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- PDB-4ge1: Structure of the tryptamine complex of the amine binding protein ... -

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Basic information

Entry
Database: PDB / ID: 4ge1
TitleStructure of the tryptamine complex of the amine binding protein of Rhodnius prolixus
ComponentsBiogenic amine-binding protein
KeywordsAmine-binding protein / Lipocalin Binding protein / Serotonin / norepinephrine / Salivary gland
Function / homology
Function and homology information


histamine binding / nitric oxide binding / extracellular region
Similarity search - Function
Nitrophorin domain / Nitrophorin / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
2-(1H-INDOL-3-YL)ETHANAMINE / Biogenic amine-binding protein
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsAndersen, J.F. / Chang, B.W. / Xu, X. / Mans, B.J. / Ribeiro, J.M.
CitationJournal: 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
DepositionAug 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Oct 16, 2024Group: 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biogenic amine-binding protein
B: Biogenic amine-binding protein
C: Biogenic amine-binding protein
D: Biogenic amine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,80010
Polymers88,9754
Non-polymers8256
Water3,171176
1
A: Biogenic amine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4042
Polymers22,2441
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Biogenic amine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4963
Polymers22,2441
Non-polymers2522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Biogenic amine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4963
Polymers22,2441
Non-polymers2522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Biogenic amine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4042
Polymers22,2441
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.257, 73.086, 80.935
Angle α, β, γ (deg.)90.000, 91.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q86PT9
#2: Chemical
ChemComp-TSS / 2-(1H-INDOL-3-YL)ETHANAMINE / TRYPTAMINE


Mass: 160.216 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.92309 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2008
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92309 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 43654 / Num. obs: 43654 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.461 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.194.60.61520260.845191.8
2.19-2.234.70.61120900.86196.3
2.23-2.274.80.48421400.915197.9
2.27-2.3250.58321730.832199
2.32-2.375.10.45821890.88199.5
2.37-2.425.20.41121810.914199.6
2.42-2.485.30.38121700.906199.4
2.48-2.555.30.33121710.952199.7
2.55-2.625.30.26222010.955199.6
2.62-2.715.30.21822081.025199.6
2.71-2.815.30.17321921.09199.7
2.81-2.925.30.14422061.183199.8
2.92-3.055.30.11422011.381199.7
3.05-3.215.30.08821801.667199.9
3.21-3.415.30.07322051.88199.8
3.41-3.685.30.06322062.164199.9
3.68-4.055.30.05922342.651199.8
4.05-4.635.20.05121962.785199.9
4.63-5.835.20.04522412.5031100
5.83-5050.03722442.483198.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.15→25.348 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.7643 / SU ML: 0.68 / σ(F): 1.34 / Phase error: 29.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 2200 5.04 %Random
Rwork0.1921 ---
obs0.195 43619 98.76 %-
all-43654 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.789 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso max: 149.12 Å2 / Biso mean: 56.0103 Å2 / Biso min: 18.92 Å2
Baniso -1Baniso -2Baniso -3
1--8.2967 Å2-0 Å2-5.3411 Å2
2---4.573 Å20 Å2
3---12.8696 Å2
Refinement stepCycle: LAST / Resolution: 2.15→25.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6183 0 60 176 6419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056392
X-RAY DIFFRACTIONf_angle_d0.9038615
X-RAY DIFFRACTIONf_chiral_restr0.073930
X-RAY DIFFRACTIONf_plane_restr0.0031098
X-RAY DIFFRACTIONf_dihedral_angle_d13.8452334
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.19510.3331240.25882313243789
2.1951-2.24610.32941320.2632541267397
2.2461-2.30230.36281370.26462554269199
2.3023-2.36450.34391280.25826012729100
2.3645-2.4340.32531280.249625982726100
2.434-2.51250.3241670.257525852752100
2.5125-2.60220.36951320.24222594272699
2.6022-2.70630.29351260.238726132739100
2.7063-2.82930.30431380.220525932731100
2.8293-2.97820.29841590.225825842743100
2.9782-3.16450.3061320.213126402772100
3.1645-3.40830.28831200.207226302750100
3.4083-3.75030.25391580.192826002758100
3.7503-4.29070.19161370.16426372774100
4.2907-5.39730.18441300.134626642794100
5.3973-25.34980.18621520.16052672282499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.5137-0.01120.3784.50690.69172.2622-0.0645-0.1679-0.78230.11840.1414-0.53870.3346-0.07850.0160.156-0.01230.04240.23930.00010.24313.6613.760151.1071
24.5801-0.68410.22714.9151-0.14383.59890.00970.1003-0.6982-0.31140.0583-0.20430.3733-0.0064-0.03650.1645-0.03290.00530.2462-0.01490.26953.81420.738745.5857
35.9245-1.1951.18546.28342.36943.6278-0.2425-0.16450.48170.49360.6077-0.66610.1233-0.0479-0.37880.25570.0292-0.07960.28930.04930.21857.32464.485755.6447
42.9729-0.0663-0.54314.7154-2.43622.2590.2032-1.2288-0.47721.24750.2083-0.29910.7920.3195-0.09370.70690.1303-0.21830.64380.06180.28619.9242.916864.8534
57.95241.03571.97694.37453.34486.94140.24660.090.1615-0.0022-0.3250.70120.281-0.44510.08750.24630.03680.01120.28430.04830.2032-4.536510.761544.102
64.1573-3.11143.55784.0068-0.9284.7983-0.41920.34441.4367-0.00980.27610.0824-1.1772-0.08830.30420.61220.1364-0.07220.42550.1131.00847.222716.551117.7249
72.76680.10770.08671.86110.48231.51480.33650.62320.8958-0.59530.07910.4625-0.2554-0.5251-0.16210.48670.2324-0.15380.68160.2816-0.03374.38542.3536.9961
83.33011.6870.55584.72412.76753.66620.23810.62010.9568-0.1472-0.50630.7379-0.6047-0.560.30530.19980.0754-0.12830.68270.13490.6033-2.667.490612.3811
97.06133.290.48275.50454.56147.95850.10550.254-0.4762-0.6563-0.72851.78120.2614-1.71450.34380.3460.0239-0.19460.80810.1020.5844-5.1403-0.57712.651
103.20350.66870.95213.50191.7014.58410.2220.53170.8062-0.5679-0.1330.1122-0.2193-0.1369-0.03460.30290.1372-0.00470.47430.17940.31826.85946.369412.1533
115.45640.68640.27530.1009-0.1092.0596-0.58420.83720.4763-1.1751-0.013-0.7362-0.71721.05660.17960.8796-0.03580.37160.50150.31040.793219.051713.85126.7675
124.9658-0.68852.29992.61351.25082.05720.42041.49340.3593-0.96840.209-0.0848-0.16160.2288-0.34240.63460.03390.03560.8110.17790.264515.2375-1.41223.7589
137.19871.121-0.38945.9881-0.19460.96570.36470.41770.58-1.1824-0.23721.45730.0689-1.02880.2290.42750.0709-0.31791.16760.06630.5483-10.15140.07584.5718
142.1496-0.9559-0.54881.6645-0.10743.97190.03240.081-1.334-0.35310.0324-0.09470.9916-0.51420.07780.3465-0.0685-0.01830.1711-0.09790.609427.2639-37.322820.1407
152.7305-1.12371.17334.25610.5492.2455-0.11440.5034-1.1065-1.07740.0039-0.57160.1656-0.0591-0.17570.4324-0.02930.16630.1681-0.17320.2929.3495-28.589513.7177
164.9708-0.34440.20642.2086-0.06532.3992-0.01670.3077-0.7411-0.60460.01-0.23610.2562-0.289-0.05910.3110.02750.07060.2693-0.07480.197423.8884-27.734915.1739
173.789-0.1890.72854.2818-0.55492.80750.17680.5695-0.7477-0.82410.01820.21320.3898-0.266-0.06080.37970.01020.01710.4178-0.13730.279621.046-29.314111.2773
183.96120.28631.28763.40291.62457.4838-0.15390.4967-0.7718-1.2447-0.3125-0.52690.0008-0.06260.03360.6283-0.02120.15060.2105-0.14780.656928.4136-37.50713.5341
195.50910.29480.51444.56151.95465.74270.0359-0.0764-0.5003-0.7111-0.1546-1.2792-0.05530.52740.28330.3195-0.00610.12520.23510.04020.705435.7212-33.107120.7585
201.10511.07232.03431.891.88144.0699-0.07510.0235-0.24780.0946-0.2127-0.36820.38560.2334-0.02210.340.08410.15380.19650.04381.350139.0408-43.209622.1403
210.3024-1.21510.02465.96780.25260.0779-0.07880.7193-1.1137-0.8804-0.4614-0.97640.52050.2407-0.17910.56030.10410.41160.3263-0.05680.876741.2766-29.170314.5746
222.95433.7091.18685.53870.46932.175-0.1525-0.27880.1328-0.06510.03450.4777-0.3223-0.45010.13470.32270.05090.05710.4098-0.02020.196417.6782-18.737218.0692
232.08742.5588-0.55026.4721-1.90441.61830.0629-0.19061.24470.2782-0.04060.147-0.9569-0.0201-0.30760.60320.0593-0.26950.3528-0.19861.255535.597112.126437.6278
242.4839-0.34310.40782.95150.18891.8687-0.2026-0.09570.9225-0.0379-0.0846-0.4959-0.36260.08350.12710.20560.0025-0.07450.20180.0680.518237.8206-0.902328.2539
256.1844-3.9531-3.32774.6145.86428.9613-0.0896-0.15370.5789-0.46590.0985-0.828-0.59270.3978-0.14950.2729-0.0189-0.06280.24920.1570.572347.1089-4.185529.418
261.48510.3164-0.89814.4651.5623.42820.0812-0.44671.2723-0.1003-0.1169-1.2025-0.42390.2436-0.04270.3859-0.0232-0.10290.2877-0.00840.773643.27913.975730.8129
271.50260.56270.56411.8160.44822.3269-0.23350.08530.5939-0.3058-0.4115-0.6755-0.65150.09640.24110.46440.0212-0.13470.18170.10360.965837.04967.63729.1195
281.1252-0.0764-0.35572.26290.5092.2517-0.14010.46711.0277-0.3581-0.346-0.5069-0.5695-0.30340.28280.38410.1528-0.0860.26710.05150.601427.71435.256422.227
293.67672.95264.70315.60831.8428.56290.3610.0146-0.61970.4421-0.0491-1.06080.35990.1412-0.26010.25340.0237-0.0140.23880.05030.4744.0203-12.672532.7247
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:67)A2 - 67
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 68:128)A68 - 128
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 129:145)A129 - 145
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 146:171)A146 - 171
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 172:196)A172 - 196
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 2:14)B2 - 14
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 15:67)B15 - 67
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 68:86)B68 - 86
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 87:100)B87 - 100
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 101:145)B101 - 145
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 146:159)B146 - 159
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 160:179)B160 - 179
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 180:195)B180 - 195
14X-RAY DIFFRACTION14CHAIN C AND (RESSEQ 4:30)C4 - 30
15X-RAY DIFFRACTION15CHAIN C AND (RESSEQ 31:53)C31 - 53
16X-RAY DIFFRACTION16CHAIN C AND (RESSEQ 54:86)C54 - 86
17X-RAY DIFFRACTION17CHAIN C AND (RESSEQ 87:114)C87 - 114
18X-RAY DIFFRACTION18CHAIN C AND (RESSEQ 115:133)C115 - 133
19X-RAY DIFFRACTION19CHAIN C AND (RESSEQ 134:145)C134 - 145
20X-RAY DIFFRACTION20CHAIN C AND (RESSEQ 146:159)C146 - 159
21X-RAY DIFFRACTION21CHAIN C AND (RESSEQ 160:179)C160 - 179
22X-RAY DIFFRACTION22CHAIN C AND (RESSEQ 180:196)C180 - 196
23X-RAY DIFFRACTION23CHAIN D AND (RESSEQ 3:14)D3 - 14
24X-RAY DIFFRACTION24CHAIN D AND (RESSEQ 15:86)D15 - 86
25X-RAY DIFFRACTION25CHAIN D AND (RESSEQ 87:100)D87 - 100
26X-RAY DIFFRACTION26CHAIN D AND (RESSEQ 101:114)D101 - 114
27X-RAY DIFFRACTION27CHAIN D AND (RESSEQ 115:132)D115 - 132
28X-RAY DIFFRACTION28CHAIN D AND (RESSEQ 133:179)D133 - 179
29X-RAY DIFFRACTION29CHAIN D AND (RESSEQ 180:196)D180 - 196

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