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- PDB-4n62: Crystal structure of hemagglutinin from an H7N9 influenza virus i... -

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Basic information

Entry
Database: PDB / ID: 4n62
TitleCrystal structure of hemagglutinin from an H7N9 influenza virus in complex with a sulfated receptor analog
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / viral envelope protein / hemagglutinin / viral fusion protein
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / 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
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5026 Å
AuthorsXu, R. / Wilson, I.A.
CitationJournal: Science / Year: 2013
Title: Preferential recognition of avian-like receptors in human influenza A H7N9 viruses.
Authors: Xu, R. / de Vries, R.P. / Zhu, X. / Nycholat, C.M. / McBride, R. / Yu, W. / Paulson, J.C. / Wilson, I.A.
History
DepositionOct 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6889
Polymers112,1504
Non-polymers2,5385
Water1,29772
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,57518
Polymers168,2246
Non-polymers5,35112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area38100 Å2
ΔGint-99 kcal/mol
Surface area59010 Å2
MethodPISA
2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
hetero molecules

C: Hemagglutinin HA1
D: Hemagglutinin HA2
hetero molecules

C: Hemagglutinin HA1
D: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,4889
Polymers168,2246
Non-polymers2,2643
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area34660 Å2
ΔGint-132 kcal/mol
Surface area57550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.806, 153.806, 153.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

21B-316-

HOH

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Components

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Hemagglutinin ... , 2 types, 4 molecules ACBD

#1: Protein Hemagglutinin HA1


Mass: 34993.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/2/2013 / Gene: HA, hemagglutinin / Plasmid: pFastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: R4NN21
#2: Protein Hemagglutinin HA2


Mass: 21081.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/2/2013 / Gene: HA, hemagglutinin / Plasmid: pFastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: R4NN21

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Sugars , 3 types, 5 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-6-O-sulfo- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose


Type: oligosaccharide / Mass: 754.667 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAc[6S]b1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O_6*OSO/3=O/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc6SO3]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 , 1 types, 72 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 17-20% PEG3350, 0.2 M ammonium acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0331 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2013 / Details: K-B pair of biomorph mirrors
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionRedundancy: 9.3 % / Number: 392387 / Rmerge(I) obs: 0.089 / Χ2: 1.02 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 42019 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.385099.710.0450.9559
4.275.3810010.0750.9879.3
3.734.2710010.0631.0249.4
3.393.7310010.091.0169.4
3.153.3910010.1241.0369.4
2.963.1510010.181.0889.4
2.822.9610010.2611.0769.4
2.692.8210010.4131.0239.4
2.592.6910010.5911.0129.4
2.52.5910010.7721.0379.4
ReflectionResolution: 2.5→50 Å / Num. obs: 42019 / % possible obs: 100 % / Rmerge(I) obs: 0.089

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.75 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.64 Å
Translation2.5 Å48.64 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5026→48.638 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 27.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 2121 5.05 %
Rwork0.2201 --
obs0.2224 41990 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.588 Å2
Refinement stepCycle: LAST / Resolution: 2.5026→48.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7600 0 167 72 7839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047928
X-RAY DIFFRACTIONf_angle_d0.85310711
X-RAY DIFFRACTIONf_dihedral_angle_d17.772954
X-RAY DIFFRACTIONf_chiral_restr0.0391180
X-RAY DIFFRACTIONf_plane_restr0.0041400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5026-2.56090.29161590.26922632X-RAY DIFFRACTION100
2.5609-2.62490.3481620.2732595X-RAY DIFFRACTION100
2.6249-2.69590.33921390.27952612X-RAY DIFFRACTION100
2.6959-2.77520.3491460.28892642X-RAY DIFFRACTION100
2.7752-2.86480.33551450.26842642X-RAY DIFFRACTION100
2.8648-2.96710.33351370.2562646X-RAY DIFFRACTION100
2.9671-3.08590.29651340.262615X-RAY DIFFRACTION100
3.0859-3.22630.32531310.25032684X-RAY DIFFRACTION100
3.2263-3.39640.29641260.2452656X-RAY DIFFRACTION100
3.3964-3.60910.24421320.23422645X-RAY DIFFRACTION100
3.6091-3.88770.27761380.21782670X-RAY DIFFRACTION100
3.8877-4.27870.23181470.19592662X-RAY DIFFRACTION100
4.2787-4.89730.20041240.18232681X-RAY DIFFRACTION100
4.8973-6.16810.24851330.19982725X-RAY DIFFRACTION100
6.1681-48.64690.2431680.19422762X-RAY DIFFRACTION99
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)
11.07191.1615-0.7332.4165-0.91850.78240.1799-0.08710.41420.07420.05940.3793-0.2910.0193-0.26140.5522-0.05980.12220.4125-0.05850.487810.639-45.7815-2.7004
21.28810.61590.45681.6597-1.24131.97540.4474-0.1930.25130.4415-0.09620.6168-0.22240.4042-0.37330.5906-0.12550.09090.5173-0.10730.673543.969-25.4129-20.6694
32.03190.38650.58723.2589-1.98352.69980.34230.4218-0.0571-0.0137-0.25090.26-0.01581.0425-0.07880.4716-0.0179-0.06840.7425-0.11150.45253.1824-21.1096-32.5334
40.46430.18580.32031.5568-1.84552.74880.18750.1452-0.1183-0.10520.37050.28570.16190.4374-0.51220.4776-0.015-0.10440.5813-0.01460.574642.7423-21.4673-34.7963
51.3923-0.0083-0.16321.805-0.66571.62770.51950.0882-0.48370.2591-0.3591-0.0470.18320.683-0.18480.5171-0.0141-0.15510.6702-0.130.460651.445-30.8312-23.5852
61.4215-0.00180.37191.61770.29890.32470.6143-0.45290.46970.4196-0.31910.1237-0.45970.2148-0.24640.7351-0.15730.20590.4507-0.05950.626723.0606-38.0009-8.6045
72.32211.1837-2.00732.6291-1.3064.0730.02390.16050.51060.00230.27240.4556-0.3266-0.54-0.21170.3720.02080.04560.3984-0.00850.60470.8978-52.7862-3.4145
84.32020.2485-1.96923.2193-0.05772.0281-0.06770.14650.04610.3137-0.03240.4443-0.2182-0.47690.14280.5191-0.00930.19920.5102-0.10260.6055-6.956-61.599310.3885
93.82121.0834-2.41941.604-1.07363.11410.0886-0.3532-0.15470.3434-0.1802-0.1625-0.39650.20620.06490.4685-0.03780.04570.5332-0.0380.42983.4119-62.479512.1029
102.94931.036-1.4512.13890.04071.5561-0.0035-0.5753-0.1740.1263-0.3274-0.0046-0.0110.15980.38660.6569-0.04290.10790.57810.05290.698629.015-40.024-18.3234
111.24990.957-1.25120.3196-1.08061.3949-0.1107-0.03930.0469-0.18920.05260.02990.2882-0.03010.03420.5705-0.03760.13630.4705-0.00870.48287.1262-62.0709-5.8311
121.72620.1420.34723.51530.31211.446-0.1864-0.3307-0.23890.41790.15780.32020.5562-0.63630.02340.611-0.05540.14640.65770.11630.4628-9.0136-79.471623.1064
130.91850.37050.46410.380.34830.3425-0.22050.391-0.015-0.049-0.0890.16550.3332-0.52030.20021.4521-0.6457-0.26361.43-0.55021.9288-20.2646-36.5998-7.3127
141.21950.03830.4010.9470.68530.93260.78270.1642-0.6463-0.3032-0.3462-0.21691.1441-0.0748-0.37331.4027-0.1157-0.22560.856-0.36821.203913.4486-15.97089.8798
152.6333-0.07830.02011.64490.95482.29460.6995-0.3770.4889-0.5442-0.0876-0.71440.00310.207-0.56241.0212-0.01330.11440.7962-0.4040.940321.3116-3.353614.7951
161.9512-1.035-0.40963.17922.71854.20930.8475-0.2578-0.0292-0.7518-0.17340.07290.4264-0.1196-0.51310.8938-0.0827-0.02280.8056-0.36811.055910.8749-3.37217.0188
171.1166-0.0365-0.06581.22980.11921.38960.68940.8268-0.0561-0.8017-0.39810.07210.4125-0.1649-0.18921.42450.14540.0910.8821-0.31221.049918.8341-10.50233.9092
180.67030.4582-0.14840.57330.54591.4071-0.01880.0295-0.7009-0.1311-0.20850.40220.50090.279-0.00941.9747-1.2584-0.73841.4271-0.77491.4442-7.5719-29.6786-0.8483
190.62070.99280.42562.39790.31140.47290.03710.05110.03090.3512-0.01820.35670.0958-0.53180.00551.5215-1.4518-0.57321.9745-0.9321.613-31.2644-36.7217-12.0456
200.17410.292-0.53050.4708-0.8741.6057-0.0339-0.05730.1849-0.06660.08640.5226-0.2019-0.1564-0.01021.93-0.5559-0.21691.3931-0.35962.5946-44.86-48.4803-24.4025
210.01540.12660.01890.89450.13660.01520.0006-0.24330.0071-0.0397-0.22160.0708-0.04330.16390.1661.7707-0.652-0.2021.7169-0.672.0688-37.0724-56.3003-24.3716
221.69550.8471.442.23151.83732.8802-0.08280.09160.1767-0.04820.0122-0.3409-0.14650.18250.05141.8091-0.3558-0.21491.5743-0.66591.8378-20.2599-42.2921-23.3353
230.89490.70290.43711.10430.08410.3599-0.17870.0274-0.264-0.0001-0.215-0.21350.07280.2440.35451.458-0.3026-0.25741.2381-0.51911.656-3.8526-18.9872-1.7707
240.51210.38730.09410.29660.43770.0484-0.35320.3741-0.4658-0.399-0.08350.41660.2539-0.73140.27391.6678-0.8936-0.21661.8051-0.68011.6345-27.5368-31.6528-21.8705
250.37850.3205-0.47841.0470.25911.1109-0.1379-0.3146-0.0645-0.2435-0.06090.0665-0.09270.28150.01261.5067-1.145-0.47841.5403-1.66472.2739-42.1954-60.0021-41.5328
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 213 )
4X-RAY DIFFRACTION4chain 'A' and (resid 214 through 237 )
5X-RAY DIFFRACTION5chain 'A' and (resid 238 through 269 )
6X-RAY DIFFRACTION6chain 'A' and (resid 270 through 308 )
7X-RAY DIFFRACTION7chain 'A' and (resid 309 through 327 )
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 22 )
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 56 )
10X-RAY DIFFRACTION10chain 'B' and (resid 57 through 74 )
11X-RAY DIFFRACTION11chain 'B' and (resid 75 through 137 )
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 172 )
13X-RAY DIFFRACTION13chain 'C' and (resid 11 through 65 )
14X-RAY DIFFRACTION14chain 'C' and (resid 66 through 132 )
15X-RAY DIFFRACTION15chain 'C' and (resid 133 through 213 )
16X-RAY DIFFRACTION16chain 'C' and (resid 214 through 237 )
17X-RAY DIFFRACTION17chain 'C' and (resid 238 through 269 )
18X-RAY DIFFRACTION18chain 'C' and (resid 270 through 308 )
19X-RAY DIFFRACTION19chain 'C' and (resid 309 through 327 )
20X-RAY DIFFRACTION20chain 'D' and (resid 4 through 13 )
21X-RAY DIFFRACTION21chain 'D' and (resid 14 through 37 )
22X-RAY DIFFRACTION22chain 'D' and (resid 38 through 56 )
23X-RAY DIFFRACTION23chain 'D' and (resid 57 through 74 )
24X-RAY DIFFRACTION24chain 'D' and (resid 75 through 137 )
25X-RAY DIFFRACTION25chain 'D' and (resid 138 through 172 )

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