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- PDB-7n08: Crystal structure of the 3D6 antibody fragment bound to the HIV-1... -

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Basic information

Entry
Database: PDB / ID: 7n08
TitleCrystal structure of the 3D6 antibody fragment bound to the HIV-1 gp41 immunodominant region
Components
  • Fab 3D6 heavy chain
  • Fab 3D6 light chain
  • HIV-1 gp41 immunodominant region
KeywordsIMMUNE SYSTEM / antibody / Fab / anti-HIV / gp41
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
HIV-1 06TG.HT008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCook, J.D. / Lee, J.E.
Funding support Canada, 5items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-115066 Canada
Canadian Institutes of Health Research (CIHR)PJT-173301 Canada
Ontario Early Researcher AwardsER-13-09-116 Canada
Canada Research Chairs950-231672 Canada
Canada Foundation for Innovation Canada
CitationJournal: Commun Biol / Year: 2022
Title: Conformational plasticity of the HIV-1 gp41 immunodominant region is recognized by multiple non-neutralizing antibodies.
Authors: Cook, J.D. / Khondker, A. / Lee, J.E.
History
DepositionMay 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: HIV-1 gp41 immunodominant region
H: Fab 3D6 heavy chain
F: HIV-1 gp41 immunodominant region
E: HIV-1 gp41 immunodominant region
L: Fab 3D6 light chain
B: Fab 3D6 light chain
A: Fab 3D6 heavy chain
D: Fab 3D6 light chain
C: Fab 3D6 heavy chain


Theoretical massNumber of molelcules
Total (without water)154,5349
Polymers154,5349
Non-polymers00
Water21,8521213
1
G: HIV-1 gp41 immunodominant region
D: Fab 3D6 light chain
C: Fab 3D6 heavy chain


Theoretical massNumber of molelcules
Total (without water)51,5113
Polymers51,5113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-38 kcal/mol
Surface area19500 Å2
MethodPISA
2
H: Fab 3D6 heavy chain
F: HIV-1 gp41 immunodominant region
L: Fab 3D6 light chain


Theoretical massNumber of molelcules
Total (without water)51,5113
Polymers51,5113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-36 kcal/mol
Surface area19440 Å2
MethodPISA
3
E: HIV-1 gp41 immunodominant region
B: Fab 3D6 light chain
A: Fab 3D6 heavy chain


Theoretical massNumber of molelcules
Total (without water)51,5113
Polymers51,5113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-37 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.825, 77.825, 218.972
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein/peptide HIV-1 gp41 immunodominant region


Mass: 1590.798 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) HIV-1 06TG.HT008 (virus)
#2: Antibody Fab 3D6 heavy chain


Mass: 26649.836 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Antibody Fab 3D6 light chain


Mass: 23270.859 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1213 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride, 20% (w/v) PEG 8000, 0.1 M Tris-HCl, pH 8.5, and 0.59 mM n-undecyl-beta-D-maltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 10, 2016
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→42.492 Å / Num. obs: 98127 / % possible obs: 97.9 % / Redundancy: 2 % / Biso Wilson estimate: 23.75 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.07 / Rrim(I) all: 0.105 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0320.668977648710.5510.6130.9091.598.6
10.95-42.492.10.02211825530.9980.0190.02925.890.5

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7N07

7n07


Resolution: 2→42.492 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2026 2017 2.06 %
Rwork0.1654 96035 -
obs0.1662 98052 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.4 Å2 / Biso mean: 32.2365 Å2 / Biso min: 7.33 Å2
Refinement stepCycle: final / Resolution: 2→42.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10254 0 0 1213 11467
Biso mean---34.71 -
Num. residues----1368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110547
X-RAY DIFFRACTIONf_angle_d1.09514391
X-RAY DIFFRACTIONf_chiral_restr0.0661626
X-RAY DIFFRACTIONf_plane_restr0.0071839
X-RAY DIFFRACTIONf_dihedral_angle_d16.9793736
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0001-2.05010.28981440.2538692199
2.0501-2.10550.28791450.2377686998
2.1055-2.16750.25291460.2222692699
2.1675-2.23740.28031330.2201687599
2.2374-2.31740.26241420.2066685898
2.3174-2.41020.26441400.1983689799
2.4102-2.51980.23421490.1886696599
2.5198-2.65270.22841440.1823688399
2.6527-2.81880.21021470.1723687798
2.8188-3.03640.221480.1666688098
3.0364-3.34190.19611380.158683297
3.3419-3.82520.1661440.1354671996
3.8252-4.81830.14121520.1146679897
4.8183-42.4920.17671450.1449673596
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.752-0.102-3.83721.1923-0.49384.33360.2708-0.4221-0.3762-0.2968-0.3222-0.028-0.00880.57250.09590.30480.0589-0.01860.26450.05340.248754.033-108.86136.393
24.46811.78664.46352.04712.07026.76860.18850.1169-0.18260.0579-0.0579-0.11730.63780.2397-0.1610.20580.05450.03430.17860.00890.209656.776-73.301-22.118
31.5321-0.27261.10530.7113-0.30754.3542-0.0459-0.00080.0147-0.00110.01210.0188-0.0533-0.04590.04110.1605-0.0011-0.00060.16210.01020.196753.744-64.984-24.032
40.58590.1661-1.14821.8608-0.77314.806-0.2134-0.2551-0.17410.0944-0.0081-0.00810.20960.25890.2340.1409-0.0223-0.03310.1491-0.01490.18448.583-71.08412.834
53.29981.5015-1.92111.0482-1.34394.0175-0.01140.09990.0141-0.04190.02480.06980.1002-0.0594-0.02250.1592-0.00640.0010.1422-0.010.166644.739-74.2519.009
62.32530.6417-3.31542.15950.28126.9503-0.1907-0.0766-0.16340.10670.0114-0.02350.50460.18580.19450.10960.0121-0.01460.19290.02940.212245-79.13417.293
72.99574.39844.12836.47836.37059.6396-0.05240.10480.07340.03980.20130.0435-0.15350.2756-0.09240.17390.02250.00350.27270.05640.235550.691-60.773-39.007
84.3935-3.1646-3.57726.95924.75256.48740.07060.11940.3185-0.15260.28130.0095-0.0412-0.4653-0.340.244-0.0096-0.04920.23550.06670.230174.039-74.371-67.011
92.17353.7565-2.1076.6403-2.85865.823-0.0083-0.4568-0.0065-0.0156-0.23290.0208-0.11-0.09380.23650.15990.0915-0.01460.25-0.05070.239531.655-56.423-14.533
103.02290.2626-0.31362.0276-1.02673.1959-0.09130.20250.1095-0.08290.11270.1588-0.0003-0.3255-0.02580.13780.0182-0.03070.24660.0020.223534.87-60.946-24.147
110.29860.08830.10060.2276-0.12912.14290.03350.01020.0274-0.0022-0.00310.0679-0.0393-0.3346-0.05450.1787-0.0019-0.00120.2163-0.0030.265636.453-62.899-5.859
128.05150.67175.94350.36970.65745.74140.06960.4469-0.03650-0.02520.0966-0.140.0552-0.03640.2077-0.02960.05130.21560.01690.231138.828-60.78711.307
132.88092.71844.16586.9346.62897.6675-0.03610.10280.11890.0879-0.0712-0.0287-0.0525-0.04720.07440.2703-0.05040.03180.23990.04450.249945.645-55.32512.979
144.64350.26982.59551.71360.59414.5423-0.13140.11480.16750.1026-0.00710.0876-0.2145-0.21040.12740.1661-0.01610.04450.14330.02920.178739.431-60.78713.062
159.5741-3.71236.75186.9504-3.64328.54710.1872-0.4588-0.68410.4739-0.02690.24680.0609-0.5793-0.11380.2912-0.06650.07770.234-0.00040.278840.57-60.58825.966
162.3445-0.65720.7735.3414-1.22863.99410.2196-0.3155-0.160.5339-0.10020.51050.1735-0.60410.07480.2561-0.11250.01930.337-0.00140.248363.997-88.857-40.959
171.5377-0.06650.56983.9304-1.643.9720.08740.0569-0.1858-0.21320.00250.17040.4327-0.342-0.10090.2103-0.0575-0.01380.207-0.02370.202167.825-88.599-50.924
180.3405-0.04120.64460.32920.16472.39720.1359-0.0582-0.0641-0.0171-0.0328-0.01420.3981-0.1993-0.10520.2005-0.0337-0.0030.17150.01160.268774.104-87.426-31.153
190.1847-0.1374-0.08574.81944.29797.2025-0.00630.04460.0436-0.10790.0480.2271-0.0924-0.4365-0.02070.21120.009-0.03570.25580.06850.280272.934-81.826-15.126
202.52622.7612.68053.66023.07732.9119-0.0661-0.04190.0918-0.3050.13410.0422-0.0872-0.0721-0.11330.30860.0142-0.0110.26290.05140.238778.278-83.56-16.575
212.931-0.7649-0.15950.6091-1.05932.9796-0.2624-0.06730.09080.0499-0.17380.59580.463-0.8740.42180.1959-0.06610.04930.45270.00750.339767.796-85.489-10.113
225.16021.12073.17567.57242.80899.2699-0.1874-0.5398-0.29320.30170.4424-0.3480.3351-0.2223-0.22540.3010.13270.0620.42320.02910.278875.822-83.153-1.427
233.5547-2.8257-1.53794.42141.44824.30220.0991-0.28580.01250.2122-0.0312-0.4703-0.1210.2919-0.14420.2036-0.0966-0.04110.29230.0290.259690.872-73.513-45.427
242.15360.41240.5141.3619-0.12644.7028-0.0467-0.0986-0.02010.0802-0.0387-0.0994-0.25440.12310.07220.1701-0.0123-0.02150.1352-0.00290.194882.364-74.562-54.232
257.2502-0.3704-3.54713.14521.22267.01160.0996-0.09940.15130.1751-0.22120.0658-0.7004-0.0730.05270.27380.0083-0.0560.1411-0.00670.172283.153-67.035-53.959
261.52580.75511.29281.6560.50724.91060.0112-0.10870.05660.0701-0.0962-0.0726-0.14480.05470.09010.147-0.00060.00710.1699-0.00360.183781.085-75.336-51.907
270.6507-0.67140.65441.9348-1.92926.23730.0509-0.06790.0060.2501-0.00470.0277-0.21540.2905-0.05190.13880.0240.01940.201-0.00170.194887.467-82.097-14.383
281.046-0.31630.78672.2097-1.53872.4121-0.09320.10810.0792-0.08140.0714-0.1970.06450.25680.00160.1863-0.0117-0.00980.2603-0.02150.143988.935-83.722-22.631
290.43730.6605-0.85856.6022-3.11983.244-0.1536-0.0202-0.0012-0.02510.1087-0.05140.16010.13660.0610.19070.0216-0.02350.3125-0.01870.18191.834-88.196-15.703
301.4990.4426-1.89941.8048-2.01246.5172-0.0973-0.119-0.13960.1067-0.0497-0.0477-0.05260.47790.19360.17420.0373-0.06230.33330.00560.264990.446-86.818-6.88
315.6384-1.41715.02410.6847-0.62055.68730.11310.7397-0.3888-0.17090.1299-0.11660.55890.3349-0.08210.4201-0.080.06050.24-0.08370.305339.5-122.29512.697
325.6479-0.27591.87473.1535-1.65234.7467-0.05050.0336-0.20470.1111-0.0311-0.20510.2066-0.03370.07090.202-0.02510.03770.1341-0.02420.160141.769-116.31820.111
334.17340.27170.75650.979-0.31173.2582-0.0798-0.2492-0.23130.12930.0499-0.00570.3065-0.30850.02230.2955-0.02490.03460.1787-0.00270.226538.328-117.48521.137
344.83262.48676.46151.62593.30278.64710.3572-0.86060.01870.3047-0.310.18790.2647-0.8441-0.04820.2439-0.06360.00730.3085-0.00710.21930.182-119.9280.711
359.2355.3818-2.14283.956-2.31555.0119-0.24020.60440.3778-0.38190.31960.1288-0.44050.0039-0.12390.2313-0.0130.06630.2365-0.00110.223842.693-105.315-22.328
364.53051.0739-1.46950.9073-1.05262.8808-0.0562-0.1242-0.24560.1115-0.1454-0.25760.0150.40840.20640.15210.0077-0.01670.30290.02180.343.732-115.421-13.007
372.28140.9813-1.33852.9873-0.69553.52490.0679-0.0346-0.0263-0.04-0.1548-0.3841-0.1890.22550.03740.1351-0.0077-0.01610.26440.04290.227240.976-114.862-14.073
386.60321.6695-1.33868.8251-5.01783.0730.07270.4350.399-0.6216-0.2406-0.5960.44390.21110.14650.31170.03290.05210.3667-0.04110.277342.064-114.998-26.986
393.828-1.0347-1.00714.6102-0.20026.16280.23910.04490.6918-0.0942-0.0091-0.1594-0.75850.3307-0.2620.261-0.0576-0.06610.15660.02320.217251.06-93.09813.236
403.48140.8058-3.62134.8574-2.65225.35410.0922-0.17580.2230.5420.1167-0.0092-0.75340.0699-0.19050.3121-0.0375-0.0490.2042-0.03670.215147.882-95.39527.561
411.11410.5353-0.08521.301-1.2484.2857-0.08230.00020.06050.00310.0178-0.054-0.05520.24320.08030.19740.0042-0.00370.2089-0.0130.210752.437-102.64421.333
423.79542.01984.02782.45192.00055.5788-0.14260.04570.0978-0.0485-0.0739-0.0534-0.46370.36060.13390.2172-0.07280.01070.26020.02050.185240.654-101.48-16.146
434.4452-0.10191.74791.3768-0.89063.5246-0.0667-0.1556-0.0140.1694-0.0824-0.0394-0.5530.02690.16040.3241-0.0244-0.00940.2142-0.00580.200138.561-99.094-8.135
445.20950.0279-0.38411.4241-0.26870.9177-0.12690.14070.26580.1309-0.09950.0457-0.45020.0440.19580.275-0.0318-0.01870.1645-0.00960.167133.323-98.319-15.611
452.47382.47662.26288.54746.34985.2130.05560.05950.1106-0.1698-0.36450.0628-0.53150.16470.15510.376-0.0146-0.00540.26530.08620.226335.775-100.785-24.614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN G AND RESID 600:610 )G600 - 610
2X-RAY DIFFRACTION2( CHAIN H AND RESID 2:33 )H2 - 33
3X-RAY DIFFRACTION3( CHAIN H AND RESID 34:109 )H34 - 109
4X-RAY DIFFRACTION4( CHAIN H AND RESID 110:134 )H110 - 134
5X-RAY DIFFRACTION5( CHAIN H AND RESID 135:188 )H135 - 188
6X-RAY DIFFRACTION6( CHAIN H AND RESID 189:221 )H189 - 221
7X-RAY DIFFRACTION7( CHAIN F AND RESID 600:610 )F600 - 610
8X-RAY DIFFRACTION8( CHAIN E AND RESID 600:610 )E600 - 610
9X-RAY DIFFRACTION9( CHAIN L AND RESID 1:18 )L1 - 18
10X-RAY DIFFRACTION10( CHAIN L AND RESID 19:69 )L19 - 69
11X-RAY DIFFRACTION11( CHAIN L AND RESID 70:126 )L70 - 126
12X-RAY DIFFRACTION12( CHAIN L AND RESID 127:148 )L127 - 148
13X-RAY DIFFRACTION13( CHAIN L AND RESID 149:161 )L149 - 161
14X-RAY DIFFRACTION14( CHAIN L AND RESID 162:202 )L162 - 202
15X-RAY DIFFRACTION15( CHAIN L AND RESID 203:212 )L203 - 212
16X-RAY DIFFRACTION16( CHAIN B AND RESID 1:18 )B1 - 18
17X-RAY DIFFRACTION17( CHAIN B AND RESID 19:75 )B19 - 75
18X-RAY DIFFRACTION18( CHAIN B AND RESID 76:126 )B76 - 126
19X-RAY DIFFRACTION19( CHAIN B AND RESID 127:161 )B127 - 161
20X-RAY DIFFRACTION20( CHAIN B AND RESID 162:186 )B162 - 186
21X-RAY DIFFRACTION21( CHAIN B AND RESID 187:202 )B187 - 202
22X-RAY DIFFRACTION22( CHAIN B AND RESID 203:212 )B203 - 212
23X-RAY DIFFRACTION23( CHAIN A AND RESID 1:17 )A1 - 17
24X-RAY DIFFRACTION24( CHAIN A AND RESID 18:59 )A18 - 59
25X-RAY DIFFRACTION25( CHAIN A AND RESID 60:75 )A60 - 75
26X-RAY DIFFRACTION26( CHAIN A AND RESID 76:111 )A76 - 111
27X-RAY DIFFRACTION27( CHAIN A AND RESID 112:145 )A112 - 145
28X-RAY DIFFRACTION28( CHAIN A AND RESID 146:175 )A146 - 175
29X-RAY DIFFRACTION29( CHAIN A AND RESID 176:203 )A176 - 203
30X-RAY DIFFRACTION30( CHAIN A AND RESID 204:221 )A204 - 221
31X-RAY DIFFRACTION31( CHAIN D AND RESID 1:18 )D1 - 18
32X-RAY DIFFRACTION32( CHAIN D AND RESID 19:48 )D19 - 48
33X-RAY DIFFRACTION33( CHAIN D AND RESID 49:99 )D49 - 99
34X-RAY DIFFRACTION34( CHAIN D AND RESID 100:111 )D100 - 111
35X-RAY DIFFRACTION35( CHAIN D AND RESID 112:126 )D112 - 126
36X-RAY DIFFRACTION36( CHAIN D AND RESID 127:161 )D127 - 161
37X-RAY DIFFRACTION37( CHAIN D AND RESID 162:202 )D162 - 202
38X-RAY DIFFRACTION38( CHAIN D AND RESID 203:212 )D203 - 212
39X-RAY DIFFRACTION39( CHAIN C AND RESID 2:17 )C2 - 17
40X-RAY DIFFRACTION40( CHAIN C AND RESID 18:33 )C18 - 33
41X-RAY DIFFRACTION41( CHAIN C AND RESID 34:111 )C34 - 111
42X-RAY DIFFRACTION42( CHAIN C AND RESID 112:145 )C112 - 145
43X-RAY DIFFRACTION43( CHAIN C AND RESID 146:175 )C146 - 175
44X-RAY DIFFRACTION44( CHAIN C AND RESID 176:203 )C176 - 203
45X-RAY DIFFRACTION45( CHAIN C AND RESID 204:220 )C204 - 220

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