PDB-4get: Crystal structure of biogenic amine binding protein from Rhodnius...

ID or keywords:

Entry

Database: PDB / ID: 4get

Title

Crystal structure of biogenic amine binding protein from Rhodnius prolixus

Components

Biogenic amine-binding protein

Keywords

Amine-binding protein /

lipocalin /

serotonin /

norepinephrine

Function / homology

Function and homology information

histamine binding /

nitric oxide binding / extracellular region
Similarity search - Function

Biological species

Rhodnius prolixus (insect)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.24 Å

Authors

Andersen, J.F. / Chang, B.W. / Xu, X. / Mans, B.J. / Ribeiro, J.M.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure and ligand-binding properties of the biogenic amine-binding protein from the saliva of a blood-feeding insect vector of Trypanosoma cruzi.
Authors: Xu, X. / Chang, B.W. / Mans, B.J. / Ribeiro, J.M. / Andersen, J.F.

History

Deposition	Aug 2, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 2, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4get.cif.gz	323.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4get.ent.gz	277 KB	Display	PDB format
PDBx/mmJSON format	4get.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ge/4get ftp://data.pdbj.org/pub/pdb/validation_reports/ge/4get	HTTPS FTP

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Related structure data

Related structure data	4ge1C 4hfoC C: citing same article (ref.)
Similar structure data	4hfo-8 4hfo-6 4ge1-2 4ge1-3 4ge1-4 4hfo-7 4hfo-4 4hfo-2 3r9e-1 4hfo-5 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

4ge1C

4hfoC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#193 - Jan 2016 Siderocalin similarity (1) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

A: Biogenic amine-binding protein

B: Biogenic amine-binding protein

C: Biogenic amine-binding protein

D: Biogenic amine-binding protein

hetero molecules

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

1

A: Biogenic amine-binding protein

hetero molecules

defined by author&software
22.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Biogenic amine-binding protein

hetero molecules

defined by author&software
22.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Biogenic amine-binding protein

hetero molecules

defined by author&software
22.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Biogenic amine-binding protein

hetero molecules

defined by author&software
22.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	68.727, 72.331, 79.491
Angle α, β, γ (deg.)	90.000, 90.040, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Biogenic amine-binding protein Mass: 22243.807 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q86PT9
#2: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.22 Å³/Da / Density % sol: 44.61 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 8.2 Details: 28-30% PEG 6000, 0.1 M Tris, pH 8.2, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-BM / Wavelength: 1 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2008

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.24→50 Å / Num. obs: 37060 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / R_merge(I) obs: 0.081 / Χ²: 0.922 / Net I/σ(I): 9.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.24-2.33	4.6	0.363	3541	0.666	1	94.1
2.33-2.42	5.2	0.298	3608	0.671	1	98.2
2.42-2.53	5.6	0.256	3674	0.696	1	99.6
2.53-2.67	5.7	0.195	3734	0.727	1	100
2.67-2.83	5.8	0.145	3743	0.785	1	100
2.83-3.05	5.8	0.106	3700	0.86	1	100
3.05-3.36	5.8	0.075	3756	1.084	1	100
3.36-3.85	5.8	0.064	3726	1.28	1	100
3.85-4.85	5.8	0.055	3754	1.253	1	100
4.85-50	5.6	0.052	3824	1.067	1	99.8

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.11	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.24→32.919 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8027 / SU ML: 0.69 / σ(F): 1.38 / Phase error: 26.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2544	1847	4.99 %	Random
R_work	0.1846	-	-	-
obs	0.188	37034	98.89 %	-
all	-	37046	-	-

Solvent computation

Shrinkage radii: 1.13 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 22.665 Å² / k_sol: 0.284 e/Å³

Displacement parameters

B_iso max: 142.44 Å² / B_iso mean: 37.4419 Å² / B_iso min: 8.43 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.6269 Å²	-0 Å²	-1.6557 Å²
2-	-	2.3292 Å²	0 Å²
3-	-	-	0.2977 Å²

Refinement step

Cycle: LAST / Resolution: 2.24→32.919 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6180	0	32	375	6587

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	6342
X-RAY DIFFRACTION	f_angle_d	0.919	8553
X-RAY DIFFRACTION	f_chiral_restr	0.073	929
X-RAY DIFFRACTION	f_plane_restr	0.003	1094
X-RAY DIFFRACTION	f_dihedral_angle_d	12.576	2325

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.24-2.3053	0.3135	132	0.2327	2443	2575	90
2.3053-2.3731	0.3501	137	0.2303	2653	2790	97
2.3731-2.4497	0.3286	147	0.2351	2697	2844	99
2.4497-2.5372	0.3006	159	0.2296	2690	2849	100
2.5372-2.6387	0.3433	147	0.2233	2701	2848	100
2.6387-2.7588	0.3136	157	0.214	2746	2903	100
2.7588-2.9041	0.2622	146	0.2034	2718	2864	100
2.9041-3.086	0.3099	123	0.197	2718	2841	100
3.086-3.324	0.2677	144	0.1924	2735	2879	100
3.324-3.6582	0.2572	138	0.1934	2751	2889	100
3.6582-4.1866	0.2122	139	0.156	2751	2890	100
4.1866-5.2711	0.18	134	0.1334	2787	2921	100
5.2711-32.9222	0.2032	144	0.1686	2797	2941	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	2.4631	-0.2489	0.2991	1.4148	0.1157	1.8644	-0.0822	-0.2945	-0.4014	0.0517	0.245	-0.2715	0.4234	-0.1723	-0.0353	0.15	0.0074	-0.0003	0.1565	-0.0004	0.2042	5.4053	1.4268	51.2264
2	2.5359	-0.2658	0.1404	2.126	0.1919	2.3633	-0.0788	-0.0641	-0.0107	-0.12	0.1591	0.086	0.3305	-0.2298	-0.0586	0.0664	-0.0181	-0.0186	0.1368	0.0133	0.0666	4.4747	2.7671	45.0923
3	3.658	-1.3859	-0.1153	3.1856	1.7467	1.5786	0.1678	-0.0759	0.2319	0.2397	0.1285	-0.195	-0.2577	-0.2976	-0.2641	0.1867	0.0614	-0.0109	0.2155	0.0569	0.0644	8.3855	4.2637	54.8094
4	0.0273	-0.0474	-0.0503	1.7013	-1.0346	0.9235	0.0095	-0.3549	-0.047	0.5831	0.2415	-0.1434	0.181	-0.1015	0.1612	0.4328	0.2436	-0.1824	0.6021	-0.0147	0.1308	11.047	2.7049	63.8256
5	4.2254	0.378	1.3736	2.3346	1.4619	5.9348	0.1127	-0.0957	0.3901	0.1743	-0.0152	-0.0731	0.0056	-0.3276	0.0292	0.0659	0.0402	-0.0056	0.2197	-0.0124	0.1354	-3.4763	10.6031	43.5121
6	0.2838	-0.2768	0.5649	0.3644	-0.3927	1.386	0.2769	0.3221	0.3964	-0.5711	-0.0691	-0.0894	-0.7577	-0.4001	-0.1524	0.5231	0.1848	0.1289	0.3653	0.0748	0.2456	6.8955	11.5692	10.1403
7	0.1678	-0.1616	-0.348	0.331	0.3485	0.7424	0.1804	0.257	0.2272	-0.2275	-0.0216	0.1784	-0.4638	-0.6826	-0.0465	0.3583	0.1841	0.0088	0.4063	0.0674	0.0994	5.41	1.0489	8.7852
8	1.5614	-1.0065	0.9322	1.1702	-1.0458	1.075	0.1944	0.0473	-0.1475	-0.1378	-0.0626	0.1283	-0.0362	-0.2768	0.1841	0.3627	0.2275	-0.3189	0.3613	0.0756	-0.05	2.4774	-3.1571	5.8257
9	2.5867	0.541	-0.0372	3.2001	1.1018	3.5597	0.3826	0.1233	-0.0122	-0.0118	-0.2797	0.5264	-0.4142	-0.6132	0.0373	0.1177	0.1241	-0.0684	0.5515	-0.0702	0.2093	-3.1067	4.0025	12.4833
10	1.9967	0.0213	0.3527	1.1576	0.2217	3.1779	0.262	0.3393	0.1711	-0.5151	-0.0448	-0.0645	-0.3151	-0.1753	-0.1046	0.2939	0.0811	0.0905	0.3178	0.0412	0.1716	7.3556	6.6984	11.551
11	2.75	1.6295	-1.4611	1.3569	-1.4454	2.0896	0.0483	0.2602	0.1096	-0.4183	-0.1014	-0.4001	-0.0945	0.1572	-0.0131	0.4988	0.0039	0.3296	0.3167	0.1559	0.5438	19.5661	13.8091	6.4868
12	4.4313	2.9161	4.3915	4.0231	2.9567	4.8752	0.1656	1.0852	-0.1003	-0.7593	0.3358	-0.2547	0.012	0.4237	-0.2144	0.4893	0.0241	0.0648	0.4538	0.0641	0.1787	15.614	-1.3026	3.3761
13	5.2101	0.0607	4.1104	3.1377	-1.6373	4.1487	0.1152	0.0727	-0.0364	-0.4405	-0.0069	0.4214	-0.1309	-0.7642	-0.0901	0.4478	0.0632	-0.1761	0.6226	0.1222	0.2349	-9.5752	-0.0375	4.4923
14	2.1742	-0.0627	-0.7332	2.3818	0.7768	2.9364	0.061	0.1141	-0.7726	-0.4717	-0.0398	0.1645	0.7494	-0.4849	-0.1526	0.3663	-0.0549	-0.1357	0.1753	0.0245	0.3569	27.8574	-36.9478	19.6901
15	2.0822	-0.1067	0.1408	1.8097	-0.3389	1.6542	0.0119	0.123	-0.5086	-0.7842	0.173	0.1859	0.4254	-0.314	0.0224	0.3114	-0.0107	0.0033	0.0974	-0.0559	0.0882	25.326	-27.2474	13.3031
16	0.3439	-0.2315	-0.2108	3.2532	-0.3961	0.2181	0.1634	0.2027	-0.449	-0.6616	-0.0337	0.1159	0.3833	-0.1247	-0.2643	0.4754	-0.0292	-0.1973	0.2906	-0.0646	0.3861	22.9888	-33.3264	11.1851
17	2.7791	0.2302	0.7464	2.2416	0.7759	2.1327	0.203	0.2664	-0.2488	-0.9112	-0.0792	-0.1738	0.2371	0.0453	-0.1025	0.4061	0.0185	-0.0298	0.1148	-0.0225	0.2864	31.6045	-35.5242	16.0144
18	4.5051	4.9045	4.5546	5.3979	5.207	5.7138	0.1516	0.0395	-0.6243	-0.55	-0.062	-0.0171	0.4995	0.0413	-0.0969	0.3928	0.0582	-0.0102	0.1493	0.028	0.569	39.5141	-42.6787	21.6696
19	0.3531	-0.339	-0.1574	2.5856	1.0715	0.444	-0.1941	0.2696	-0.4764	-0.3289	0.0929	-0.4251	0.2731	0.1934	-0.2982	0.4231	0.1336	0.3821	0.1647	-0.095	0.3148	41.8018	-28.9688	14.0472
20	6.7654	0.8422	1.075	3.4252	0.5714	3.88	0.0619	-0.3656	-0.0383	-0.2881	0.0221	0.4928	0.1786	-0.4906	0.0676	0.1543	0.0013	-0.0487	0.1613	0.0382	0.1092	18.2403	-18.5765	17.5297
21	5.3115	3.8142	-4.8377	4.5993	-3.7144	6.4176	0.0509	-0.1008	0.3316	0.0978	-0.1265	-0.0781	-0.7942	0.1846	-0.0813	0.331	-0.0609	-0.0783	0.1513	-0.124	0.571	37.2509	12.6828	36.1417
22	1.6458	0.1602	0.4895	2.2233	1.1054	1.7668	0.0122	-0.0406	0.5124	-0.0994	-0.0182	-0.391	-0.2696	0.0056	0.0218	0.1085	-0.0024	-0.012	0.1055	0.0399	0.2947	37.0714	-1.0636	25.3351
23	2.2602	-1.1377	-1.0468	3.8265	3.0072	5.4885	0.0942	-0.3312	0.4938	0.1545	0.246	-0.4596	-0.2316	0.3287	-0.3204	0.1289	-0.0087	-0.03	0.1898	0.0012	0.2816	42.5935	-0.0085	33.9783
24	3.4138	-1.7846	-1.3344	6.7116	3.6445	2.8874	-0.0564	-0.1748	0.4929	-0.0963	0.1653	-0.2372	-0.1327	0.2109	-0.1019	0.0883	-0.0178	-0.0181	0.1664	0.0579	0.3492	47.8016	-4.0542	28.7629
25	1.4184	0.014	0.2217	0.5184	0.4154	0.7036	0.0006	0.1218	0.505	-0.1529	-0.1783	-0.3837	-0.2364	-0.0048	0.1136	0.1892	-0.0045	0.021	0.129	0.0177	0.5424	40.6201	6.3325	28.8825
26	0.9511	0.4653	-0.0134	0.3727	0.5867	2.5546	0.1822	-0.0384	0.3972	-0.0169	-0.3549	0.0305	-0.2958	-0.4724	0.0865	0.1899	0.0647	-0.0487	0.1406	-0.0735	0.4147	26.1833	7.3424	25.984
27	1.1566	0.7089	1.2199	0.4398	0.7505	1.2823	-0.2294	0.2176	0.3514	-0.3812	-0.0548	0.0723	-0.3966	-0.3214	-0.0748	0.3019	0.0914	0.1725	0.172	0.1072	0.2334	30.3555	2.114	15.8111
28	7.7969	1.777	2.9992	0.7145	0.3232	4.076	0.0877	-0.3667	-0.1168	0.1566	0.0116	-0.6005	0.1056	0.0652	-0.0945	0.1322	-0.0157	-0.0431	0.1206	0.0209	0.357	44.2303	-12.659	31.3783

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 2:53)	A	2 - 53
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 54:128)	A	54 - 128
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 129:145)	A	129 - 145
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 146:171)	A	146 - 171
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 172:196)	A	172 - 196
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 2:30)	B	2 - 30
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 31:53)	B	31 - 53
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 54:67)	B	54 - 67
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 68:100)	B	68 - 100
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 101:145)	B	101 - 145
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 146:159)	B	146 - 159
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 160:179)	B	160 - 179
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 180:195)	B	180 - 195
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESSEQ 4:30)	C	4 - 30
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESSEQ 31:100)	C	31 - 100
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESSEQ 101:114)	C	101 - 114
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESSEQ 115:145)	C	115 - 145
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESSEQ 146:159)	C	146 - 159
19	X-RAY DIFFRACTION	19	CHAIN C AND (RESSEQ 160:179)	C	160 - 179
20	X-RAY DIFFRACTION	20	CHAIN C AND (RESSEQ 180:196)	C	180 - 196
21	X-RAY DIFFRACTION	21	CHAIN D AND (RESSEQ 2:14)	D	2 - 14
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESSEQ 15:67)	D	15 - 67
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESSEQ 68:86)	D	68 - 86
24	X-RAY DIFFRACTION	24	CHAIN D AND (RESSEQ 87:100)	D	87 - 100
25	X-RAY DIFFRACTION	25	CHAIN D AND (RESSEQ 101:133)	D	101 - 133
26	X-RAY DIFFRACTION	26	CHAIN D AND (RESSEQ 134:159)	D	134 - 159
27	X-RAY DIFFRACTION	27	CHAIN D AND (RESSEQ 160:179)	D	160 - 179
28	X-RAY DIFFRACTION	28	CHAIN D AND (RESSEQ 180:195)	D	180 - 195

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

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Yorodumi