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- PDB-5lbs: structural basis of Zika and Dengue virus potent antibody cross-n... -

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Basic information

Entry
Database: PDB / ID: 5lbs
Titlestructural basis of Zika and Dengue virus potent antibody cross-neutralization
Components
  • (BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 ...) x 2
  • envelope protein E
KeywordsIMMUNE SYSTEM-VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX / ZIKA VIRUS / BROADLY NEUTRALIZING ANTIBODY
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / molecular adaptor activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / centrosome / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus ...Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Genome polyprotein / Polyprotein
Similarity search - Component
Biological speciesZika virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsVaney, M.C. / Rouvinski, A. / Barba-Spaeth, G. / Rey, F.A.
Citation
Journal: Nature / Year: 2016
Title: Structural basis of potent Zika-dengue virus antibody cross-neutralization.
Authors: Barba-Spaeth, G. / Dejnirattisai, W. / Rouvinski, A. / Vaney, M.C. / Medits, I. / Sharma, A. / Simon-Loriere, E. / Sakuntabhai, A. / Cao-Lormeau, V.M. / Haouz, A. / England, P. / Stiasny, K. ...Authors: Barba-Spaeth, G. / Dejnirattisai, W. / Rouvinski, A. / Vaney, M.C. / Medits, I. / Sharma, A. / Simon-Loriere, E. / Sakuntabhai, A. / Cao-Lormeau, V.M. / Haouz, A. / England, P. / Stiasny, K. / Mongkolsapaya, J. / Heinz, F.X. / Screaton, G.R. / Rey, F.A.
#1: Journal: Nature / Year: 2015
Title: Recognition determinants of broadly neutralizing human antibodies against dengue viruses.
Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. ...Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. / Petres, S. / Shepard, W.E. / Despres, P. / Arenzana-Seisdedos, F. / Dussart, P. / Mongkolsapaya, J. / Screaton, G.R. / Rey, F.A.
#2: Journal: Nat Immunol / Year: 2015
Title: A new class of highly potent, broadly neutralizing antibodies isolated from viremic patients infected with dengue virus.
Authors: Wanwisa Dejnirattisai / Wiyada Wongwiwat / Sunpetchuda Supasa / Xiaokang Zhang / Xinghong Dai / Alexander Rouvinski / Amonrat Jumnainsong / Carolyn Edwards / Nguyen Than Ha Quyen / Thaneeya ...Authors: Wanwisa Dejnirattisai / Wiyada Wongwiwat / Sunpetchuda Supasa / Xiaokang Zhang / Xinghong Dai / Alexander Rouvinski / Amonrat Jumnainsong / Carolyn Edwards / Nguyen Than Ha Quyen / Thaneeya Duangchinda / Jonathan M Grimes / Wen-Yang Tsai / Chih-Yun Lai / Wei-Kung Wang / Prida Malasit / Jeremy Farrar / Cameron P Simmons / Z Hong Zhou / Felix A Rey / Juthathip Mongkolsapaya / Gavin R Screaton /
Abstract: Dengue is a rapidly emerging, mosquito-borne viral infection, with an estimated 400 million infections occurring annually. To gain insight into dengue immunity, we characterized 145 human monoclonal ...Dengue is a rapidly emerging, mosquito-borne viral infection, with an estimated 400 million infections occurring annually. To gain insight into dengue immunity, we characterized 145 human monoclonal antibodies (mAbs) and identified a previously unknown epitope, the envelope dimer epitope (EDE), that bridges two envelope protein subunits that make up the 90 repeating dimers on the mature virion. The mAbs to EDE were broadly reactive across the dengue serocomplex and fully neutralized virus produced in either insect cells or primary human cells, with 50% neutralization in the low picomolar range. Our results provide a path to a subunit vaccine against dengue virus and have implications for the design and monitoring of future vaccine trials in which the induction of antibody to the EDE should be prioritized.
History
DepositionJun 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Derived calculations
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Aug 17, 2016Group: Database references
Revision 2.0Jun 12, 2019Group: Atomic model / Data collection / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / database_PDB_rev / database_PDB_rev_record
Item: _atom_site.occupancy / _audit_author.name
Revision 2.1Jan 10, 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: envelope protein E
B: envelope protein E
H: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
I: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
L: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
M: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,93420
Polymers157,9636
Non-polymers97114
Water3,243180
1
A: envelope protein E
H: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
L: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
hetero molecules

A: envelope protein E
H: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
L: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,14924
Polymers157,9636
Non-polymers1,18518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
2
B: envelope protein E
I: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
M: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
hetero molecules

B: envelope protein E
I: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
M: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,72016
Polymers157,9636
Non-polymers75710
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Unit cell
Length a, b, c (Å)60.799, 121.353, 257.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-942-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein envelope protein E /


Mass: 48492.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Strain: Mr 766 / Cell (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A120IIH9, UniProt: A0A024B7W1*PLUS

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Antibody , 2 types, 4 molecules HILM

#2: Antibody BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8


Mass: 14617.839 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ScFv fragment, heavy chain / Source: (gene. exp.) Homo sapiens (human) / Cell (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)
#3: Antibody BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8


Mass: 15871.365 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SCFV fragment, light chain / Source: (gene. exp.) Homo sapiens (human) / Cell (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)

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Non-polymers , 3 types, 194 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 1.26M (NH4)2SO4 0.1M CHES pH 9.5 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.41→40 Å / Num. obs: 74842 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 35.74 Å2 / Net I/σ(I): 6.7
Reflection shellResolution: 2.41→2.46 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UTA

4uta


Resolution: 2.41→39.96 Å / Cor.coef. Fo:Fc: 0.9155 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.297 / SU Rfree Blow DPI: 0.209 / SU Rfree Cruickshank DPI: 0.212
Details: The DEBYE and STARANISO progams developped by Global Phasing Ltd. were applied to the AIMLESS scaled data without truncation of the resolution. These corrected anisotropic amplitudes were ...Details: The DEBYE and STARANISO progams developped by Global Phasing Ltd. were applied to the AIMLESS scaled data without truncation of the resolution. These corrected anisotropic amplitudes were used for further cycles of refinements with BUSTER.
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 3203 4.91 %RANDOM
Rwork0.1937 ---
obs0.1949 65260 87.25 %-
Displacement parametersBiso mean: 55.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.9083 Å20 Å20 Å2
2---1.6734 Å20 Å2
3----0.2349 Å2
Refine analyzeLuzzati coordinate error obs: 0.363 Å
Refinement stepCycle: 1 / Resolution: 2.41→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9576 0 59 180 9815
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089862HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9113363HARMONIC2.5
X-RAY DIFFRACTIONt_dihedral_angle_d3296SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes205HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1443HARMONIC5
X-RAY DIFFRACTIONt_it9862HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion18.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1272SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10248SEMIHARMONIC4
LS refinement shellResolution: 2.41→2.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2552 120 5.48 %
Rwork0.23 2071 -
all0.2314 2191 -
obs--40.32 %
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)
14.899-0.403-2.24021.793-0.50947.17620.24151.151-0.1502-0.2216-0.7169-0.33050.31851.18110.4754-0.25460.2461-0.02770.38280.0707-0.32493.3839166.90832.3725
26.1335-1.77840.83361.9004-1.92665.7165-0.01510.3412-0.12710.0172-0.14760.19-0.2886-1.1760.16270.4520.0970.1065-0.1506-0.0819-0.360951.1889133.26144.0424
33.6839-0.18955.4490-0.77469.97750.037-0.3319-0.1139-0.0653-0.00010.01980.43341.0874-0.0369-0.29420.2165-0.08330.45150.0141-0.322370.3014172.911-9.979
40.02440.10431.766602.218415.5701-0.0406-0.41840.13730.126-0.12720.09580.1863-0.56650.16780.62720.06970.027-0.0465-0.1121-0.394647.2213127.52-2.8105
56.0814-1.60022.33693.35-0.45595.6631-0.1701-0.0134-0.1420.48510.0726-0.03110.18220.19020.0975-0.0543-0.0049-0.0465-0.2232-0.0089-0.241584.7258167.22454.4554
64.6777-1.6563-1.18794.0543-0.57997.9185-0.4157-0.53220.37320.65650.2813-0.3875-0.55930.47770.13450.61210.0427-0.0281-0.3911-0.0895-0.266770.6722132.57559.0076
702.46264.1287.8765-0.10440.75950.13010.6138-0.5038-0.0286-0.3318-0.47650.49650.10070.20170.08760.0827-0.19610.0144-0.018-0.09493.7633162.98960.7542
80.43154.13822.90151.283-1.544200.0555-0.34910.60190.21080.1008-0.3035-0.23150.2077-0.15630.36550.1399-0.0295-0.168-0.0396-0.36363.0963136.5466.2415
92.6289-0.33380.73185.91461.1915.2798-0.02950.3940.1545-0.6551-0.05330.2274-0.9622-0.30130.08270.06980.0516-0.0203-0.05770.0607-0.259967.7341195.80829.681
101.24170.3941-0.12554.04361.61963.65430.1001-0.10250.05850.4136-0.0567-0.0223-0.2515-0.0889-0.04340.07990.00560.0128-0.09650.0253-0.090672.894193.52851.1555
112.2923-0.99050.71155.8188-0.35366.25940.1610.5067-0.1384-1.0932-0.15610.31570.53060.0009-0.00490.37220.0054-0.0968-0.2997-0.0926-0.320772.499104.31728.4725
121.3085-0.49790.48235.4783-1.84773.60710.0160.0150.0020.0685-0.1636-0.198-0.2740.32990.14760.1875-0.0759-0.0264-0.1692-0.0456-0.134679.7077106.79149.1974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1:46 138:194 287:302}
2X-RAY DIFFRACTION2{B|1:46 138:194 287:302}
3X-RAY DIFFRACTION3{A|47:137 195:286}
4X-RAY DIFFRACTION4{B|47:137 195:286}
5X-RAY DIFFRACTION5{A|303:403}
6X-RAY DIFFRACTION6{B|303:403}
7X-RAY DIFFRACTION7{A|437:446}
8X-RAY DIFFRACTION8{B|437:443}
9X-RAY DIFFRACTION9tls_H_ScFv
10X-RAY DIFFRACTION10{L|1:110}
11X-RAY DIFFRACTION11{I|1:113}
12X-RAY DIFFRACTION12{M|1:110}

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