PDB-3pnd: FAD binding by ApbE protein from Salmonella enterica: a new class...

ID or keywords:

Entry

Database: PDB / ID: 3pnd

Title

FAD binding by ApbE protein from Salmonella enterica: a new class of FAD binding proteins

Components

Thiamine biosynthesis lipoprotein ApbE

Keywords

PROTEIN BINDING / Apbe / FAD / flavoprotein / oxidoreductase / FAD binding domain / T-fold

Function / homology

Function and homology information

FAD:protein FMN transferase / transferase activity / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Boyd, J.M. / Endrizzi, J.A. / Hamilton, T.L. / Christopherson, M.R. / Mulder, D.W. / Downs, D.M. / Peters, J.W.

Citation

Journal: J.Bacteriol. / Year: 2011
Title: FAD binding by ApbE protein from Salmonella enterica: a new class of FAD-binding proteins.
Authors: Boyd, J.M. / Endrizzi, J.A. / Hamilton, T.L. / Christopherson, M.R. / Mulder, D.W. / Downs, D.M. / Peters, J.W.

History

Deposition	Nov 18, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 5, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 2, 2011	Group: Database references
Revision 1.3	Sep 6, 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 / 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_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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PDBx/mmCIF format	3pnd.cif.gz	506.7 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	3pnd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pn/3pnd ftp://data.pdbj.org/pub/pdb/validation_reports/pn/3pnd	HTTPS FTP

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Related structure data

Related structure data	2o18S 1vrm S: Starting model for refinement
Similar structure data	1tny-2 5lsw-d 1n4r-9 1pgi-d 4gtx-1 1tnz-3 1n4p-5 6pw0-2 1tnu-1 3pz2-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	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Thiamine biosynthesis lipoprotein ApbE

B: Thiamine biosynthesis lipoprotein ApbE

C: Thiamine biosynthesis lipoprotein ApbE

D: Thiamine biosynthesis lipoprotein ApbE

hetero molecules

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

1

A: Thiamine biosynthesis lipoprotein ApbE

B: Thiamine biosynthesis lipoprotein ApbE

hetero molecules

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

2

C: Thiamine biosynthesis lipoprotein ApbE

D: Thiamine biosynthesis lipoprotein ApbE

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.103, 120.850, 212.058
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	32 - 348
2	1	1	4	B	32 - 348
3	1	1	4	C	32 - 348
4	1	1	4	D	32 - 348

#1: Protein	Thiamine biosynthesis lipoprotein ApbE Mass: 36985.777 Da / Num. of mol.: 4 / Fragment: unp residues 21-350 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: apbE, STM2266 / Plasmid: pApbe10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(A1) / References*: UniProt: P41780
#2: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.82 Å³/Da / Density % sol: 56.37 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 8.5 Details: 0.5M LiSO4, 18% polyethylene glycol (PEG) 4000 in 100 mM Tris-HCl, and 10-20 mg/ml as purified FAD bound ApbE, pH 8.5, VAPOR DIFFUSION, temperature 277K

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Data collection

Diffraction

Mean temperature: 75 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-1 / Wavelength: 0.98789

Detector

Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 11, 2008

Radiation

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

Radiation wavelength

Wavelength: 0.98789 Å / Relative weight: 1

Reflection

Resolution: 2.75→32.6 Å / Num. all: 44268 / Num. obs: 44268 / % possible obs: 99.7 % / Redundancy: 4.2 % / R_merge(I) obs: 0.093 / R_sym value: 0.093 / Net I/σ(I): 14.7

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.75-2.82	4.3	0.4	1.9	13860	3235	0.4	99.9
2.82-2.9	4.3	0.338	2.2	13295	3127	0.338	99.8
2.9-2.98	4.3	0.278	2.7	13078	3072	0.278	99.8
2.98-3.07	4.2	0.231	3.2	12561	2976	0.231	99.8
3.07-3.18	4.2	0.191	3.9	12193	2885	0.191	99.8
3.18-3.29	4.3	0.154	4.7	11967	2812	0.154	99.7
3.29-3.41	4.2	0.122	6	11491	2710	0.122	99.8
3.41-3.55	4.2	0.114	6.2	10833	2588	0.114	99.8
3.55-3.71	4.2	0.097	4.4	10445	2502	0.097	99.7
3.71-3.89	4.2	0.083	7.3	10091	2400	0.083	99.7
3.89-4.1	4.2	0.071	10	9596	2289	0.071	99.7
4.1-4.35	4.1	0.06	11.7	9018	2186	0.06	100
4.35-4.65	4.1	0.054	12.8	8354	2048	0.054	100
4.65-5.02	4.1	0.056	12	7791	1917	0.056	99.8
5.02-5.5	4	0.062	10.8	7057	1766	0.062	99.7
5.5-6.15	3.9	0.058	11.7	6183	1588	0.058	99.4
6.15-7.1	3.6	0.047	14.7	5144	1429	0.047	98.8
7.1-8.7	4.1	0.035	17	5067	1233	0.035	100
8.7-12.3	4	0.03	19.8	3913	977	0.03	100
12.3-32.599	3.8	0.033	12	2009	528	0.033	91.6

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.2.25	data scaling
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O18

2o18

Resolution: 2.75→32.6 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.886 / WR_factor R_free: 0.2134 / WR_factor R_work: 0.1709 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8392 / SU B: 26.902 / SU ML: 0.254 / SU R Cruickshank DPI: 3.9893 / SU R_free: 0.3555 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2544	2226	5 %	RANDOM
R_work	0.2024	-	-	-
obs	0.205	44205	99.59 %	-

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 max: 127.17 Å² / B_iso mean: 38.128 Å² / B_iso min: 1 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.57 Å²	0 Å²	0 Å²
2-	-	1.75 Å²	0 Å²
3-	-	-	-1.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→32.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9674	0	432	329	10435

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.022	10286
X-RAY DIFFRACTION	r_angle_refined_deg	0.899	1.997	14035
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.663	5	1255
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.412	24.196	429
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.293	15	1660
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.665	15	66
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	1544
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	7568
X-RAY DIFFRACTION	r_mcbond_it	2.114	6	6237
X-RAY DIFFRACTION	r_mcangle_it	3.261	30	10022
X-RAY DIFFRACTION	r_scbond_it	2.934	6	4049
X-RAY DIFFRACTION	r_scangle_it	4.603	30	4012

Refine LS restraints NCS

Ens-ID: 1 / Number: 2370 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	MEDIUM POSITIONAL	0.47	0.5
2	B	MEDIUM POSITIONAL	0.42	0.5
3	C	MEDIUM POSITIONAL	0.53	0.5
4	D	MEDIUM POSITIONAL	0.55	0.5
1	A	MEDIUM THERMAL	0.24	2
2	B	MEDIUM THERMAL	0.23	2
3	C	MEDIUM THERMAL	0.25	2
4	D	MEDIUM THERMAL	0.24	2

LS refinement shell

Resolution: 2.75→2.821 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.353	160	-
R_work	0.294	3052	-
all	-	3212	-
obs	-	-	99.81 %

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	13.8129	-5.8667	-2.6106	9.7548	-8.2266	12.4926	0.2965	-0.508	0.8925	0.1819	0.1649	-0.1428	-0.4452	0.1774	-0.4614	0.0987	-0.0458	0.0612	0.0422	-0.0414	0.0839	29.4951	123.8799	7.2804
2	1.4599	0.2774	0.0779	1.9534	-0.2167	0.949	-0.0351	0.2036	-0.0255	-0.3566	0.0131	-0.101	0.1147	0.0883	0.0221	0.0758	-0.0015	0.0229	0.0466	-0.0072	0.0084	19.5395	96.6569	4.4315
3	1.8936	0.2581	-0.0387	2.1122	0.3361	1.4094	-0.0668	-0.0398	0.2754	0.0885	-0.0213	0.0542	-0.3515	-0.1965	0.0881	0.1491	0.0324	0.0058	0.0756	-0.0269	0.0882	16.4063	120.4935	8.2578
4	0.0842	-0.1775	0.2725	0.6812	-1.4212	3.2274	0.0753	0.07	0.0057	-0.154	0.0309	0.0452	0.2322	-0.2492	-0.1061	0.0937	0.0122	0.0075	0.2257	0.0232	0.1261	7.9348	107.951	-10.0839
5	2.6803	-0.1728	0.1364	0.9822	0.0639	3.7128	-0.0038	-0.2093	-0.0086	0.0666	-0.0254	0.3436	-0.0085	-0.5068	0.0292	0.0058	0.0065	0.0254	0.1262	-0.0019	0.1244	1.7975	113.3289	2.2075
6	3.6676	-5.5602	1.9934	17.8864	-4.3965	2.3428	-0.0843	-0.0845	-0.1055	0.4174	-0.0515	-0.5249	-0.2871	-0.114	0.1358	0.1716	0.0151	-0.0112	0.078	-0.0206	0.0779	2.6287	116.0351	37.9079
7	0.949	-0.1412	0.2081	2.1583	0.143	0.6298	-0.0182	-0.1307	0.0531	0.1389	0.0781	0.0155	-0.1497	-0.0908	-0.0599	0.0581	0.0092	0.0244	0.0675	-0.0077	0.015	9.3776	101.3742	33.334
8	0.9803	0.7841	0.7792	1.8299	-0.6985	2.0872	0.067	0.0159	-0.0567	0.0258	-0.1398	-0.1828	0.0945	0.2039	0.0728	0.0624	-0.008	0.0079	0.0758	-0.0451	0.0945	23.7687	103.706	42.8717
9	13.3448	-0.6046	28.0979	5.4241	-9.7401	72.5797	0.8444	0.4405	0.3027	0.0353	-1.8847	-0.5333	2.0869	3.8326	1.0403	0.5227	0.1734	-0.445	0.7636	-0.178	0.8475	29.9754	109.4654	49.1999
10	2.7452	-0.3767	-0.7878	0.7337	-2.1872	8.7051	0.0902	-0.0071	0.3221	0.1487	-0.1446	-0.1569	-0.3456	0.3454	0.0543	0.143	-0.1362	-0.0191	0.1527	-0.0359	0.2456	30.0918	116.3867	39.456
11	0.0235	0.4915	-0.0112	11.9712	-0.3045	0.0092	0.0066	-0.0371	0.0162	-0.6607	-0.0358	-0.2571	0.0186	-0.0289	0.0292	0.2969	-0.021	0.018	0.6923	-0.1562	0.3821	34.8681	126.6701	75.6805
12	23.3821	-15.8788	-8.5853	19.0298	4.4448	18.5458	-0.4194	-0.6901	0.1273	-0.7217	0.2678	0.1338	0.1229	2.0017	0.1517	0.1709	0.0083	-0.0856	0.2402	0.0021	0.1126	20.5223	133.4713	85.314
13	2.1528	0.1434	-0.0854	1.0536	-0.1041	1.1646	-0.0248	-0.147	-0.1162	0.1583	0.0128	-0.0513	-0.0309	0.0232	0.012	0.025	0.0049	-0.0054	0.0109	0.007	0.0081	-2.6244	126.6792	87.3321
14	9.7815	4.3682	-6.9646	1.9615	-3.117	4.9667	0.1846	-0.0176	0.4411	0.0241	0.0937	0.1609	-0.0525	-0.0374	-0.2783	0.4959	-0.1265	0.0338	0.5643	-0.0134	0.4159	21.5972	109.4346	103.2058
15	1.2332	-0.0405	-0.3557	0.9814	0.2759	2.0817	-0.0882	-0.0716	-0.2993	0.0259	0.0007	-0.2617	0.4017	0.0956	0.0875	0.1029	-0.0037	0.0176	0.0715	-0.0031	0.1863	4.867	110.2079	93.673
16	7.3398	-2.1602	0.0797	1.0856	0.609	0.9834	0.1238	0.0072	-0.6405	0.0253	-0.0041	0.1289	0.2251	0.0135	-0.1198	0.2138	0.0001	-0.0489	0.0252	-0.0128	0.0736	0.4307	105.0187	59.8295
17	1.6419	0.4814	-0.6752	1.3199	-0.7767	2.4914	0.0273	0.3153	0.0526	-0.3782	-0.0277	0.1372	0.2411	-0.369	0.0005	0.1351	0.0243	-0.0213	0.1374	-0.0412	0.0549	-15.4641	121.3874	57.8164
18	2.3549	-1.8369	1.6191	2.8448	-0.061	2.1684	-0.0873	0.0052	-0.0111	0.1614	0.127	-0.1061	-0.0294	0.0746	-0.0397	0.0651	0.0509	-0.0421	0.1349	-0.0602	0.1102	12.06	113.7061	65.0505
19	4.5833	3.6513	-4.4714	7.3044	-4.4364	4.9002	-0.1033	0.6838	0.1338	-0.2646	-0.0407	-0.3646	0.1583	-0.518	0.1439	0.0505	0.0553	-0.0102	0.2545	0.0386	0.1941	15.8238	123.2365	61.948
20	1.3313	-0.2084	0.2777	1.3267	0.2251	3.599	-0.0111	0.1947	0.0973	-0.1818	0.0538	-0.1116	-0.2771	0.0415	-0.0427	0.0834	-0.0124	0.0245	0.0383	-0.0036	0.0492	4.9183	130.704	53.1577

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	32 - 37
2	X-RAY DIFFRACTION	2	A	38 - 186
3	X-RAY DIFFRACTION	3	A	187 - 250
4	X-RAY DIFFRACTION	4	A	251 - 284
5	X-RAY DIFFRACTION	5	A	285 - 348
6	X-RAY DIFFRACTION	6	B	31 - 47
7	X-RAY DIFFRACTION	7	B	48 - 255
8	X-RAY DIFFRACTION	8	B	256 - 324
9	X-RAY DIFFRACTION	9	B	325 - 329
10	X-RAY DIFFRACTION	10	B	330 - 348
11	X-RAY DIFFRACTION	11	C	26 - 31
12	X-RAY DIFFRACTION	12	C	32 - 37
13	X-RAY DIFFRACTION	13	C	38 - 235
14	X-RAY DIFFRACTION	14	C	236 - 240
15	X-RAY DIFFRACTION	15	C	241 - 348
16	X-RAY DIFFRACTION	16	D	33 - 89
17	X-RAY DIFFRACTION	17	D	90 - 188
18	X-RAY DIFFRACTION	18	D	189 - 233
19	X-RAY DIFFRACTION	19	D	234 - 250
20	X-RAY DIFFRACTION	20	D	251 - 348

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