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- PDB-6urm: Crystal structure of vaccine-elicited receptor-binding site targe... -

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Basic information

Entry
Database: PDB / ID: 6urm
TitleCrystal structure of vaccine-elicited receptor-binding site targeting antibody LPAF-a.01 in complex with Hemagglutinin H1 A/California/04/2009
Components
  • Hemagglutinin
  • The heavy chain of antibody LPAF-a.01
  • The light chain of antibody LPAF-a.01
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Influenza / antibody / receptor-binding site / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsZhou, T. / Cheung, S.F. / Kwong, P.D.
CitationJournal: Cell Rep / Year: 2020
Title: Identification and Structure of a Multidonor Class of Head-Directed Influenza-Neutralizing Antibodies Reveal the Mechanism for Its Recurrent Elicitation.
Authors: Cheung, C.S. / Fruehwirth, A. / Paparoditis, P.C.G. / Shen, C.H. / Foglierini, M. / Joyce, M.G. / Leung, K. / Piccoli, L. / Rawi, R. / Silacci-Fregni, C. / Tsybovsky, Y. / Verardi, R. / ...Authors: Cheung, C.S. / Fruehwirth, A. / Paparoditis, P.C.G. / Shen, C.H. / Foglierini, M. / Joyce, M.G. / Leung, K. / Piccoli, L. / Rawi, R. / Silacci-Fregni, C. / Tsybovsky, Y. / Verardi, R. / Wang, L. / Wang, S. / Yang, E.S. / Zhang, B. / Zhang, Y. / Chuang, G.Y. / Corti, D. / Mascola, J.R. / Shapiro, L. / Kwong, P.D. / Lanzavecchia, A. / Zhou, T.
History
DepositionOct 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Hemagglutinin
H: The heavy chain of antibody LPAF-a.01
L: The light chain of antibody LPAF-a.01
C: Hemagglutinin
D: The heavy chain of antibody LPAF-a.01
E: The light chain of antibody LPAF-a.01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,01315
Polymers207,2126
Non-polymers1,8019
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.408, 260.836, 66.453
Angle α, β, γ (deg.)90.000, 96.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules FC

#1: Protein Hemagglutinin


Mass: 56648.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Cell line (production host): GNTI-/- / Production host: Homo sapiens (human) / References: UniProt: A0A3S7XTA4, UniProt: C3W5S1*PLUS

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Antibody , 2 types, 4 molecules HDLE

#2: Antibody The heavy chain of antibody LPAF-a.01


Mass: 24416.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody The light chain of antibody LPAF-a.01


Mass: 22541.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)

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Sugars , 3 types, 3 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 105 molecules

#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 1.76 Å3/Da / Density % sol: 30.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M (NH4)2SO4 and 23.57% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen cryo jet / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 37436 / % possible obs: 90.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.094 / Rrim(I) all: 0.199 / Χ2: 2.034 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.73.20.73314220.5610.4280.8540.71871.8
2.7-2.743.50.6415720.6450.3610.7390.7876.2
2.74-2.83.70.60115930.7530.330.690.80677.2
2.8-2.853.80.52117270.80.2760.5930.93383.6
2.85-2.9240.52418120.7780.2760.5961.00388.9
2.92-2.984.20.48918610.7830.2570.5561.0889.1
2.98-3.064.20.43318720.8260.2280.4931.16390.7
3.06-3.144.20.37819260.90.2020.4321.22595.1
3.14-3.234.10.3318880.9250.1770.3771.44490.4
3.23-3.3440.318770.9240.1610.3421.8491.3
3.34-3.464.40.26519600.950.1390.3011.84695.6
3.46-3.64.60.23320040.9620.120.2642.08496.9
3.6-3.764.50.21620480.9630.1130.2462.27198.6
3.76-3.964.40.18119860.9620.0960.2072.59296.6
3.96-4.214.20.14520080.9760.0790.1662.75697
4.21-4.534.10.11519110.9810.0640.1323.03593.9
4.53-4.993.60.10219200.9830.0620.123.46692
4.99-5.714.60.10820080.9860.0570.1233.12796.9
5.71-7.194.80.1120630.9820.0580.1252.91898.8
7.19-504.20.07619780.9890.0430.0883.42994.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K9O

5k9o


Resolution: 2.65→40.063 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.71
RfactorNum. reflection% reflection
Rfree0.2619 1996 5.35 %
Rwork0.2146 --
obs0.2172 37343 88.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 198.07 Å2 / Biso mean: 66.3948 Å2 / Biso min: 22.03 Å2
Refinement stepCycle: final / Resolution: 2.65→40.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9981 0 113 99 10193
Biso mean--80.22 51.06 -
Num. residues----1303
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.65-2.69880.3592710.3012127545
2.6988-2.77180.31541250.2958219976
2.7718-2.85330.34371340.2791236283
2.8533-2.94540.32031420.2799250089
2.9454-3.05060.33491460.2847259090
3.0506-3.17270.33741500.2698266194
3.1727-3.31710.32151450.2504257090
3.3171-3.49190.28381550.2321273595
3.4919-3.71050.24651560.2214275998
3.7105-3.99670.23421560.2051275297
3.9967-4.39850.24441550.1805275595
4.3985-5.03390.20891480.1651262093
5.0339-6.33810.2351590.1871280398
6.3381-40.0630.23261540.1881276696
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)
18.51310.42431.67545.68140.86761.7445-0.16970.43170.5443-0.91670.21221.4308-0.4088-0.3843-0.34371.25320.46640.15840.46880.50570.86-9.57951.834-6.8797
20.1670.9487-0.85058.157-7.93857.8273-0.1780.4630.0125-1.8905-0.28030.30410.7088-0.00290.47891.13810.2045-0.0670.80350.33110.8716-8.884452.2008-9.9588
32.91840.02130.68368.9995-4.06122.60330.20460.32020.353-0.4367-0.23151.2075-0.0722-0.2035-0.01211.30170.26350.29280.49210.0650.675-4.70353.48851.6141
41.1460.739-0.71140.5456-0.52780.49520.24050.36430.0969-1.0619-0.2604-0.1856-0.3117-0.1680.15831.33560.20330.24430.57870.12270.53527.395542.1651-8.6327
55.84315.1345-2.36274.5351-1.97761.5571-0.4240.47010.3931-0.83940.52860.66550.228-0.2277-0.0941.06820.17430.12180.46940.16090.5348-4.894435.6218-2.7463
62.2497-1.38371.56311.63-1.10771.12250.27980.50050.3761-0.0898-0.04050.0597-0.4750.2625-0.09411.28640.18670.30720.5790.18420.593512.768543.689-4.7975
75.6989-1.03830.63421.58161.65242.57490.0612-0.08830.17030.3594-0.0892-0.3215-0.370.4730.02970.8740.05290.07970.36780.05010.421711.684544.81766.2226
80.9905-0.20860.52634.1927-2.89362.83920.09030.22440.3553-0.14880.21640.3516-0.143-0.0702-0.0051.0260.13270.30930.15020.31880.48181.916144.20259.2215
91.80780.63022.37185.153-2.30955.14740.14870.27580.55790.0271-0.1959-0.2028-0.7809-0.28170.09871.01650.18840.35960.47730.17190.67087.128353.9148-5.4953
103.22080.425-0.24325.7263-1.42321.4454-0.2805-0.26010.05550.09870.13690.1213-0.4251-0.11080.14020.82470.08160.01830.29170.05590.43215.588612.258222.5407
111.2942-0.9959-0.07926.6551-2.68622.72220.0513-0.11190.14120.75690.19620.4818-0.5901-0.3207-0.27920.6830.06480.06720.34650.02450.38442.592812.291523.6849
127.8972-0.4063-3.53928.88691.6694.8672-0.35360.898-0.514-1.2503-0.2078-0.8147-0.53930.88470.45130.41590.0041-0.02890.6636-0.05790.348727.3737-17.57038.8135
135.5747-1.1066-0.3791.0771.05382.7529-0.085-0.00260.07410.10820.11950.086-0.4010.0616-0.04770.5362-0.0401-0.01530.24580.04890.258918.0313-10.037616.2159
145.31411.4484-2.91143.63840.58168.4219-0.1242-0.31210.1123-0.1120.4277-0.5972-0.21051.1497-0.2970.42050.0198-0.06740.2662-0.06320.272126.8208-11.474917.9126
152.27972.2805-0.64762.87210.7164.0760.14050.20980.1287-0.21970.09260.26740.0627-0.0217-0.24230.77640.1144-0.07330.28230.06760.48211.183315.32241.1569
162.19291.40280.69782.1712-1.26382.7110.1058-0.02060.0438-0.4067-0.06620.48230.49950.11460.0010.71730.0879-0.10560.27690.08810.5461-0.192314.11951.6262
171.8945-0.57050.23940.43360.65161.9388-0.40170.18980.14430.32480.024-0.0322-0.9729-0.03930.3980.6946-0.0681-0.01940.2412-0.02880.306216.3109-13.9025-0.56
183.816-0.78660.75816.3783-1.6597.15350.09320.0041-0.12730.24220.0786-0.1172-0.0118-0.2539-0.12120.4487-0.00320.00630.2424-0.05790.226514.766-22.38496.7988
193.717-1.179-1.80147.75591.92286.26780.2965-0.1874-0.20171.2749-0.42732.58730.0422-0.71070.10331.43190.11750.70250.46650.01581.2216-14.190444.491831.2235
200.82680.44330.25980.6708-0.71981.7834-0.0255-0.3216-0.36740.79170.45080.96010.0758-0.8967-0.66541.73310.34090.52840.73270.40441.0389-11.132843.291629.1658
211.8844-0.71781.27411.8272-0.90892.0475-0.4207-0.3067-0.29690.924-0.05510.10670.48170.19360.30211.41310.3080.1920.51150.18730.46040.347755.788234.5329
220.6261-0.2770.57881.3295-1.20831.5243-0.0453-0.2884-0.01890.43350.2233-0.12690.5240.33870.22171.49020.54510.28970.30410.48630.48226.56751.143925.7837
232.4080.59851.38911.9812-1.23412.17680.1179-0.274-0.16890.71810.3401-0.06660.05860.00030.18211.67670.50580.32660.4350.34620.51555.978843.678431.3504
242.3923-0.65730.93990.9967-0.66164.2219-0.2177-0.4583-1.17540.69640.03320.14241.3297-0.7298-0.01271.2840.12810.28270.65190.27860.9289-2.497942.213534.4796
253.624-1.28580.54035.5711-2.16913.1334-0.3070.1542-0.4049-0.52840.01630.15510.44060.2330.24920.69570.08280.07790.30480.05630.30124.272181.82595.6286
262.95962.4598-0.6487.9931-1.30111.7771-0.2649-0.1079-0.2938-0.06860.0596-0.0110.31210.40440.20830.49650.1116-0.00080.35920.03410.2495.470986.19217.3657
272.01830.40582.08654.9847-2.00836.99370.0509-1.42630.00641.03830.13390.07060.1108-0.6634-0.15960.70490.1105-0.18240.8506-0.04470.232422.5192114.262624.7528
287.9974-1.07371.15033.5427-0.76234.6009-0.2783-0.39520.0320.0420.2453-0.11240.10950.26260.02190.50820.0165-0.05170.2794-0.00620.177720.5664107.090316.6763
293.71120.4530.87067.34792.36852.05210.039-0.17450.16720.1854-0.39390.40330.4778-0.04390.31640.79720.08190.15630.29280.0910.4024-5.565282.118226.0035
301.78131.90940.10164.37380.46570.0649-0.1133-0.2451-0.1670.1176-0.07580.01310.14270.15870.19630.72840.06390.05630.38190.05310.26013.431895.1226.7301
313.70311.3372-0.85216.4538-0.92023.5462-0.10870.1740.367-0.92790.23370.213-0.6363-0.4475-0.17550.49220.0924-0.05980.4105-0.00340.25729.216119.21925.6382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 57 through 71 )F57 - 71
2X-RAY DIFFRACTION2chain 'F' and (resid 72 through 90 )F72 - 90
3X-RAY DIFFRACTION3chain 'F' and (resid 90A through 114 )F90
4X-RAY DIFFRACTION4chain 'F' and (resid 115 through 138 )F115 - 138
5X-RAY DIFFRACTION5chain 'F' and (resid 139 through 148 )F139 - 148
6X-RAY DIFFRACTION6chain 'F' and (resid 149 through 175 )F149 - 175
7X-RAY DIFFRACTION7chain 'F' and (resid 176 through 213 )F176 - 213
8X-RAY DIFFRACTION8chain 'F' and (resid 214 through 237 )F214 - 237
9X-RAY DIFFRACTION9chain 'F' and (resid 238 through 268 )F238 - 268
10X-RAY DIFFRACTION10chain 'H' and (resid 1 through 52 )H1 - 52
11X-RAY DIFFRACTION11chain 'H' and (resid 53 through 119 )H53 - 119
12X-RAY DIFFRACTION12chain 'H' and (resid 120 through 135 )H120 - 135
13X-RAY DIFFRACTION13chain 'H' and (resid 136 through 175 )H136 - 175
14X-RAY DIFFRACTION14chain 'H' and (resid 176 through 215 )H176 - 215
15X-RAY DIFFRACTION15chain 'L' and (resid 1 through 60 )L1 - 60
16X-RAY DIFFRACTION16chain 'L' and (resid 61 through 105 )L61 - 105
17X-RAY DIFFRACTION17chain 'L' and (resid 106 through 121 )L106 - 121
18X-RAY DIFFRACTION18chain 'L' and (resid 122 through 210 )L122 - 210
19X-RAY DIFFRACTION19chain 'C' and (resid 59 through 71 )C59 - 71
20X-RAY DIFFRACTION20chain 'C' and (resid 72 through 111 )C72 - 111
21X-RAY DIFFRACTION21chain 'C' and (resid 112 through 163 )C112 - 163
22X-RAY DIFFRACTION22chain 'C' and (resid 164 through 228 )C164 - 228
23X-RAY DIFFRACTION23chain 'C' and (resid 229 through 247 )C229 - 247
24X-RAY DIFFRACTION24chain 'C' and (resid 248 through 268 )C248 - 268
25X-RAY DIFFRACTION25chain 'D' and (resid 1 through 71 )D1 - 71
26X-RAY DIFFRACTION26chain 'D' and (resid 72 through 119 )D72 - 119
27X-RAY DIFFRACTION27chain 'D' and (resid 120 through 134 )D120 - 134
28X-RAY DIFFRACTION28chain 'D' and (resid 135 through 215 )D135 - 215
29X-RAY DIFFRACTION29chain 'E' and (resid 1 through 47 )E1 - 47
30X-RAY DIFFRACTION30chain 'E' and (resid 48 through 150 )E48 - 150
31X-RAY DIFFRACTION31chain 'E' and (resid 151 through 209 )E151 - 209

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