PDB-1o8c: CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH

ID or keywords:

Entry

Database: PDB / ID: 1o8c

Title

CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH

Components

YHDH

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / POSSIBLE NADPH-DEPENDENT QUINONE OXIDOREDUCTASE

Function / homology

Function and homology information

acrylyl-CoA reductase (NADPH) / acryloyl-CoA reductase (NADPH) activity / protein homodimerization activity / cytoplasm
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

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

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of Escherichia Coli Yhdh, a Putative Quinone Oxidoreductase
Authors: Sulzenbacher, G. / Roig-Zamboni, V. / Pagot, F. / Grisel, S. / Salomoni, A. / Valencia, C. / Campanacci, V. / Vincentelli, R. / Tegoni, M. / Eklund, H. / Cambillau, C.

History

Deposition	Nov 26, 2002	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 21, 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	Dec 13, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1o8c.cif.gz	262.7 KB	Display	PDBx/mmCIF format
PDB format	pdb1o8c.ent.gz	214.6 KB	Display	PDB format
PDBx/mmJSON format	1o8c.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	1o8c_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	1o8c_full_validation.pdf.gz	1.5 MB	Display
Data in XML	1o8c_validation.xml.gz	49.9 KB	Display
Data in CIF	1o8c_validation.cif.gz	68.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o8/1o8c ftp://data.pdbj.org/pub/pdb/validation_reports/o8/1o8c	HTTPS FTP

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Related structure data

Related structure data	1o89SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5gxf-d 4rvu-1 2vwg-1 6grc-d 3sc1-2 5cnq-d 4q0j-d 3s3f-d 4rvu-2 2eer-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) 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	#13 - Jan 2001 Alcohol Dehydrogenase similarity (7) #34 - Oct 2002 Dihydrofolate Reductase similarity (1) #32 - Aug 2002 Chaperones similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: YHDH

B: YHDH

C: YHDH

D: YHDH

hetero molecules

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

1

A: YHDH

D: YHDH

hetero molecules

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

2

B: YHDH

C: YHDH

hetero molecules

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

Unit cell

Length a, b, c (Å)	189.313, 189.313, 98.654
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.167319, -0.950808, -0.260705), (0.648768, 0.305297, -0.69706), (0.742363, -0.052505, 0.667936)	-57.0945, 174.5057, 122.2391
2	given	(0.4345, 0.90055, -0.01494), (0.90057, -0.43464, -0.00784), (-0.01355, -0.01004, -0.99986)	-93.74427, 149.89442, 46.29948
3	given	(-0.78097, 0.56435, 0.26758), (0.56755, 0.46243, 0.68121), (0.2607, 0.68387, -0.68144)	37.4186, 21.2013, -76.13287

Details

TWO COMPLETE DIMERS ARE PRESENT IN THE ASYMMETRIC UNIT,ONE IS FORMED BY CHAINS A,D, THE OTHER BY CHAINS B,C

#1: Protein	YHDH / B3253 / YHDH / PUTATIVE QUINONE OXIDOREDUCTASE Mass: 37294.473 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: P26646
#2: Chemical	ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H₂O
Compound details	THIS ENTRY IS FROM A STRUCTURAL GENOMICS EXPERIMENT, POSSIBLY A NADPH-DEPENDENT QUINONE OXIDOREDUCTASE
Sequence details	RESIDUES -20 TO 0 AND 10 TO 12 MISSING FROM DECK OF COORDINATES. RESIDUES -20 TO 1 ARE FROM THE ...RESIDUES -20 TO 0 AND 10 TO 12 MISSING FROM DECK OF COORDINATES. RESIDUES -20 TO 1 ARE FROM THE EXPRESSION TAG AT THE N-TERMINUS

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.4 Å³/Da / Density % sol: 63 %
Crystal grow	pH: 5.5 Details: 8.5 % PEG 8K, 0.1 M NA-ACETATE PH 5.5, 0.01 MM ZNCL2, 5 MM NADPH

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
Detector	Type: ADSC CCD / Detector: CCD / Date: Jun 27, 2002
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.934 Å / Relative weight: 1
Reflection	Resolution: 2.6→43.7 Å / Num. obs: 62012 / % possible obs: 100 % / Redundancy: 6.1 % / R_merge(I) obs: 0.05 / Net I/σ(I): 8.3
Reflection shell	Resolution: 2.6→2.67 Å / Redundancy: 5.9 % / R_merge(I) obs: 0.192 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: NATIVE YHD, PDB ID CODE 1O89

1o89

Resolution: 2.6→158.11 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.932 / SU B: 7.165 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.202	3140	5.1 %	RANDOM
R_work	0.171	-	-	-
obs	0.173	58842	100 %	-

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_aniso -1	B_aniso -2	B_aniso -3
1-	0.2 Å²	0.1 Å²	0 Å²
2-	-	0.2 Å²	0 Å²
3-	-	-	-0.31 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→158.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9752	0	192	348	10292

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.021	10136
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	9329
X-RAY DIFFRACTION	r_angle_refined_deg	1.226	1.98	13797
X-RAY DIFFRACTION	r_angle_other_deg	0.776	3	21635
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.897	5	1291
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	0.067	0.2	1578
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	11285
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1963
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	1761
X-RAY DIFFRACTION	r_nbd_other	0.231	0.2	10613
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	5924
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	369
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	0.172	0.2	35
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.254	0.2	119
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.156	0.2	9
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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: 2.6→2.67 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.256	254
R_work	0.208	4318

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	2.0418	-0.7633	-0.188	5.7796	0.9111	3.4336	0.2037	0.1866	0.0343	-0.5016	-0.1564	-0.0062	-0.403	-0.1224	-0.0473	0.3091	0.171	-0.0432	0.217	-0.0001	0.1536	32.005	116.611	-12.795
2	2.144	-0.4736	-0.1653	0.8397	-0.3858	0.7943	0.0341	-0.2518	-0.1664	0.0738	-0.0022	0.1315	-0.1291	0.1034	-0.0319	0.2314	0.0389	-0.0326	0.2574	0.036	0.2872	43.349	103.892	11.73
3	5.7962	2.4849	-3.4397	7.3603	-0.804	9.2778	0.103	0.1794	-0.6877	-0.133	-0.2098	0.273	0.4904	-0.3378	0.1067	0.1647	0.0976	-0.1787	0.1504	-0.0107	0.292	32.656	99.688	-3.748
4	1.9571	-1.9887	1.0542	5.0827	-0.9619	4.9272	0.0811	-0.4046	0.0429	0.1286	-0.0093	0.3937	-0.2598	-0.6613	-0.0718	0.3784	0.1278	-0.0054	0.3141	-0.0066	0.3307	26.921	119.113	1.625
5	4.0516	0.2451	-0.9738	3.8449	-1.0818	5.4192	0.1543	0.1702	-0.0637	-0.1935	-0.1251	0.1571	-0.2687	-0.151	-0.0292	0.2934	0.0017	-0.0289	0.0888	-0.0131	0.1958	14.464	180.379	24.03
6	-0.0288	-0.0758	-0.0686	2.999	0.3577	1.9379	-0.0174	-0.0817	0.0664	0.4267	0.0168	-0.3657	-0.1617	0.4225	0.0005	0.3919	-0.0298	-0.0313	0.3166	0.0343	0.2861	26.315	164.402	46.353
7	5.7544	1.1565	2.8911	8.4575	6.66	15.9619	-0.1869	-0.4129	0.1159	0.3103	-0.1838	0.6042	-0.3625	-0.5394	0.3707	0.3051	0.0617	0.0799	0.1269	0.0933	0.2097	10.279	174.045	41.689
8	6.4104	-1.4063	1.9949	5.8024	0.193	3.0966	0.0782	-0.1266	0.4723	0.2153	-0.19	-0.5955	-0.5128	0.4733	0.1118	0.4854	-0.1107	-0.0079	0.3252	0.0486	0.3843	25.988	185.011	33.211
9	4.0782	-2.1331	-0.278	6.1495	0.3857	3.1901	-0.2672	-0.1872	-0.0415	1.3906	0.3174	0.0631	0.214	0.2694	-0.0502	0.7878	0.2447	0.0885	0.2076	0.0417	0.1259	25.399	128.213	57.419
10	1.2617	0.0156	0.3468	2.8293	0.6737	0.8468	-0.0594	0.1273	-0.1425	-0.1862	0.0348	0.2033	0.0629	0.2561	0.0246	0.2775	0.0519	0.0127	0.2362	0.0272	0.2761	18.532	143.624	32.95
11	9.436	1.8822	3.2231	7.3435	3.61	7.8356	-0.166	0.0017	-0.0219	0.9708	0.1565	1.2482	0.3409	-0.1785	0.0095	0.3739	0.1236	0.2378	0.1418	0.1577	0.3888	10.289	135.987	48.624
12	2.4878	-0.8584	1.1084	6.0434	-1.6559	4.0547	-0.0948	0.3386	-0.4546	0.0555	0.1336	0.1295	0.6684	-0.0021	-0.0389	0.5131	0.1829	0.083	0.3167	-0.0143	0.3595	25.134	122.312	43.071
13	4.6938	-0.0473	0.9465	3.9222	0.5822	3.5846	-0.0096	-0.0948	-0.3894	0.2646	0.0396	0.3133	0.0843	0.2309	-0.0299	0.1029	0.0835	0.0228	0.2384	0.0724	0.2757	74.868	84.519	20.72
14	3.3862	-1.867	0.2608	0.5744	-0.2002	1.6708	0.3236	0.5789	0.2683	-0.2758	-0.3367	-0.1965	-0.1149	0.4644	0.0131	0.2935	0.1038	-0.0021	0.4869	0.0587	0.284	65.384	101.855	-1.797
15	8.8199	-1.2511	-5.6099	6.942	0.3924	13.7749	0.3194	0.6988	-1.2136	-0.7082	-0.5129	0.5498	0.8568	0.1287	0.1935	0.2623	0.2124	-0.2317	0.3215	-0.0894	0.354	67.115	83.296	3.083
16	8.4708	-4.5062	0.4588	7.4771	-2.611	3.6722	0.0622	0.2247	0.261	-0.0971	0.0594	-0.4153	-0.204	0.3122	-0.1217	0.2099	0.0072	0.0223	0.4474	-0.0124	0.3167	83.963	92.747	11.287

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 125
2	X-RAY DIFFRACTION	2	A	126 - 268
3	X-RAY DIFFRACTION	3	A	269 - 292
4	X-RAY DIFFRACTION	4	A	293 - 324
5	X-RAY DIFFRACTION	5	B	1 - 125
6	X-RAY DIFFRACTION	6	B	126 - 268
7	X-RAY DIFFRACTION	7	B	269 - 292
8	X-RAY DIFFRACTION	8	B	293 - 324
9	X-RAY DIFFRACTION	9	C	2 - 125
10	X-RAY DIFFRACTION	10	C	126 - 268
11	X-RAY DIFFRACTION	11	C	269 - 292
12	X-RAY DIFFRACTION	12	C	293 - 324
13	X-RAY DIFFRACTION	13	D	1 - 125
14	X-RAY DIFFRACTION	14	D	126 - 268
15	X-RAY DIFFRACTION	15	D	269 - 292
16	X-RAY DIFFRACTION	16	D	293 - 324

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