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- PDB-6tcp: Crystal structure of the omalizumab Fab Leu158Pro light chain mut... -

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Basic information

Entry
Database: PDB / ID: 6tcp
TitleCrystal structure of the omalizumab Fab Leu158Pro light chain mutant - crystal form II
Components(Omalizumab Fab Leu158Pro light chain ...) x 2
KeywordsIMMUNE SYSTEM / Fab / Antibody / immunoglobulin
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMitropoulou, A.N. / Ceska, T. / Beavil, A.J. / Henry, A.J. / McDonnell, J.M. / Sutton, B.J. / Davies, A.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100090 United Kingdom
Wellcome Trust085944 United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Engineering the Fab fragment of the anti-IgE omalizumab to prevent Fab crystallization and permit IgE-Fc complex crystallization.
Authors: Mitropoulou, A.N. / Ceska, T. / Heads, J.T. / Beavil, A.J. / Henry, A.J. / McDonnell, J.M. / Sutton, B.J. / Davies, A.M.
History
DepositionNov 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
L: Omalizumab Fab Leu158Pro light chain mutant
H: Omalizumab Fab Leu158Pro light chain mutant
A: Omalizumab Fab Leu158Pro light chain mutant
B: Omalizumab Fab Leu158Pro light chain mutant
C: Omalizumab Fab Leu158Pro light chain mutant
D: Omalizumab Fab Leu158Pro light chain mutant
E: Omalizumab Fab Leu158Pro light chain mutant
F: Omalizumab Fab Leu158Pro light chain mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,49131
Polymers194,3158
Non-polymers2,17623
Water5,386299
1
L: Omalizumab Fab Leu158Pro light chain mutant
H: Omalizumab Fab Leu158Pro light chain mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,34110
Polymers48,5792
Non-polymers7638
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-60 kcal/mol
Surface area18710 Å2
MethodPISA
2
A: Omalizumab Fab Leu158Pro light chain mutant
B: Omalizumab Fab Leu158Pro light chain mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0477
Polymers48,5792
Non-polymers4685
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-62 kcal/mol
Surface area18600 Å2
MethodPISA
3
C: Omalizumab Fab Leu158Pro light chain mutant
D: Omalizumab Fab Leu158Pro light chain mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0517
Polymers48,5792
Non-polymers4725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-52 kcal/mol
Surface area18500 Å2
MethodPISA
4
E: Omalizumab Fab Leu158Pro light chain mutant
F: Omalizumab Fab Leu158Pro light chain mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0517
Polymers48,5792
Non-polymers4725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-61 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.112, 162.043, 164.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 8 molecules LACEHBDF

#1: Antibody
Omalizumab Fab Leu158Pro light chain mutant


Mass: 23906.244 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Omalizumab Fab Leu158Pro light chain mutant / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human)
#2: Antibody
Omalizumab Fab Leu158Pro light chain mutant


Mass: 24672.490 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Omalizumab Fab heavy chain / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 322 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 4000, 0.2M magnesium sulphate and 10% glycerol. Crystals were cryoprotected in 20% PEG 4000, 0.2M magnesium sulphate and 18% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.5→82.21 Å / Num. obs: 74746 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.105 / Net I/σ(I): 8.9
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.464 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4509 / CC1/2: 0.562 / Rpim(I) all: 0.602 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TCM
Resolution: 2.5→81.022 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.26
RfactorNum. reflection% reflection
Rfree0.2388 3770 5.05 %
Rwork0.2123 --
obs0.2137 74660 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.63 Å2 / Biso mean: 36.3553 Å2 / Biso min: 5.44 Å2
Refinement stepCycle: final / Resolution: 2.5→81.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12814 0 128 299 13241
Biso mean--61.11 30.32 -
Num. residues----1728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213296
X-RAY DIFFRACTIONf_angle_d0.52918181
X-RAY DIFFRACTIONf_chiral_restr0.0422036
X-RAY DIFFRACTIONf_plane_restr0.0042327
X-RAY DIFFRACTIONf_dihedral_angle_d11.8137759
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.53170.37261270.31622592100
2.5317-2.5650.30371410.31582604100
2.565-2.60010.37721270.30212583100
2.6001-2.63730.38211340.31822563100
2.6373-2.67660.37071340.30582631100
2.6766-2.71840.34791200.29342611100
2.7184-2.7630.31371250.30082603100
2.763-2.81070.28571150.28282612100
2.8107-2.86180.30841570.2745260899
2.8618-2.91680.33051320.27322567100
2.9168-2.97640.27831650.27142588100
2.9764-3.04110.29751350.27622598100
3.0411-3.11180.26431470.26592606100
3.1118-3.18970.27481470.24192595100
3.1897-3.27590.22671430.22042608100
3.2759-3.37230.25351180.21482641100
3.3723-3.48110.21971470.20582641100
3.4811-3.60560.24761680.19752580100
3.6056-3.74990.21741310.18982623100
3.7499-3.92060.22881420.18132625100
3.9206-4.12730.21381400.17272647100
4.1273-4.38580.17111400.1517262299
4.3858-4.72440.17421420.13832650100
4.7244-5.19980.16771560.1482657100
5.1998-5.9520.18391550.16632662100
5.952-7.49810.21291440.19262715100
7.4981-81.0220.20491380.19032858100
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)
10.0997-0.01570.13280.005-0.01880.1833-0.0062-0.0476-0.0076-0.0857-0.01020.0380.0229-0.08090.01310.0685-0.00050.02180.0326-0.00370.064337.7758-16.14527.7065
20.0094-0.0214-0.01070.0532-0.01460.0767-0.0170.05710.0038-0.01930.02760.0076-0.0066-0.1228-0.01950.1004-0.00210.01980.08810.01510.121429.2426-8.63081.361
30.181-0.10760.06560.1685-0.02680.11860.06450.0441-0.0836-0.0326-0.00150.08130.13230.11310.09690.0930.03070.07070.0584-0.0370.046636.4232-11.40192.8301
40.0016-0.0008-0.00220.00840.00420.00390.04840.0149-0.02530.00190.1141-0.02430.0485-0.016200.2286-0.0251-0.01120.19920.01390.21922.4505-11.394211.1707
50.02230.0038-0.01520.00240.00110.01250.0087-0.02670.00390.02460.0623-0.0434-0.0820.06650.05940.0825-0.00870.02740.2515-0.09940.092753.501-7.61739.547
60.0689-0.01720.02230.02290.02240.0488-0.06840.0035-0.00950.03620.0143-0.0462-0.02130.0041-0.07830.3657-0.1040.01470.3026-0.11460.116159.05077.182725.912
70.0105-0.0063-0.00390.00880.00720.0052-0.1229-0.0672-0.06250.0522-0.0077-0.03180.02490.024700.2632-0.013-0.00060.2458-0.04230.141555.89950.905223.1386
80.07520.0097-0.028-0.0011-0.00720.01470.0761-0.13870.02970.08190.0411-0.06950.03610.2110.09340.2343-0.046-0.17140.3135-0.1546-0.136564.06095.75428.9242
90.0025-0.0093-0.00740.05220.04990.048-0.0044-0.06920.096-0.02770.02310.0063-0.05610.0101-0.00070.3683-0.03710.08360.2012-0.06060.10924.958110.25718.9255
100.0336-0.0106-0.0030.0133-0.01030.03920.0343-0.02640.15370.021-0.10250.0162-0.0907-0.0316-0.02780.16950.0729-0.00240.19350.00130.187818.97192.792611.2838
110.01520.00310.00490.00840.00260.0021-0.063-0.08830.0932-0.0197-0.08520.0669-0.0849-0.0402-0.02350.40930.15690.00440.3552-0.04860.307414.9675.688816.0134
120.15080.05090.01070.0719-0.08480.21090.0776-0.07210.00440.0370.02670.1299-0.0503-0.00360.11730.11930.0909-0.00080.1368-0.05760.170923.72440.978413.0041
130.0608-0.0022-0.03320.1103-0.01950.04930.0439-0.09990.1781-0.0663-0.14590.0677-0.0111-0.1101-0.14160.387-0.04780.0080.3293-0.07910.158248.38112.940322.0843
140.00110.0040.00090.00850.0041-0.00040.03320.00580.0478-0.06740.004-0.0073-0.0611-0.029400.39020.0215-0.00730.2886-0.060.369249.192921.711819.0156
150.07290.0836-0.00210.0879-0.01250.05320.00660.0483-0.06050.03040.05120.01380.07990.01930.13290.1025-0.04150.00970.09160.01360.114250.5374-9.566676.2375
160.1046-0.0010.02950.0466-0.03670.1226-0.0236-0.0142-0.02270.01850.0222-0.07580.0205-0.06220.03280.0878-0.01060.01040.1251-0.04630.16345.3642-8.884369.3816
170.1747-0.02360.06150.03760.01330.14330.11360.1648-0.2488-0.15520.06520.099-0.0019-0.11270.08330.21480.0354-0.05450.3381-0.00990.184520.74012.662254.014
180.0098-0.012-0.02630.03020.03940.19450.04820.06480.09110.0252-0.00380.0733-0.0359-0.06330.01140.25590.01130.01120.4261-0.05380.064155.192110.220557.1035
190.05650.0202-0.01850.0258-0.02860.02150.02470.09720.1529-0.0614-0.0313-0.0499-0.0697-0.03720.00210.1198-0.0341-0.02130.1804-0.06870.128460.78795.4965.0636
200.0220.00560.0130.0125-0.00140.0235-0.02190.0585-0.0463-0.0289-0.0221-0.0132-0.0604-0.011-0.07440.2388-0.0670.11710.207-0.08190.086969.00064.739461.4687
210.0081-0.0055-0.00260.00180.00110.0016-0.01610.01760.04250.00550.0034-0.06330.0168-0.007900.2911-0.0380.01610.3007-0.03770.12760.88915.346154.3645
220.12740.0469-0.13340.1990.15530.39330.05030.1441-0.0713-0.01580.0563-0.1216-0.129-0.08330.29380.0965-0.07030.00140.1552-0.0263-0.039650.02226.297762.2104
230.0318-0.00140.02880.05260.0480.08520.06290.18130.12360.14620.0674-0.0541-0.19170.18210.14880.4483-0.0030.05440.29380.00680.16131.934713.711558.3847
240.0166-0.00040.00750.0194-0.01640.0166-0.0291-0.02780.10430.0991-0.0336-0.0259-0.04870.0013-0.04760.16040.03230.01730.11180.02370.133947.7324-22.08993.1993
250.0390.0051-0.00730.0644-0.00840.0018-0.04860.0142-0.0462-0.05920.05430.07330.006-0.0218-0.00220.06460.0364-0.0590.0859-0.03380.151751.654-32.9161-1.1036
260.0277-0.00690.00650.06480.03750.0168-0.0501-0.1471-0.05780.03150.02850.14780.03950.0194-0.01350.08760.0137-0.00310.10320.02570.157845.336-31.50954.1036
270.00850.0062-0.01470.0156-0.0210.03130.00180.0063-0.05670.0075-0.0267-0.012-0.0781-0.00450.00330.1515-0.0325-0.03850.1440.02440.168558.8241-29.8888-4.8311
280.00390.0151-0.00230.0411-0.00430.0002-0.0336-0.0781-0.0394-0.00720.0446-0.0760.0086-0.03160.01510.20310.05320.07820.20380.01970.111845.3864-20.70421.8458
290.0160.02-0.00440.1931-0.09790.0492-0.024-0.13830.00320.07090.1623-0.01680.06330.19970.0650.28430.1283-0.05410.4272-0.03670.118261.6451-19.671537.4096
300.0127-0.0210.01420.0429-0.03490.0265-0.0191-0.14910.05360.16640.21490.019-0.05980.0470.00410.39070.0582-0.04310.385-0.04120.204157.9596-18.275130.4044
310.0024-0.0013-0.00030.02220.00810.00280.0129-0.08070.02850.12260.0281-0.0385-0.02060.18840.07540.45710.1481-0.11720.5676-0.1940.227161.8102-14.646741.7919
320.0467-0.0368-0.03710.02560.02310.1209-0.0242-0.1345-0.05090.10450.1153-0.04780.060.14050.12440.00420.1135-0.01690.0580.00620.337368.4636-42.60275.8132
330.0477-0.0399-0.01420.14420.04890.0685-0.0195-0.0236-0.1308-0.22120.0226-0.1683-0.1020.0353-0.0110.06470.0510.00070.0539-0.03390.242367.6577-38.42461.0417
340.13980.12740.12690.11460.10780.1085-0.1454-0.1574-0.20020.31360.3169-0.04590.12770.17540.10220.47730.24340.00030.51520.03080.291366.4835-32.111632.3512
350.11730.13130.02790.1558-0.00540.02680.08940.0424-0.28720.0810.0465-0.1073-0.0730.00010.31320.105-0.08940.013-0.08920.03030.224736.7721-29.210679.844
360.0178-0.0287-0.01720.03590.00420.0711-0.00180.2824-0.0765-0.158-0.0131-0.0269-0.0095-0.04260.03640.28530.0053-0.06790.3971-0.09090.215223.5707-20.551645.8744
370.03780.040.00470.05250.00640.00480.00410.0515-0.09930.0520.01110.06590.0675-0.03440.02190.0686-0.11570.0412-0.04420.06940.49318.4398-41.332680.2435
380.02420.00190.00180.0628-0.03020.0722-0.0687-0.0027-0.00970.0830.00620.0513-0.0199-0.0504-0.08660.13290.03570.06520.02230.020.490413.6708-38.845881.2783
390.0310.0214-0.00620.0136-0.00450.00820.0187-0.0078-0.03020.0374-0.0227-0.0740.00460.0093-0.01340.0647-0.0537-0.01720.09660.04160.461526.2814-39.854680.6447
400.028-0.06080.0480.1179-0.12060.1512-0.07140.1986-0.2074-0.26920.22710.07980.2901-0.07290.13250.3107-0.0859-0.02180.399-0.15420.40118.2961-35.188750.0895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 25 )L1 - 25
2X-RAY DIFFRACTION2chain 'L' and (resid 26 through 65 )L26 - 65
3X-RAY DIFFRACTION3chain 'L' and (resid 66 through 94 )L66 - 94
4X-RAY DIFFRACTION4chain 'L' and (resid 95 through 105 )L95 - 105
5X-RAY DIFFRACTION5chain 'L' and (resid 106 through 117 )L106 - 117
6X-RAY DIFFRACTION6chain 'L' and (resid 118 through 154 )L118 - 154
7X-RAY DIFFRACTION7chain 'L' and (resid 155 through 176 )L155 - 176
8X-RAY DIFFRACTION8chain 'L' and (resid 177 through 217 )L177 - 217
9X-RAY DIFFRACTION9chain 'H' and (resid 1 through 17 )H1 - 17
10X-RAY DIFFRACTION10chain 'H' and (resid 18 through 60 )H18 - 60
11X-RAY DIFFRACTION11chain 'H' and (resid 61 through 83 )H61 - 83
12X-RAY DIFFRACTION12chain 'H' and (resid 84 through 119 )H84 - 119
13X-RAY DIFFRACTION13chain 'H' and (resid 120 through 196 )H120 - 196
14X-RAY DIFFRACTION14chain 'H' and (resid 197 through 222 )H197 - 222
15X-RAY DIFFRACTION15chain 'A' and (resid 1 through 94 )A1 - 94
16X-RAY DIFFRACTION16chain 'A' and (resid 95 through 117 )A95 - 117
17X-RAY DIFFRACTION17chain 'A' and (resid 118 through 217 )A118 - 217
18X-RAY DIFFRACTION18chain 'B' and (resid 1 through 17 )B1 - 17
19X-RAY DIFFRACTION19chain 'B' and (resid 18 through 53 )B18 - 53
20X-RAY DIFFRACTION20chain 'B' and (resid 54 through 76 )B54 - 76
21X-RAY DIFFRACTION21chain 'B' and (resid 77 through 91 )B77 - 91
22X-RAY DIFFRACTION22chain 'B' and (resid 92 through 142 )B92 - 142
23X-RAY DIFFRACTION23chain 'B' and (resid 143 through 222 )B143 - 222
24X-RAY DIFFRACTION24chain 'C' and (resid 1 through 25 )C1 - 25
25X-RAY DIFFRACTION25chain 'C' and (resid 26 through 52 )C26 - 52
26X-RAY DIFFRACTION26chain 'C' and (resid 53 through 94 )C53 - 94
27X-RAY DIFFRACTION27chain 'C' and (resid 95 through 105 )C95 - 105
28X-RAY DIFFRACTION28chain 'C' and (resid 106 through 117 )C106 - 117
29X-RAY DIFFRACTION29chain 'C' and (resid 118 through 154 )C118 - 154
30X-RAY DIFFRACTION30chain 'C' and (resid 155 through 178 )C155 - 178
31X-RAY DIFFRACTION31chain 'C' and (resid 179 through 216 )C179 - 216
32X-RAY DIFFRACTION32chain 'D' and (resid 1 through 40 )D1 - 40
33X-RAY DIFFRACTION33chain 'D' and (resid 41 through 119 )D41 - 119
34X-RAY DIFFRACTION34chain 'D' and (resid 120 through 222 )D120 - 222
35X-RAY DIFFRACTION35chain 'E' and (resid 1 through 105 )E1 - 105
36X-RAY DIFFRACTION36chain 'E' and (resid 106 through 216 )E106 - 216
37X-RAY DIFFRACTION37chain 'F' and (resid 1 through 60 )F1 - 60
38X-RAY DIFFRACTION38chain 'F' and (resid 61 through 98 )F61 - 98
39X-RAY DIFFRACTION39chain 'F' and (resid 99 through 119 )F99 - 119
40X-RAY DIFFRACTION40chain 'F' and (resid 120 through 223 )F120 - 223

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