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- PDB-4gd9: Circular Permuted Streptavidin N49/G48 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4gd9
TitleCircular Permuted Streptavidin N49/G48
ComponentsStreptavidin
KeywordsBiotin-Binding Protein / biotin / circular permutation
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLe Trong, I. / Chu, V. / Xing, Y. / Lybrand, T.P. / Stayton, P.S. / Stenkamp, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin.
Authors: Le Trong, I. / Chu, V. / Xing, Y. / Lybrand, T.P. / Stayton, P.S. / Stenkamp, R.E.
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 15, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name / _software.name
Revision 1.3Sep 13, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
C: Streptavidin
D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,85210
Polymers54,6834
Non-polymers1,1696
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint-57 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.720, 85.890, 100.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Streptavidin


Mass: 13670.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical
ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsResidues 13-49 have been renumbered to 213-249 to ensure sequential residue numbering of the peptide

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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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.0 M ammonium phosphate, 0.1 M Tris-chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9794 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 83070 / Num. obs: 83070 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.067 / Χ2: 1.115 / Net I/σ(I): 25.081
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.320.8615370.92419.3
1.32-1.350.56113510.941123.5
1.35-1.370.58619830.943134.3
1.37-1.40.51723960.97141.6
1.4-1.430.51628140.962148.8
1.43-1.460.42232221.029155.9
1.46-1.50.33636191.354162.7
1.5-1.540.27642320.96173.3
1.54-1.590.23547891.001182.5
1.59-1.640.20553241.046192.3
1.64-1.70.16856811.048197.6
1.7-1.760.1356671.051197.8
1.76-1.840.14356991.106198.4
1.84-1.940.16538761.276166.6
1.94-2.060.12157861.257199
2.06-2.220.09958081.19199.4
2.22-2.450.08344571.148175.8
2.45-2.80.06558401.092198.8
2.8-3.530.05554881.085192.4
3.53-500.04645010.964172.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QCB
Resolution: 1.5→36.94 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.45 / SU B: 2.483 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 3343 5 %RANDOM
Rwork0.2006 ---
obs0.2021 63726 100 %-
all-63726 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.85 Å2 / Biso mean: 25.9489 Å2 / Biso min: 13.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3683 0 70 366 4119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023878
X-RAY DIFFRACTIONr_bond_other_d0.0010.022405
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.9125300
X-RAY DIFFRACTIONr_angle_other_deg1.98335845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8235489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.75623.58162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01815520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.951520
X-RAY DIFFRACTIONr_chiral_restr0.1240.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02876
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 183 -
Rwork0.207 3698 -
all-3881 -
obs--72.04 %
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)
18.4516-1.77921.30530.6461.26869.06040.0476-0.23630.2321-0.06710.0797-0.0937-0.40080.1875-0.12730.1413-0.0296-0.05410.1856-0.0060.181442.9706-1.972934.1844
24.34521.6095-0.38853.1667-0.54820.9963-0.0749-0.0329-0.11070.02060.0419-0.1706-0.0192-0.01560.0330.0798-0.0008-0.00640.1299-0.02760.101640.7862-6.706431.0137
35.25093.2928-2.42877.5561-4.51513.9533-0.0079-0.2097-0.28260.1608-0.0619-0.10460.07070.05790.06970.04590.01210.00250.1143-0.03380.090841.3087-11.329628.1682
417.6898-0.9526-6.240227.2127-8.16756.3276-0.1144-1.305-0.22241.7225-0.1497-0.55250.3950.62880.26420.64880.0516-0.0330.1790.00270.116744.8635-20.089830.5966
50.57880.13260.09733.3411-0.2060.52750.0444-0.03580.04060.0842-0.0779-0.0728-0.01760.02730.03350.0234-0.0073-0.00420.1256-0.00590.128241.6851-4.035823.7981
68.5929-2.91173.47999.8784.65.16620.0724-0.3085-0.67070.28260.22740.20880.2327-0.034-0.29980.035-0.01780.01180.16110.02550.195139.1882-24.053520.856
71.39030.57070.91797.49161.42710.9466-0.0348-0.06880.08750.0455-0.02140.1187-0.0399-0.01720.05620.0085-0.01780.01250.1143-0.00730.121935.5284-3.897724.6265
810.1434-4.57622.728111.943116.095131.579-0.0918-0.66130.02930.3891-0.09250.13310.1301-0.85460.18430.4561-0.02090.05110.2024-0.05320.153134.0973.645237.5322
90.79390.46820.30361.36221.00133.8689-0.01230.024-0.07850.0150.01040.0786-0.0095-0.02620.00190.00680.0019-0.00050.1203-0.00690.131431.2759-10.877420.6671
1019.3996-10.0561-6.633412.01954.71966.95320.2010.9422-0.3469-0.5199-0.29770.02740.0325-0.25940.09670.0956-0.0065-0.02070.2065-0.02840.155324.857-20.69038.0748
111.460.82462.03336.52765.97739.54530.0315-0.0038-0.06940.037-0.08870.2030.0669-0.1360.05720.0024-0.00660.01170.115-0.00290.134326.6323-13.12920.2922
1217.62663.72987.15748.05494.931813.6284-0.2293-0.94460.01240.440.0496-0.1319-0.00020.12120.17970.11350.01610.00640.1435-0.00730.141836.8566-4.118936.0235
134.4673-1.40390.37111.2345-0.19161.80140.06680.128-0.0296-0.12760.0207-0.0537-0.020.0512-0.08750.0695-0.01250.01260.1414-0.02180.129942.6566-7.5654.2404
142.62984.2062-3.845713.7055-3.31776.7771-0.1211-0.2632-0.1931-0.0102-0.2008-0.29380.28870.47540.32190.02450.02230.01940.1611-0.01080.166448.334-9.522813.0394
1519.0582-2.46374.107611.8745-4.36146.0132-0.23210.3531.11640.11640.1478-0.0681-0.5228-0.14720.08430.1824-0.00790.00640.1148-0.00980.144638.2594.13326.2989
1614.66861.57231.79718.4486-2.070618.7320.24711.01280.8995-1.7776-0.1205-0.3182-0.8040.3779-0.12660.24890.00820.0570.21790.03490.203645.38277.83456.7951
171.111-0.4072-0.19642.2866-0.2180.86030.05820.0683-0.1056-0.149-0.0722-0.09970.15210.01830.0140.04770.00640.00460.1304-0.0150.122641.0445-12.535113.0865
189.34271.0313-4.929620.1527-6.349713.67970.02850.17840.1053-0.3194-0.091-0.1337-0.43910.29780.06250.039-0.0210.0110.1441-0.02480.160845.408211.603413.3781
190.69980.0066-0.27281.96030.62920.8398-0.050.0486-0.0073-0.0590.01120.15170.03050.01610.03870.01480.0065-0.00330.118-0.00990.1236.9692-5.506311.4492
207.9301-6.951-13.27216.332711.742622.26410.07140.8295-0.2166-0.2888-0.4780.2362-0.1705-1.28310.40660.3654-0.162-0.06570.32450.00390.127934.9798-13.14291.0226
211.1923-0.13360.1262.83383.07195.7824-0.0156-0.04070.13870.08110.01820.04290.0091-0.0369-0.00260.0201-0.00110.00520.1058-0.0010.135530.84570.680117.4418
2217.41587.93442.958613.10294.80026.87050.0222-0.77980.36710.4078-0.20070.12540.0147-0.1950.17840.05770.00290.02310.1809-0.04920.172624.25018.170427.4803
233.8201-1.671-2.75151.08731.68513.97040.14130.21050.1027-0.1808-0.0613-0.0289-0.149-0.0903-0.080.062-0.00780.00770.08730.00720.135934.3358-3.85527.2498
242.9066-2.9014-3.176211.53858.69787.00650.0503-0.2556-0.16950.35780.0257-0.27510.21840.1284-0.0760.1414-0.02180.01250.25280.00740.226745.0225-17.5995-1.9176
255.8189-1.4950.22420.4152-0.46985.55180.0024-0.0971-0.3408-0.0130.04230.09220.3031-0.0448-0.04470.13010.01550.02670.18420.0090.18214.1436-9.360132.4526
269.7618-2.65911.50122.163-2.44367.60510.0043-0.48650.38460.42230.0391-0.0274-0.4806-0.1975-0.04340.197200.03280.1587-0.05120.160214.17092.44532.8901
276.41296.45840.543614.11222.21762.155-0.1085-0.10770.0815-0.31660.00610.1426-0.1883-0.22290.10240.11070.02360.01530.17710.01650.12932.4172-6.365727.3941
283.8006-1.35350.35551.99311.75372.6001-0.1367-0.01650.4711-0.1223-0.05050.1036-0.4069-0.06790.18720.17330.0080.10640.163-0.01020.26536.52741.789925.4887
291.0697-0.52980.19721.8139-0.38480.3784-0.02-0.08440.00440.21660.04480.1633-0.0615-0.0492-0.02480.06020.00540.01730.1288-0.00620.13167.2972-6.850823.9616
307.9543-4.3576-3.153717.0912.22324.43750.0571-0.05580.3614-0.3715-0.0751-0.1233-0.1926-0.18980.0180.04690.0176-0.00190.1275-0.0060.20944.195112.013517.774
311.3166-0.28690.1465.3006-2.79842.4478-0.036-0.07650.05440.1911-0.0116-0.0638-0.1001-0.02180.04760.0317-0.00630.00430.1099-0.01930.117712.5386-3.696222.8784
327.6588-0.9134-1.092511.1481-10.339532.0524-0.2597-1.00310.05561.0879-0.2942-0.38810.49460.50620.55390.2887-0.02830.00680.24720.01480.147513.6102-9.635337.5992
331.3030.8066-0.97433.9249-4.32688.7062-0.00350.03090.1434-0.09820.0366-0.00810.1565-0.0536-0.03310.0115-0.0024-0.00170.1045-0.00750.139718.3966-0.355817.736
3424.9863-12.28796.7557.1836-8.199522.76170.24530.94970.2085-0.2771-0.4789-0.13010.62750.37310.23370.2294-0.0535-0.01040.17930.05150.146725.20755.55985.0286
352.95071.5532-3.86972.8948-4.072112.259-0.0085-0.02050.06950.1267-0.042-0.0914-0.09790.03790.05050.0214-0.0017-0.00430.0895-0.01620.145122.0520.610719.7362
362.6174-2.4276-0.31622.60250.4128.5111-0.079-0.5503-0.14670.32060.2990.3997-0.3613-0.1679-0.220.2997-0.07190.13240.3026-0.13780.29257.4869-5.009436.5353
3710.2371.515-0.75520.27480.45446.46320.05550.14360.3262-0.0330.01130.0526-0.4013-0.1078-0.06690.1331-0.0143-0.04280.16680.01860.16376.3403-5.3550.9209
385.5493-2.0913-0.8183.06911.00140.7930.00960.1828-0.1953-0.0752-0.0730.11310.0021-0.01770.06340.0830.0070.00810.1454-0.0030.110610.5866-12.18723.9949
397.08040.14891.043511.91881.14986.0423-0.16950.07370.42320.0620.14140.6068-0.4464-0.23530.02810.05090.0109-0.01890.1465-0.00050.16670.5393-0.810710.3528
4017.2694-7.6649-4.589411.01725.67132.9603-0.1361-0.3062-0.6376-0.0550.12760.0237-0.02110.0880.00850.0346-0.00420.00770.12860.0040.141910.5371-17.94597.9407
4118.4856-11.2967-3.737519.7532-2.31974.68510.24571.2748-0.7099-1.691-0.53541.05051.2894-0.72470.28970.4659-0.12760.02280.2556-0.08990.20924.1122-22.46558.4025
421.24030.2646-0.16233.4555-0.36160.8106-0.02340.12440.1698-0.26180.02560.1208-0.0932-0.0108-0.00230.06060.0064-0.01980.130.00160.14698.72-1.440910.2524
4312.61984.50162.652220.668-0.965417.38490.13420.2613-0.55940.0805-0.09980.31260.8743-0.1853-0.03450.0698-0.0182-0.02030.13450.00470.19344.3811-25.012515.7751
441.2850.7612-0.14824.9225-2.08831.60020.00990.0074-0.0072-0.0436-0.0557-0.0027-0.0181-0.00990.04580.01980.01370.00050.106-0.0050.115812.9932-10.621513.8007
4513.51718.9009-0.69628.0682-2.91341.2742-0.48941.2264-0.2865-1.26990.5029-0.2962-0.5650.9074-0.01340.72250.0019-0.00250.30810.04920.13615.0072-1.3949-3.8896
461.1922-0.09790.53552.005-2.31996.3752-0.04880.0081-0.03510.00770.0311-0.0813-0.0433-0.01360.01770.01440.00590.00510.0917-0.01330.129918.0354-11.406616.0164
472.1507-0.64572.67072.6604-3.610510.78390.0134-0.1249-0.10040.1092-0.0902-0.0768-0.07860.15540.07690.00770.00340.00630.1164-0.01070.15122.9983-14.908121.2437
4813.5519-5.69364.91953.3485-1.596211.73740.35350.9364-0.4791-0.66840.01350.4611-0.40130.0935-0.3670.3384-0.1599-0.09970.28630.08970.20599.8695-8.4443-2.9266
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A214 - 222
2X-RAY DIFFRACTION2A223 - 236
3X-RAY DIFFRACTION3A237 - 248
4X-RAY DIFFRACTION4A49 - 54
5X-RAY DIFFRACTION5A55 - 83
6X-RAY DIFFRACTION6A84 - 88
7X-RAY DIFFRACTION7A89 - 96
8X-RAY DIFFRACTION8A97 - 103
9X-RAY DIFFRACTION9A104 - 115
10X-RAY DIFFRACTION10A116 - 120
11X-RAY DIFFRACTION11A121 - 128
12X-RAY DIFFRACTION12A129 - 133
13X-RAY DIFFRACTION13B213 - 235
14X-RAY DIFFRACTION14B236 - 242
15X-RAY DIFFRACTION15B243 - 248
16X-RAY DIFFRACTION16B49 - 54
17X-RAY DIFFRACTION17B55 - 79
18X-RAY DIFFRACTION18B80 - 84
19X-RAY DIFFRACTION19B85 - 100
20X-RAY DIFFRACTION20B101 - 105
21X-RAY DIFFRACTION21B106 - 115
22X-RAY DIFFRACTION22B116 - 120
23X-RAY DIFFRACTION23B121 - 135
24X-RAY DIFFRACTION24B136 - 143
25X-RAY DIFFRACTION25C213 - 221
26X-RAY DIFFRACTION26C222 - 227
27X-RAY DIFFRACTION27C228 - 236
28X-RAY DIFFRACTION28C237 - 248
29X-RAY DIFFRACTION29C50 - 79
30X-RAY DIFFRACTION30C80 - 84
31X-RAY DIFFRACTION31C85 - 99
32X-RAY DIFFRACTION32C100 - 104
33X-RAY DIFFRACTION33C105 - 115
34X-RAY DIFFRACTION34C116 - 120
35X-RAY DIFFRACTION35C121 - 129
36X-RAY DIFFRACTION36C130 - 143
37X-RAY DIFFRACTION37D213 - 222
38X-RAY DIFFRACTION38D223 - 233
39X-RAY DIFFRACTION39D234 - 240
40X-RAY DIFFRACTION40D241 - 248
41X-RAY DIFFRACTION41D49 - 54
42X-RAY DIFFRACTION42D55 - 79
43X-RAY DIFFRACTION43D80 - 84
44X-RAY DIFFRACTION44D85 - 96
45X-RAY DIFFRACTION45D97 - 103
46X-RAY DIFFRACTION46D104 - 115
47X-RAY DIFFRACTION47D116 - 129
48X-RAY DIFFRACTION48D130 - 134

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