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- PDB-5dzb: 6beta1 -

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Basic information

Entry
Database: PDB / ID: 5dzb
Title6beta1
Components6beta1
KeywordsDE NOVO PROTEIN / synthetic protein / loop design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsKabasakal, B.V. / MacDonald, J.T. / Murray, W.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension.
Authors: MacDonald, J.T. / Kabasakal, B.V. / Godding, D. / Kraatz, S. / Henderson, L. / Barber, J. / Freemont, P.S. / Murray, J.W.
History
DepositionSep 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6beta1
B: 6beta1
C: 6beta1
D: 6beta1
E: 6beta1
F: 6beta1


Theoretical massNumber of molelcules
Total (without water)161,1866
Polymers161,1866
Non-polymers00
Water00
1
A: 6beta1
B: 6beta1


Theoretical massNumber of molelcules
Total (without water)53,7292
Polymers53,7292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-15 kcal/mol
Surface area18140 Å2
MethodPISA
2
C: 6beta1
D: 6beta1


Theoretical massNumber of molelcules
Total (without water)53,7292
Polymers53,7292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-15 kcal/mol
Surface area18300 Å2
MethodPISA
3
E: 6beta1
F: 6beta1


Theoretical massNumber of molelcules
Total (without water)53,7292
Polymers53,7292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-14 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.960, 86.530, 362.320
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
6beta1


Mass: 26864.357 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pRSETA / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 7.5 / Details: 20% v/v 1,4 butanediol HEPES pH 7.5, 0.2 M NaCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.33→90.58 Å / Num. all: 355691 / Num. obs: 26271 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.08 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.61
Reflection shellResolution: 3.33→3.42 Å / Redundancy: 7.17 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.88 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted structure

Resolution: 3.33→90.58 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 1350 5.03 %throughout
Rwork0.1967 ---
obs0.2002 26860 98.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.33→90.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10212 0 0 0 10212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910296
X-RAY DIFFRACTIONf_angle_d1.42513980
X-RAY DIFFRACTIONf_dihedral_angle_d14.6926204
X-RAY DIFFRACTIONf_chiral_restr0.0891638
X-RAY DIFFRACTIONf_plane_restr0.0091938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.33-3.44910.34051290.29192492X-RAY DIFFRACTION100
3.4491-3.58710.30041150.24592572X-RAY DIFFRACTION100
3.5871-3.75040.33881530.22972492X-RAY DIFFRACTION100
3.7504-3.94810.22981410.17342524X-RAY DIFFRACTION100
3.9481-4.19550.23011390.15522532X-RAY DIFFRACTION99
4.1955-4.51940.22421210.16052494X-RAY DIFFRACTION97
4.5194-4.97420.23341390.18022412X-RAY DIFFRACTION94
4.9742-5.69390.28971370.18422591X-RAY DIFFRACTION98
5.6939-7.17330.2431340.23062633X-RAY DIFFRACTION100
7.1733-90.61350.27941420.19622768X-RAY DIFFRACTION99
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)
12.2315-1.3191-1.2511.50772.3914.34861.13391.32640.1959-1.1346-0.2278-0.01120.12810.4811-0.61091.2681-0.4776-0.00581.64520.03510.753817.8017-26.5698-31.3702
25.6234-0.39120.21235.1397-0.82695.8698-0.1330.20590.68730.00990.05770.0705-1.83490.48450.07281.0744-0.225-0.02760.98940.04850.890716.0286-20.4758-23.202
32.3205-0.85460.63091.30380.56133.69680.4978-0.1132-0.4111-0.4921-0.02850.98751.5531-0.432-0.35511.0659-0.13970.02130.64790.11421.213811.1642-28.325-18.2618
48.8542-0.30351.40597.2908-0.20728.0398-0.41591.38680.4638-1.09560.0039-0.4793-0.60151.76730.29270.8593-0.23220.04191.07120.07180.903717.1243-20.9518-13.7192
56.9415-0.49031.29764.73611.63523.7122-0.7606-0.41910.56140.49550.60330.7162-0.4570.186-0.15580.6418-0.0874-0.01160.7140.11291.00279.9744-23.8929-9.15
64.30050.8222-1.67132.77520.43868.3016-0.1129-0.50650.3550.2152-0.18870.0711-0.38530.52320.23780.74760.0814-0.05710.750.03090.920613.5018-19.27490.8998
73.38592.20642.49071.47911.72462.80960.00850.0263-1.4862-0.5927-0.25920.12552.1705-0.12580.10770.95340.42-0.04630.91990.160.97799.4417-25.568611.1426
87.67160.23080.0913.2662-0.29646.95280.38810.97741.0121-0.6357-0.3477-0.3571-0.2930.8315-0.01680.91330.0297-0.2280.8356-0.15141.01914.6233-15.947212.6399
96.0773-0.00330.6433.3041-0.03484.0336-0.1451-1.72640.06650.46190.4634-0.2405-0.3044-0.4654-0.29010.75340.167-0.0571.1544-0.13140.880711.9569-19.906218.9942
102.92294.22030.14596.6496-1.27187.0722-0.34981.7897-0.1870.09280.21040.2669-1.4894-1.51740.05031.03960.4257-0.05211.2423-0.14240.908713.3002-14.552228.5345
110.21760.53550.11751.35730.47970.5227-0.3745-0.55182.16760.7873-0.27133.0449-0.23940.0310.13222.1621.57340.96294.68171.46853.6227-6.3714-28.799489.7448
122.11760.649-0.81849.51520.32833.9327-0.5025-1.3543-0.03922.14611.62161.5071-0.0206-1.1347-0.8941.41150.30320.19182.65840.16531.40260.9685-28.906882.3834
137.07515.90383.33779.80954.49289.0581-0.94330.8886-0.1348-0.3554-0.26611.13870.2837-0.45291.06041.0427-0.15140.07652.3709-0.27941.1285-5.8602-32.321475.1172
148.18241.59950.55783.811-0.79043.24280.6037-1.32830.02280.3401-0.91880.6609-0.6327-2.58130.36181.09280.14590.04382.6616-0.13210.99191.7251-25.185973.5905
151.5381-0.80390.37597.9046-0.18440.11860.46970.1658-0.3742-1.9169-1.0331.47490.7705-0.68590.62980.9355-0.1901-0.06712.9098-0.26411.06310.0166-31.02266.8409
163.80530.01640.26963.5041-2.32244.89180.12310.19030.23220.4368-0.19460.5089-0.4889-1.58820.0471.09570.2764-0.0161.8763-0.14211.01785.9495-24.695759.0392
171.33212.5632-0.95048.9453-0.03329.03930.3601-0.34130.4587-1.0479-0.79311.18611.5049-1.00170.64620.86580.2761-0.07762.06770.01960.80271.9888-26.257147.134
184.0362-0.87590.08564.3940.76153.2017-0.2293-1.2669-0.02980.98180.0849-0.3138-0.4397-0.69510.2181.06610.16220.00941.3113-0.02790.945911.0742-20.477348.7666
196.2228-0.8861-0.78734.62080.46785.08690.81260.60350.3556-0.4532-0.82040.1347-0.7221-1.7023-0.07661.07940.3218-0.20861.2657-0.11520.92918.6509-21.598741.3677
203.62370.635-0.55023.62922.0496.3619-0.48320.03840.3342-0.12570.47690.2015-0.68310.19690.05241.06540.0987-0.17881.00180.08590.833515.8254-17.958233.8318
218.3108-1.65992.55540.81340.31032.31920.3996-0.39062.11450.3470.69070.02220.4495-0.2076-0.91992.00720.04260.19983.4164-0.05561.76123.779114.864965.4984
224.3072-2.0968-0.37023.1752-1.55272.2792-0.4652-1.2948-0.57550.3303-0.01890.60220.3746-0.57380.37631.00950.1190.13562.15040.00491.027510.107213.292257.2243
232.8189-2.43662.50592.5705-2.12122.2374-1.04211.0248-0.35530.6516-0.09240.54690.8795-2.4821.38441.0535-0.17850.22112.3813-0.00221.09472.035710.079350.973
243.75490.79780.62843.1679-0.18163.1460.1738-1.08590.36980.0424-0.6310.4748-0.6123-1.10480.40380.87190.21530.0061.5311-0.19461.005810.13716.015647.9669
251.85312.38460.32446.18041.5910.89190.1209-0.4546-0.3007-2.4223-0.09310.63290.78420.55990.0831.0637-0.20210.08821.7340.02610.86047.16739.843342.1383
264.7557-0.98370.38013.4935-0.38075.0873-0.0759-0.62150.0561-0.0118-0.19570.1014-0.1379-0.71540.18940.89440.1192-0.06141.1948-0.04750.848212.841214.577133.1333
272.17880.83150.69053.19011.25657.7513-0.52560.4832-0.7298-0.96190.94491.96930.7195-2.0321-0.35091.07860.2107-0.24041.2273-0.07410.95657.375412.393322.0076
283.7865-0.860.58435.54570.80714.5774-0.3196-0.36810.25130.64960.3925-0.1523-0.7602-0.1875-0.17171.14690.2564-0.00111.1451-0.09290.960817.200717.150622.0677
293.3028-1.3252-0.18687.08790.16054.80460.1361-0.19390.4451-0.7686-0.32910.8216-0.8658-2.11880.23890.94810.3404-0.13151.1726-0.14550.844313.711615.575615.0592
304.2225-0.4142-4.25242.54381.77168.5814-0.032-0.3931-0.4158-0.2596-0.30720.3682-0.72210.63370.54920.75130.1422-0.19060.73290.03970.881320.165218.04786.4459
315.24061.116-3.49894.67313.64626.6549-0.70852.19880.3206-0.83050.871-0.349-0.3819-0.9105-0.33491.2063-0.48140.00421.63180.01140.672714.29478.1038-58.3189
322.69831.45850.57135.98860.0555.1214-0.09970.04720.1749-0.5355-0.32960.0257-0.5137-0.19210.4340.9896-0.0257-0.02661.17160.00360.924113.357414.0885-49.9844
334.312-1.3297-0.00510.45320.43916.2485-0.01640.2287-0.7691-0.2967-0.7403-0.02131.0391-1.54520.74920.965-0.2073-0.08090.6217-0.05521.0878.81676.4132-44.3564
346.732-1.91210.18166.2722-0.03485.90350.04111.0214-0.1588-0.3899-0.179-0.040.27380.86140.03510.6736-0.0777-0.01661.0538-0.00030.833315.543413.3767-40.6027
352.2322-1.1929-0.84451.98790.31549.5605-1.08370.2949-0.20470.97940.6951-0.03990.701-1.69690.39180.888-0.04780.01820.93610.05820.85518.687310.895-34.9867
362.931-0.59210.19873.51520.00167.26930.01050.0665-0.13850.332-0.152-0.0205-0.48080.14990.07230.828-0.0834-0.02750.9419-0.0050.884813.726415.4309-25.7423
374.77954.7487-1.44715.89760.65046.12570.8360.6801-1.6847-0.197-0.16730.2390.6034-0.8789-0.52641.15740.0628-0.02670.83410.0470.637210.46319.6547-14.8533
387.128-2.5725-1.08488.41530.46225.89010.30220.71680.3934-1.6857-0.6548-0.3177-1.2946-0.350.2591.05890.0144-0.16190.7742-0.10860.869116.426118.7811-14.3337
392.91422.34460.79733.32460.2023.7922-0.5403-0.0895-0.25330.15670.8937-0.18920.1191-0.0174-0.23150.99150.1941-0.00440.81690.0530.920314.359815.3301-7.5301
400.3695-0.8078-0.95325.23853.54015.47620.1020.40710.0394-0.9514-0.13190.1135-1.0630.43030.00571.15840.0881-0.04420.57130.18150.942717.421.271.3411
418.6783-1.8369-0.83055.2601-0.25493.26720.8721.79220.3498-1.6148-0.0393-0.09281.32051.3121-0.58631.2620.2178-0.01691.0852-0.0920.797339.8962-1.910315.3658
425.81630.2752-1.53167.1769-1.49755.11680.2537-0.05060.3117-0.5521-0.26110.2635-0.80670.1642-0.03280.8740.0875-0.04360.9963-0.03130.741334.77771.781423.5336
433.3153.00510.86912.9755-0.53286.75090.07890.1803-1.78050.72890.1532-0.00341.24440.6431-0.47190.71420.0690.10461.0251-0.0771.057437.2232-6.636229.7156
449.1947-2.3276-0.68998.4569-0.25277.28680.61190.46990.1673-0.2383-0.4881-0.0007-0.50771.0955-0.11510.73470.01550.04230.954-0.02250.722236.82913.379432.8228
455.6813-0.53830.43186.073-1.01358.24240.7107-0.10970.5035-0.296-0.3708-0.86110.8715-0.0215-0.00810.6790.19250.14960.8866-0.00640.757533.8328-3.044238.5684
463.3694-1.1359-0.55094.45161.61565.4373-0.04730.021-0.10150.2849-0.06180.0316-0.23250.40910.10350.78350.08440.00631.14230.02170.838733.94094.335847.6475
478.71543.0901-0.90778.4146-1.41624.9512-0.2313-0.087-1.49230.5752-0.4261-1.48121.56661.7380.5710.91350.2011-0.08061.07840.04380.889735.3985-1.31358.9447
485.3582.4979-0.24784.9112-1.22483.5150.23880.4774-0.43570.6180.2814-0.0112-0.13830.2855-0.34190.83120.04380.09841.49560.0170.962733.02629.414658.7094
495.82630.28310.22233.9230.28764.28750.2426-1.51070.05190.3725-0.0717-0.54680.1199-0.8163-0.2120.95220.0255-0.04881.22850.11720.771233.8455.839765.7888
506.8228-1.5166-2.45775.7438-1.31165.8901-0.292-0.3367-0.23650.32540.1645-0.1131-1.8719-0.14990.16781.1833-0.028-0.17850.6404-0.04320.68131.165212.844774.067
516.448-6.0736-0.53825.94070.16827.7976-1.5947-1.50780.83491.77741.28050.00691.0953-1.8867-0.02931.4163-0.18710.09660.9735-0.03790.850620.47417.0183138.5156
522.5991-0.45921.05527.4615-1.32734.44440.40830.02920.16530.1277-0.6123-0.081-0.2240.71390.17060.88390.00810.10661.19390.01630.783426.95419.404130.4746
535.92034.49470.49516.42032.95255.0042-0.345-1.8497-1.4367-0.0176-0.10660.1330.5571-0.070.38090.7866-0.28680.16031.11210.05521.051124.16930.6483125.1507
545.24271.9620.21835.3736-0.55654.1020.3443-1.1823-0.06420.2237-0.55510.2197-0.6542-0.53180.18681.0177-0.0957-0.01871.4074-0.02130.823225.96510.0156120.8913
556.514-1.49091.67367.2795-0.25318.15140.89390.8315-0.0549-0.2621-0.5098-0.43830.4231.6003-0.31010.80990.02850.09011.309-0.04350.618828.74822.6919116.3905
563.714-0.2157-0.10573.37220.6924.18430.15530.1916-0.1638-0.2107-0.2136-0.0401-0.28410.03510.04870.9469-0.04950.00171.20440.06250.888130.37388.8091106.5674
573.104-2.88312.64632.8263-2.38652.45140.4215-0.48660.34830.0034-0.6841-0.11362.3533-1.24520.32530.82580.06340.03121.1631-0.05440.773729.11451.76296.084
582.40331.5829-0.47274.60992.02725.93970.3082-0.89291.1719-0.4214-0.1110.5946-0.11240.113-0.23131.0547-0.00390.14941.25730.01640.933632.627812.06195.0625
593.1974-1.42981.09895.0105-1.03833.07920.19670.6956-0.1428-0.2771-0.25040.2922-0.23680.82310.00441.0231-0.07280.04241.3323-0.07630.869131.89797.65888.4957
606.45151.8552-0.35235.69090.08174.7033-0.02110.79120.22860.5571-0.390.0785-1.34290.37360.45971.0951-0.085-0.00150.85790.01730.776835.42812.930979.3394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 21:34)
2X-RAY DIFFRACTION2(chain A and resseq 35:65)
3X-RAY DIFFRACTION3(chain A and resseq 66:72)
4X-RAY DIFFRACTION4(chain A and resseq 73:102)
5X-RAY DIFFRACTION5(chain A and resseq 103:113)
6X-RAY DIFFRACTION6(chain A and resseq 114:186)
7X-RAY DIFFRACTION7(chain A and resseq 187:193)
8X-RAY DIFFRACTION8(chain A and resseq 194:206)
9X-RAY DIFFRACTION9(chain A and resseq 207:235)
10X-RAY DIFFRACTION10(chain A and resseq 236:253)
11X-RAY DIFFRACTION11(chain B and resseq 21:34)
12X-RAY DIFFRACTION12(chain B and resseq 35:65)
13X-RAY DIFFRACTION13(chain B and resseq 66:72)
14X-RAY DIFFRACTION14(chain B and resseq 73:102)
15X-RAY DIFFRACTION15(chain B and resseq 103:113)
16X-RAY DIFFRACTION16(chain B and resseq 114:186)
17X-RAY DIFFRACTION17(chain B and resseq 187:193)
18X-RAY DIFFRACTION18(chain B and resseq 194:206)
19X-RAY DIFFRACTION19(chain B and resseq 207:235)
20X-RAY DIFFRACTION20(chain B and resseq 236:253)
21X-RAY DIFFRACTION21(chain C and resseq 21:34)
22X-RAY DIFFRACTION22(chain C and resseq 35:65)
23X-RAY DIFFRACTION23(chain C and resseq 66:72)
24X-RAY DIFFRACTION24(chain C and resseq 73:102)
25X-RAY DIFFRACTION25(chain C and resseq 103:113)
26X-RAY DIFFRACTION26(chain C and resseq 114:186)
27X-RAY DIFFRACTION27(chain C and resseq 187:193)
28X-RAY DIFFRACTION28(chain C and resseq 194:206)
29X-RAY DIFFRACTION29(chain C and resseq 207:235)
30X-RAY DIFFRACTION30(chain C and resseq 236:253)
31X-RAY DIFFRACTION31(chain D and resseq 21:34)
32X-RAY DIFFRACTION32(chain D and resseq 35:65)
33X-RAY DIFFRACTION33(chain D and resseq 66:72)
34X-RAY DIFFRACTION34(chain D and resseq 73:102)
35X-RAY DIFFRACTION35(chain D and resseq 103:113)
36X-RAY DIFFRACTION36(chain D and resseq 114:186)
37X-RAY DIFFRACTION37(chain D and resseq 187:193)
38X-RAY DIFFRACTION38(chain D and resseq 194:206)
39X-RAY DIFFRACTION39(chain D and resseq 207:235)
40X-RAY DIFFRACTION40(chain D and resseq 236:253)
41X-RAY DIFFRACTION41(chain E and resseq 21:34)
42X-RAY DIFFRACTION42(chain E and resseq 35:65)
43X-RAY DIFFRACTION43(chain E and resseq 66:72)
44X-RAY DIFFRACTION44(chain E and resseq 73:102)
45X-RAY DIFFRACTION45(chain E and resseq 103:113)
46X-RAY DIFFRACTION46(chain E and resseq 114:186)
47X-RAY DIFFRACTION47(chain E and resseq 187:193)
48X-RAY DIFFRACTION48(chain E and resseq 194:206)
49X-RAY DIFFRACTION49(chain E and resseq 207:235)
50X-RAY DIFFRACTION50(chain E and resseq 236:253)
51X-RAY DIFFRACTION51(chain F and resseq 21:34)
52X-RAY DIFFRACTION52(chain F and resseq 35:65)
53X-RAY DIFFRACTION53(chain F and resseq 66:72)
54X-RAY DIFFRACTION54(chain F and resseq 73:102)
55X-RAY DIFFRACTION55(chain F and resseq 103:113)
56X-RAY DIFFRACTION56(chain F and resseq 114:186)
57X-RAY DIFFRACTION57(chain F and resseq 187:193)
58X-RAY DIFFRACTION58(chain F and resseq 194:206)
59X-RAY DIFFRACTION59(chain F and resseq 207:235)
60X-RAY DIFFRACTION60(chain F and resseq 236:253)

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