1999
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	13928
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2393
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	2708
X-RAY DIFFRACTION	r_nbd_other	0.229	0.2	13724
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	6987
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	1328
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.157	0.2	5
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.147	0.2	16
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.246	0.2	84
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.211	0.2	57
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	0.432	1.5	7815
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.837	2	12642
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.391	3	4892
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.404	4.5	4677
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

LS refinement shell

Resolution: 2→2.05 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.201	319
R_work	0.182	9589

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	2.7377	2.412	0.5875	3.975	-0.1037	0.7151	0.0964	0.1847	0.0392	-0.0669	-0.1194	0.1011	0.0183	0.015	0.023	0.2844	-0.0228	0.0145	0.2551	-0.0614	0.3893	103.18	-33.146	26.33
2	1.2885	-0.1961	0.3673	1.0253	-0.054	1.1012	0.0215	0.2686	0.0901	-0.1754	-0.0691	-0.2048	-0.022	0.064	0.0476	0.3084	-0.0567	0.0408	0.3129	0.0438	0.3399	103.528	-13.561	16.484
3	0.8553	-0.2058	0.1074	0.799	-0.0354	0.3394	-0.0717	0.0444	-0.0294	-0.0032	0.0449	-0.0443	-0.0096	-0.0146	0.0268	0.3115	-0.0425	-0.0174	0.2738	-0.0032	0.3869	96.726	-23.764	36.917
4	1.167	-0.4255	0.4097	1.3803	-0.2742	0.8527	-0.0471	0.0263	-0.0768	-0.0512	0.1057	0.0809	-0.0185	-0.1357	-0.0586	0.3011	-0.062	-0.01	0.2872	0.0141	0.3414	79.806	-22.363	33.27
5	3.6331	2.0585	2.5383	4.7155	3.446	2.1392	0.0345	0.0682	-0.1668	-0.1069	-0.0972	-0.2838	0.1612	0.0993	0.0627	0.2281	-0.0598	0.007	0.1909	0.0112	0.2313	96.261	-11.616	26.392
6	0.9881	1.5772	-1.0204	5.3472	-2.3203	1.3882	-0.0729	0.1292	-0.0041	-0.0929	0.0841	-0.048	-0.0221	-0.0678	-0.0112	0.4026	-0.0589	-0.027	0.3143	0.0215	0.2446	78.298	12.701	31.354
7	0.4681	-0.3218	-0.1221	1.5403	0.535	1.136	0.0601	0.0279	0.0265	-0.1633	0.0573	-0.1823	-0.1892	0.1254	-0.1174	0.365	-0.0963	0.0225	0.3099	0.04	0.2756	88.806	17.923	13.054
8	0.0943	-0.0288	0.0068	0.9663	0.0938	0.5304	0.063	-0.0015	-0.0182	-0.085	-0.0259	0.0581	-0.0999	-0.0935	-0.037	0.4056	-0.0147	-0.023	0.331	0.0329	0.2633	66.749	16.969	21.79
9	0.5177	-0.1636	-0.2726	0.68	0.0789	1.7539	-0.013	0.0335	-0.0709	-0.075	-0.0006	0.0459	0.0626	-0.1791	0.0136	0.3436	-0.0525	-0.0318	0.3381	0.0316	0.2615	62.298	3.114	12.28
10	4.2766	5.6972	0.1252	-0.5503	-0.7747	6.7755	0.1059	-0.0333	0.1584	-0.1536	-0.2143	-0.0186	-0.0425	-0.0014	0.1084	0.3072	-0.0356	0.0117	0.2253	0.0776	0.1314	76.892	17.735	9.257
11	-0.0392	-0.3812	0.6114	3.8379	-1.5773	1.397	-0.0086	-0.0086	-0.0318	0.213	0.0677	0.1064	-0.2296	-0.0683	-0.0591	0.4204	-0.0458	0.0261	0.3369	0.0381	0.2627	78.671	21.594	33.051
12	1.2849	1.0826	-0.0326	2.3894	-0.0333	0.5882	0.0814	-0.0336	0.0189	0.1332	-0.0022	-0.1664	0.0186	0.0184	-0.0792	0.3402	-0.0285	-0.0212	0.2697	0.0053	0.2961	91.507	14.061	50.658
13	0.0412	0.0014	-0.2667	2.166	-0.7067	0.7489	0.0071	0.0351	-0.018	0.0176	0.029	-0.0628	-0.0618	-0.0964	-0.0361	0.377	-0.0167	-0.016	0.3211	0.0205	0.275	67.195	17.751	42.825
14	0.889	0.2913	0.3015	1.5627	0.5924	1.5359	0.0123	0.0168	0.118	0.0579	-0.0345	0.0051	-0.0311	-0.1771	0.0223	0.3309	0.0369	-0.0135	0.2839	0.042	0.2896	63.094	31.774	52.445
15	2.2037	1.6728	1.0011	4.1812	2.1109	1.1893	-0.0181	0.1846	-0.0785	0.0412	-0.02	-0.2598	0.1163	0.0716	0.0381	0.3058	-0.0364	-0.0271	0.2419	-0.017	0.3769	110.84	-30.299	30.279
16	2.2241	-0.3524	0.5091	1.1917	-0.3354	1.0836	0.0277	0.5303	-0.4187	-0.3581	-0.0879	-0.2031	0.1536	0.1659	0.0603	0.33	-0.0083	0.1231	0.2963	-0.1794	0.3965	119.659	-48.288	21.101
17	1.3674	0.1509	0.3676	1.5221	-0.1297	0.0245	-0.0548	0.0377	-0.2167	0.0199	0.0042	-0.0585	-0.0116	0.0115	0.0506	0.3031	-0.0225	0.0044	0.2292	-0.026	0.4306	107.161	-41.508	40.385
18	2.4934	-0.0806	0.016	1.3835	-0.0146	0.4268	-0.0626	-0.197	-0.2785	0.1117	0.0638	-0.1473	0.0137	0.0386	-0.0012	0.2825	0.006	-0.0233	0.2191	0.0297	0.4094	120.573	-43.568	51.066
19	-1.047	-4.8109	3.6626	-4.8059	2.1736	5.5744	-0.347	0.3438	-0.4524	-0.5779	0.5328	-0.5848	-0.5008	-0.3879	-0.1859	0.1907	-0.0842	0.0646	0.0749	-0.1529	0.4324	116.589	-52.118	32.524

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-2 - 14
2	X-RAY DIFFRACTION	2	A	15 - 183
3	X-RAY DIFFRACTION	3	A	184 - 263
4	X-RAY DIFFRACTION	4	A	264 - 387
5	X-RAY DIFFRACTION	5	E	501
6	X-RAY DIFFRACTION	6	B	-2 - 14
7	X-RAY DIFFRACTION	7	B	15 - 183
8	X-RAY DIFFRACTION	8	B	184 - 263
9	X-RAY DIFFRACTION	9	B	264 - 387
10	X-RAY DIFFRACTION	10	F	502
11	X-RAY DIFFRACTION	11	C	-2 - 14
12	X-RAY DIFFRACTION	12	C	15 - 183
13	X-RAY DIFFRACTION	13	C	184 - 263
14	X-RAY DIFFRACTION	14	C	264 - 387
15	X-RAY DIFFRACTION	15	D	-2 - 14
16	X-RAY DIFFRACTION	16	D	15 - 183
17	X-RAY DIFFRACTION	17	D	184 - 263
18	X-RAY DIFFRACTION	18	D	264 - 387
19	X-RAY DIFFRACTION	19	H	503

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Assembly

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 1503 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi