PDB-3l5a: Crystal structure of a probable NADH-dependent flavin oxidoreduct...

ID or keywords:

Entry

Database: PDB / ID: 3l5a

Title

Crystal structure of a probable NADH-dependent flavin oxidoreductase from Staphylococcus aureus

Components

NADH/flavin oxidoreductase/NADH oxidase

Keywords

OXIDOREDUCTASE / old yellow enzyme family / OYE-like FMN-binding domain / TIM barrel

Function / homology

Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / TRIETHYLENE GLYCOL / :

Function and homology information

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.65 Å

Authors

Lam, R. / Gordon, R.D. / Vodsedalek, J. / Battaile, K.P. / Grebemeskel, S. / Lam, K. / Romanov, V. / Chan, T. / Mihajlovic, V. / Thompson, C.M. ...

Citation

Journal: To be Published
Title: Crystal structure of a probable NADH-dependent flavin oxidoreductase from Staphylococcus aureus
Authors: Lam, R. / Gordon, R.D. / Vodsedalek, J. / Battaile, K.P. / Grebemeskel, S. / Lam, K. / Romanov, V. / Chan, T. / Mihajlovic, V. / Thompson, C.M. / Guthrie, J. / Pai, E.F. / Chirgadze, N.Y.

History

Deposition	Dec 21, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 22, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3l5a.cif.gz	99.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3l5a.ent.gz	72.5 KB	Display	PDB format
PDBx/mmJSON format	3l5a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3l5a_validation.pdf.gz	440.3 KB	Display	wwPDB validaton report
Full document	3l5a_full_validation.pdf.gz	443.1 KB	Display
Data in XML	3l5a_validation.xml.gz	20.8 KB	Display
Data in CIF	3l5a_validation.cif.gz	29.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l5/3l5a ftp://data.pdbj.org/pub/pdb/validation_reports/l5/3l5a	HTTPS FTP

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Related structure data

Similar structure data	5ah0-2 4gl3-d 3eu8-4 2ybp-2 6rtv-2 5jy9-1 3eu8-2 6ru2-2 5jy8-2 2os2-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: NADH/flavin oxidoreductase/NADH oxidase

hetero molecules

48 kDa, 1 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)	69.941, 75.342, 80.736
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	NADH/flavin oxidoreductase/NADH oxidase Mass: 47546.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: JH1 / Gene: SaurJH1_0381 / Plasmid: pW2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIPL / References: UniProt: A6TYH5
#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.01 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG200, 0.1M MES, 5mM I3C, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 17-BM / Wavelength: 0.9792 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 2, 2009 / Details: Si(111) double-crystal monochromator

Radiation

Monochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 1.65→50 Å / Num. obs: 51898 / % possible obs: 99.7 % / Redundancy: 14.3 % / R_merge(I) obs: 0.097 / Χ²: 1.929 / Net I/σ(I): 14.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
1.65-1.69	11.4	0.405	3278	0.807	96.5
1.69-1.73	12.8	0.376	3413	0.835	99.4
1.73-1.78	14	0.303	3421	0.888	100
1.78-1.83	14.6	0.262	3406	0.981	100
1.83-1.89	14.8	0.224	3464	1.057	100
1.89-1.96	14.8	0.183	3414	1.292	100
1.96-2.03	14.9	0.145	3442	1.487	100
2.03-2.13	14.8	0.127	3450	1.757	100
2.13-2.24	14.9	0.111	3449	1.859	100
2.24-2.38	14.9	0.106	3460	2.07	100
2.38-2.56	14.9	0.103	3471	2.234	100
2.56-2.82	14.9	0.098	3481	2.676	100
2.82-3.23	14.8	0.087	3510	2.842	100
3.23-4.07	14.7	0.073	3552	2.826	100
4.07-50	13.9	0.077	3687	4.681	99.2

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Phasing

Phasing

Method:

SAD

Phasing MAD

D res high: 1.65 Å / D res low: 34.97 Å / FOM acentric: 0.585 / FOM centric: 0.214 / Reflection acentric: 47024 / Reflection centric: 4793

Phasing MAD set

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Lowest resolution (Å)	Reflection acentric	Reflection centric
ISO_1	0	0	1.65	34.97	47024	4793
ANO_1	0.41	0	1.65	34.97	46752	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	Reflection acentric	Reflection centric
ISO_1	7.23-34.97	0	461	219
ISO_1	5.17-7.23	0	909	240
ISO_1	4.23-5.17	0	1195	237
ISO_1	3.67-4.23	0	1432	238
ISO_1	3.29-3.67	0	1654	246
ISO_1	3-3.29	0	1839	239
ISO_1	2.78-3	0	1976	239
ISO_1	2.6-2.78	0	2156	238
ISO_1	2.46-2.6	0	2316	247
ISO_1	2.33-2.46	0	2436	245
ISO_1	2.22-2.33	0	2563	244
ISO_1	2.13-2.22	0	2708	237
ISO_1	2.05-2.13	0	2803	245
ISO_1	1.97-2.05	0	2926	242
ISO_1	1.9-1.97	0	3044	241
ISO_1	1.84-1.9	0	3146	235
ISO_1	1.79-1.84	0	3242	256
ISO_1	1.74-1.79	0	3368	244
ISO_1	1.69-1.74	0	3434	236
ISO_1	1.65-1.69	0	3416	225
ANO_1	7.23-34.97	0.229	457	0
ANO_1	5.17-7.23	0.181	909	0
ANO_1	4.23-5.17	0.259	1195	0
ANO_1	3.67-4.23	0.271	1432	0
ANO_1	3.29-3.67	0.26	1654	0
ANO_1	3-3.29	0.25	1839	0
ANO_1	2.78-3	0.257	1976	0
ANO_1	2.6-2.78	0.255	2156	0
ANO_1	2.46-2.6	0.281	2316	0
ANO_1	2.33-2.46	0.31	2436	0
ANO_1	2.22-2.33	0.356	2563	0
ANO_1	2.13-2.22	0.384	2708	0
ANO_1	2.05-2.13	0.421	2803	0
ANO_1	1.97-2.05	0.493	2926	0
ANO_1	1.9-1.97	0.564	3044	0
ANO_1	1.84-1.9	0.624	3146	0
ANO_1	1.79-1.84	0.689	3242	0
ANO_1	1.74-1.79	0.764	3368	0
ANO_1	1.69-1.74	0.837	3381	0
ANO_1	1.65-1.69	0.892	3201	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	54.198	3.27	14.37	SE	18.08	2.76
2	63.89	-8.173	13.904	SE	15.52	2.47
3	55.966	6.765	18.483	SE	18.45	2.64
4	45.192	-2.852	11.306	SE	17.38	2.41
5	63.042	-23.179	15.835	SE	16.44	2.2
6	46.162	5.041	27.143	SE	19.9	2.27
7	42.266	-5.139	10.613	SE	18.15	1.77
8	69.415	1.419	17.358	SE	20.99	1.53
9	42.879	-6.458	23.391	SE	33.87	1.53
10	60.599	-26.802	28.036	SE	33.64	1.39
11	31.403	29.178	17.852	SE	29.25	1.37
12	31.623	33.144	11.893	SE	42.55	1.7
13	41.47	30.593	12.27	SE	58.3	1.23
14	16.121	60.176	13.023	SE	21.72	0.26

Phasing MAD shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
7.23-34.97	0.764	0.243	461	219
5.17-7.23	0.739	0.209	909	240
4.23-5.17	0.68	0.202	1195	237
3.67-4.23	0.656	0.196	1432	238
3.29-3.67	0.67	0.185	1654	246
3-3.29	0.678	0.184	1839	239
2.78-3	0.681	0.207	1976	239
2.6-2.78	0.686	0.217	2156	238
2.46-2.6	0.683	0.228	2316	247
2.33-2.46	0.674	0.221	2436	245
2.22-2.33	0.65	0.216	2563	244
2.13-2.22	0.636	0.206	2708	237
2.05-2.13	0.622	0.203	2803	245
1.97-2.05	0.591	0.203	2926	242
1.9-1.97	0.569	0.208	3044	241
1.84-1.9	0.532	0.266	3146	235
1.79-1.84	0.505	0.233	3242	256
1.74-1.79	0.468	0.217	3368	244
1.69-1.74	0.433	0.215	3434	236
1.65-1.69	0.393	0.222	3416	225

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 51817

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.95-100	66.5	0.731	511
5.94-7.95	60.5	0.838	694
4.95-5.94	54.7	0.875	867
4.33-4.95	51.5	0.894	990
3.9-4.33	56.9	0.907	1101
3.57-3.9	52.8	0.91	1197
3.32-3.57	52	0.902	1300
3.11-3.32	51.4	0.901	1376
2.94-3.11	50.7	0.896	1469
2.79-2.94	51.9	0.898	1528
2.66-2.79	50.5	0.902	1619
2.55-2.66	49.4	0.91	1692
2.46-2.55	47.8	0.904	1747
2.37-2.46	46.6	0.914	1820
2.29-2.37	48.3	0.913	1883
2.22-2.29	49.3	0.918	1935
2.15-2.22	50.2	0.915	1993
2.09-2.15	50.2	0.916	2055
2.04-2.09	52.4	0.91	2100
1.99-2.04	52.5	0.909	2152
1.94-1.99	53.6	0.893	2199
1.9-1.94	55.7	0.885	2269
1.85-1.9	58	0.878	2330
1.82-1.85	57	0.88	2347
1.78-1.82	58.3	0.876	2416
1.75-1.78	62.9	0.871	2433
1.71-1.75	64.1	0.874	2497
1.68-1.71	68.3	0.834	2537
1.65-1.68	69.5	0.783	2760

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	refmac_5.5.0102	refinement
PDB_EXTRACT	3.005	data extraction
JDirector		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.65→34.964 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.954 / WR_factor R_free: 0.195 / WR_factor R_work: 0.182 / ESU R: 0.092 / ESU R Free: 0.083 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection
R_free	0.1915	2642	5.099 %
R_work	0.1812	-	-
obs	-	51815	99.671 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 24.733 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.022 Å²	0 Å²	0 Å²
2-	-	-0.003 Å²	0 Å²
3-	-	-	-0.019 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→34.964 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2989	0	30	279	3298

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	3090
X-RAY DIFFRACTION	r_angle_refined_deg	1.252	1.959	4173
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.658	5	382
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.899	23.862	145
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.968	15	516
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.404	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	454
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	2349
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	1493
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	2133
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.113	0.2	258
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.186	0.2	60
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.111	0.2	30
X-RAY DIFFRACTION	r_mcbond_it	0.714	1.5	1899
X-RAY DIFFRACTION	r_mcangle_it	1.338	2	3059
X-RAY DIFFRACTION	r_scbond_it	2.173	3	1191
X-RAY DIFFRACTION	r_scangle_it	3.618	4.5	1113

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.65-1.693	0.263	178	0.226	3463	3777	96.399
1.693-1.739	0.232	177	0.201	3493	3682	99.674
1.739-1.789	0.205	202	0.182	3410	3612	100
1.789-1.844	0.217	164	0.179	3333	3497	100
1.844-1.905	0.225	183	0.183	3198	3381	100
1.905-1.971	0.209	170	0.175	3116	3286	100
1.971-2.045	0.215	175	0.178	2992	3167	100
2.045-2.129	0.198	180	0.175	2869	3049	100
2.129-2.223	0.165	144	0.167	2801	2945	100
2.223-2.331	0.175	136	0.175	2672	2808	100
2.331-2.456	0.214	110	0.171	2569	2679	100
2.456-2.605	0.2	124	0.182	2440	2564	100
2.605-2.783	0.225	136	0.187	2258	2394	100
2.783-3.005	0.174	112	0.188	2102	2214	100
3.005-3.289	0.191	94	0.185	1984	2078	100
3.289-3.673	0.16	97	0.175	1803	1900	100
3.673-4.234	0.171	95	0.166	1576	1671	100
4.234-5.166	0.15	72	0.166	1359	1431	100
5.166-7.228	0.213	58	0.22	1091	1149	100
7.228-34.964	0.178	35	0.207	644	702	96.724

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