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- PDB-3lr2: Self-assembly of spider silk proteins is controlled by a pH-sensi... -

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Basic information

Entry
Database: PDB / ID: 3lr2
TitleSelf-assembly of spider silk proteins is controlled by a pH-sensitive relay
ComponentsMajor ampullate spidroin 1
KeywordsSTRUCTURAL PROTEIN / dragline spider silk / self-assembly / pH-dependence / NT wild-type
Function / homology
Function and homology information


identical protein binding
Similarity search - Function
Spidroin, N-terminal domain / Spidroin, N-terminal / Major ampullate spidroin 1, spider silk protein 1, N-term / Spidroin, N-terminal domain superfamily / Enzyme I; Chain A, domain 2 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Major ampullate spidroin 1
Similarity search - Component
Biological speciesEuprosthenops australis (spider)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAskarieh, G. / Hedhammar, H. / Nordling, K. / Johansson, J. / Knight, S.D. / Rising, A. / Casals, C. / Saenz, A.
CitationJournal: Nature / Year: 2010
Title: Self-assembly of spider silk proteins is controlled by a pH-sensitive relay.
Authors: Askarieh, G. / Hedhammar, M. / Nordling, K. / Saenz, A. / Casals, C. / Rising, A. / Johansson, J. / Knight, S.D.
History
DepositionFeb 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Major ampullate spidroin 1
B: Major ampullate spidroin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5364
Polymers28,3672
Non-polymers1682
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-21 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.379, 68.379, 97.857
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

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Components

#1: Protein Major ampullate spidroin 1


Mass: 14183.714 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Euprosthenops australis (spider) / Gene: MaSp1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q05H60
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: ammonium sulphate, PEG 400, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONESRF ID14-21
SYNCHROTRONESRF ID14-42
Detector
TypeIDDetector
ADSC QUANTUM 3151CCD
2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→59.23 Å / Num. obs: 27832
Reflection shellResolution: 1.7→1.744 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 8.4 / Rsym value: 0.06

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→59.2 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.547 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1486 5.1 %RANDOM
Rwork0.16 ---
obs0.163 27832 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.7→59.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 11 126 1989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222023
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9472786
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0385306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81127.12373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70215357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.855152
X-RAY DIFFRACTIONr_chiral_restr0.0880.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021526
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.21022
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21451
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2101
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3251.51374
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.94422202
X-RAY DIFFRACTIONr_scbond_it3.5183711
X-RAY DIFFRACTIONr_scangle_it5.0474.5549
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 117 -
Rwork0.165 2054 -
obs--99.95 %
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)
115.1709-1.5674-7.053920.28152.056411.76940.0422-0.4223-0.2121-0.0230.01450.44790.1312-0.4097-0.05670.0513-0.0154-0.01750.1265-0.00060.026118.994612.50776.3212
28.6475-0.09291.18492.30220.00952.66130.00210.02950.13740.096-0.08390.0135-0.0367-0.06340.08170.11780.00350.0060.07770.00110.049225.096515.94856.3062
36.2985-1.2791.49558.5053-0.51153.7422-0.1795-0.00720.0159-0.04420.04140.048-0.06230.0760.13810.1128-0.018-0.00410.06820.01350.015434.360911.80927.6492
420.3632-16.84497.8814.0286-5.795810.1344-0.7483-0.32870.54140.90680.2453-0.7012-0.0599-0.01480.5030.106-0.0175-0.04470.04890.01960.009640.23938.272812.6681
53.14530.2643-3.42911.0369-7.40078.33110.034-0.05430.0380.0683-0.3082-0.50510.07990.29540.27430.04020.01920.00170.03950.05080.056446.50783.93946.1153
616.6587-8.92324.61212.40834.89938.39660.3720.15280.5707-0.3291-0.3472-0.61970.11-0.0885-0.02480.085900.02760.05020.06250.067743.19049.89372.3388
721.9625-5.5345-0.14423.0201-2.10452.82060.21840.59250.0006-0.1829-0.3021-0.175-0.0452-0.00180.08370.1160.02240.01040.10460.02320.05435.963314.3674-1.1638
810.7231-7.24035.65896.6749-0.82488.5437-0.08560.52250.5175-0.1349-0.1187-0.225-0.12650.35550.20430.09480.01650.00730.11160.04870.069128.972119.9066-3.1502
96.7438-1.7718.07915.5255-3.17049.7516-0.17150.13530.2688-0.1489-0.0511-0.11730.01970.28920.22250.06480.04220.01620.13590.03210.053621.719221.8796-6.2007
1014.747-8.6231-2.850312.2140.90067.9615-0.04650.2753-0.34510.2937-0.0040.39160.1789-0.56720.05050.0706-0.0246-0.00230.1327-0.00810.054719.610711.4109-2.9244
1112.8097-4.4158.91341.7811-3.576311.8116-0.140.16590.17030.2518-0.0362-0.21750.07780.05280.17620.12520.0002-0.02270.0602-0.01560.052928.35437.9924-0.5325
124.7159-4.1435-2.7727.53094.48976.36490.15630.23470.0204-0.1545-0.191-0.0936-0.00120.06890.03470.1290.00710.01770.09650.02860.038435.29033.0638-0.9257
1321.51321.44925.18653.86923.39543.71040.29440.6475-0.1583-0.0857-0.3086-0.24220.41870.20340.01420.14320.0880.02810.08340.02560.029443.5657-0.8319-0.7941
1417.28671.9797-4.97062.3826-4.05687.07090.0570.021-0.416-0.044-0.341-0.01420.42750.17950.2840.11290.05510.02590.0250.04060.02643.8415-4.18387.4502
157.6336-5.3825-3.38568.07265.04713.9512-0.0433-0.1202-0.05020.1264-0.02940.10440.1305-0.09120.07270.1108-0.00930.0190.06320.02040.030135.93460.645210.9544
167.5277-5.2087-3.54858.63512.89137.2651-0.05-0.08930.01740.08010.1316-0.1326-0.14650.0598-0.08160.1156-0.01050.00080.0640.00940.048829.33947.726913.5593
170.1562-1.1471-0.674711.23823.51323.6509-0.04060.0846-0.0744-0.22340.03240.3796-0.1708-0.23830.00820.11810.0123-0.00030.09130.01380.088822.85827.509513.6514
184.91-2.7834-5.05626.00913.92710.50420.0642-0.2075-0.0027-0.2588-0.0680.0504-0.0577-0.12140.00380.101-0.0172-0.00840.02880.00160.032625.4907-1.08168.7595
197.8579-0.9963-5.90393.3573-1.27579.1467-0.00940.07920.0515-0.29120.02620.00420.051-0.2809-0.01690.1694-0.0071-0.00170.0058-0.00160.002230.3606-3.76043.0085
2011.1205-6.14772.613630.2822-0.187211.85560.16340.3298-0.1976-1.2202-0.0866-0.10870.96660.0435-0.07680.22950.04790.0463-0.0448-0.0227-0.02635.7509-7.744-2.8523
2118.39065.16922.307133.16331.206811.9650.0696-0.4244-1.1021-0.3128-0.3369-0.25410.35660.75010.26720.11160.02860.01320.0277-0.00160.052842.33243.1569-16.0186
2217.1095-1.87745.03814.93390.35297.5295-0.43680.083-0.0248-0.00920.07790.017-0.40620.15430.3590.1396-0.01630.00390.0570.00480.036640.451310.8581-17.3508
237.19745.2939-2.599.62761.78526.8922-0.14880.1102-0.01760.0299-0.0634-0.0655-0.173-0.38360.21220.11770.0127-0.00350.0811-0.00980.025732.82348.6435-19.5489
2419.23093.1247-0.56898.96275.64767.8784-0.21240.03990.3038-0.180.05580.1728-0.7459-0.47810.15660.1134-0.0011-0.00550.1449-0.01830.039425.47316.8162-20.3884
2523.472517.1677-10.302518.379-5.658926.2919-0.42840.98790.1479-0.48810.10680.19650.3129-1.3330.32160.01960.0078-0.0770.206-0.05020.103318.23693.0234-20.7991
2616.445911.8274.97819.32712.098910.9361-0.02830.23310.595-0.096-0.2731.0986-0.2848-0.71530.30130.010.0164-0.04620.2457-0.07980.121215.7519.6017-14.8319
2712.94398.36970.8076.8587-0.06089.75880.17480.39270.1055-0.15910.03780.1070.068-0.2287-0.21270.07560.0042-0.02160.1117-0.01350.053523.375212.085-12.008
288.04483.6132-2.38243.56122.3036.5753-0.00060.0480.3045-0.0433-0.20960.0717-0.0902-0.25690.21020.11150.0168-0.00950.12750.0090.090230.859615.7141-11.5247
2912.43123.51082.12551.90161.55295.6184-0.05150.05590.24270.08-0.00070.0834-0.1328-0.00230.05220.1028-0.0115-0.00320.07880.02430.065839.509118.0254-10.5719
301.85664.7751-0.09712.3349-0.52421.42690.0895-0.0527-0.03280.0503-0.1758-0.2496-0.04250.08560.08640.1079-0.02-0.00250.11110.0130.069745.470114.2791-7.6623
3117.42284.48832.19853.0891-0.45753.8617-0.0804-0.2671-0.2294-0.01150.0419-0.12440.2585-0.11030.03850.1281-0.0191-0.00350.07410.0090.037739.44285.8382-7.9621
3210.6822.84663.35631.21172.43716.307-0.14420.1604-0.1487-0.15280.06730.2197-0.23850.08090.0770.1255-0.0247-0.00890.1051-0.00560.063927.88484.8173-9.0683
3313.016-7.37283.69386.916-1.08591.43150.04350.0062-0.2079-0.0816-0.18170.31780.2683-0.42830.13820.0563-0.090.0230.1814-0.0570.067318.48443.5617-7.2538
3417.2407-8.1815-1.451316.14613.53672.97310.3409-0.4914-0.48040.4668-0.56790.73931.3344-0.74430.2270.0439-0.2560.0330.279-0.08230.090413.4196-2.1191-12.4538
3514.92963.9303-6.88841.6635-0.96744.3164-0.1983-0.0593-0.2642-0.2208-0.1461-0.10350.357-0.19790.34440.1245-0.06610.00180.1292-0.03990.084424.0285-1.9369-17.8614
3612.94490.8640.51667.9437-0.717413.6166-0.00480.2020.1292-0.35940.16370.04630.0907-0.2168-0.15890.1421-0.01880.01960.0581-0.01010.055733.57351.81-24.1045
378.0571-3.1013-4.920417.0567-1.75694.9326-0.2004-0.2318-0.02970.44980.0217-0.69030.0490.37850.17870.1391-0.0095-0.00520.0854-0.01630.034138.3029-0.5595-21.9422
3822.7096-2.6173-19.9414.975-7.119833.9414-0.5881-0.5629-0.6312-0.1646-0.0794-0.34351.9620.76040.66760.23560.01920.06250.07190.05210.048433.4709-5.8994-14.458
3921.765-3.0704-7.79489.5629-2.594911.7522-0.3460.0056-0.43570.2149-0.2762-0.07351.01190.22060.62220.219-0.05090.0350.03610.01080.011827.9107-4.885-8.8495
4018.40773.39522.06971.8479-2.999714.19460.52370.1271-0.33840.2456-0.55210.20151.4948-0.55360.02840.2191-0.17730.09360.0603-0.05140.037921.3236-4.7865-2.6395
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 10
2X-RAY DIFFRACTION2A11 - 19
3X-RAY DIFFRACTION3A20 - 24
4X-RAY DIFFRACTION4A25 - 30
5X-RAY DIFFRACTION5A31 - 37
6X-RAY DIFFRACTION6A38 - 42
7X-RAY DIFFRACTION7A43 - 49
8X-RAY DIFFRACTION8A50 - 55
9X-RAY DIFFRACTION9A56 - 61
10X-RAY DIFFRACTION10A62 - 68
11X-RAY DIFFRACTION11A69 - 73
12X-RAY DIFFRACTION12A74 - 79
13X-RAY DIFFRACTION13A80 - 85
14X-RAY DIFFRACTION14A86 - 93
15X-RAY DIFFRACTION15A94 - 100
16X-RAY DIFFRACTION16A101 - 107
17X-RAY DIFFRACTION17A108 - 113
18X-RAY DIFFRACTION18A114 - 118
19X-RAY DIFFRACTION19A119 - 124
20X-RAY DIFFRACTION20A125 - 130
21X-RAY DIFFRACTION21B7 - 11
22X-RAY DIFFRACTION22B12 - 17
23X-RAY DIFFRACTION23B18 - 22
24X-RAY DIFFRACTION24B23 - 27
25X-RAY DIFFRACTION25B28 - 33
26X-RAY DIFFRACTION26B34 - 39
27X-RAY DIFFRACTION27B40 - 45
28X-RAY DIFFRACTION28B46 - 50
29X-RAY DIFFRACTION29B51 - 57
30X-RAY DIFFRACTION30B58 - 63
31X-RAY DIFFRACTION31B64 - 71
32X-RAY DIFFRACTION32B72 - 78
33X-RAY DIFFRACTION33B79 - 84
34X-RAY DIFFRACTION34B85 - 91
35X-RAY DIFFRACTION35B92 - 102
36X-RAY DIFFRACTION36B103 - 107
37X-RAY DIFFRACTION37B108 - 113
38X-RAY DIFFRACTION38B114 - 118
39X-RAY DIFFRACTION39B119 - 124
40X-RAY DIFFRACTION40B125 - 130

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