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- PDB-7mlm: Crystal structure of mouse TLR4/MD-2 in complex with sulfatides -

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Basic information

Entry
Database: PDB / ID: 7mlm
TitleCrystal structure of mouse TLR4/MD-2 in complex with sulfatides
Components
  • Lymphocyte antigen 96
  • Toll-like receptor 4,Variable lymphocyte receptor B
KeywordsIMMUNE SYSTEM / Innate immunity / endogenous ligands / Toll-like receptors
Function / homology
Function and homology information


MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / Toll Like Receptor 4 (TLR4) Cascade / Heme signaling / nitric oxide production involved in inflammatory response / Regulation of TLR by endogenous ligand / MHC class II biosynthetic process / TRIF-mediated programmed cell death / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / TRAF6-mediated induction of TAK1 complex within TLR4 complex ...MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / Toll Like Receptor 4 (TLR4) Cascade / Heme signaling / nitric oxide production involved in inflammatory response / Regulation of TLR by endogenous ligand / MHC class II biosynthetic process / TRIF-mediated programmed cell death / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / lipopolysaccharide immune receptor activity / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of matrix metallopeptidase secretion / Toll-like receptor 4 binding / IKK complex recruitment mediated by RIP1 / mast cell activation / detection of lipopolysaccharide / positive regulation of lymphocyte proliferation / regulation of dendritic cell cytokine production / lipopolysaccharide receptor complex / negative regulation of interleukin-23 production / cellular response to oxidised low-density lipoprotein particle stimulus / wound healing involved in inflammatory response / lymphocyte proliferation / B cell proliferation involved in immune response / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / activation of NF-kappaB-inducing kinase activity / positive regulation of stress-activated MAPK cascade / intestinal epithelial structure maintenance / positive regulation of interleukin-13 production / positive regulation of interleukin-1 production / macrophage activation / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / microglia differentiation / nucleotide-binding oligomerization domain containing 2 signaling pathway / NAD+ nucleosidase activity, cyclic ADP-ribose generating / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / positive regulation of platelet activation / positive regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of interleukin-17 production / positive regulation of cytokine production involved in inflammatory response / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of cold-induced thermogenesis / positive regulation of macrophage cytokine production / positive regulation of smooth muscle cell migration / MyD88-dependent toll-like receptor signaling pathway / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of reactive oxygen species biosynthetic process / cellular response to lipoteichoic acid / negative regulation of type II interferon production / negative regulation of interleukin-6 production / B cell proliferation / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / phagocytosis / phagocytic cup / stress-activated MAPK cascade / positive regulation of chemokine production / JNK cascade / cellular response to platelet-derived growth factor stimulus / ruffle / positive regulation of B cell proliferation / ERK1 and ERK2 cascade / neurogenesis / nitric oxide biosynthetic process / positive regulation of interleukin-12 production / positive regulation of smooth muscle cell proliferation / activation of innate immune response / positive regulation of interferon-beta production / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / response to bacterium / lipopolysaccharide binding / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of type II interferon production / cellular response to amyloid-beta / positive regulation of inflammatory response / positive regulation of nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / cellular response to lipopolysaccharide / regulation of inflammatory response / response to lipopolysaccharide
Similarity search - Function
Lymphocyte antigen 96 / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Toll-like receptor / : / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain ...Lymphocyte antigen 96 / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Toll-like receptor / : / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
Chem-ZKM / Variable lymphocyte receptor B / Lymphocyte antigen 96 / Toll-like receptor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Eptatretus burgeri (inshore hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.104 Å
AuthorsSu, L. / Beutler, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Sulfatides are endogenous ligands for the TLR4-MD-2 complex.
Authors: Su, L. / Athamna, M. / Wang, Y. / Wang, J. / Freudenberg, M. / Yue, T. / Wang, J. / Moresco, E.M.Y. / He, H. / Zor, T. / Beutler, B.
History
DepositionApr 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 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

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Assembly

Deposited unit
A: Toll-like receptor 4,Variable lymphocyte receptor B
C: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,23111
Polymers92,9542
Non-polymers4,2779
Water4,720262
1
A: Toll-like receptor 4,Variable lymphocyte receptor B
C: Lymphocyte antigen 96
hetero molecules

A: Toll-like receptor 4,Variable lymphocyte receptor B
C: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,46322
Polymers185,9084
Non-polymers8,55418
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area17870 Å2
ΔGint11 kcal/mol
Surface area59030 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint15 kcal/mol
Surface area31860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.094, 164.293, 89.296
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein Toll-like receptor 4,Variable lymphocyte receptor B


Mass: 71649.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Gene: Tlr4, Lps, VLRB / Cell line (production host): High Five (BTI-Tn-5B1-4) / Production host: Trichoplusia ni
References: UniProt: Q9QUK6, UniProt: Q4G1L2, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: Protein Lymphocyte antigen 96 / Ly-96 / ESOP-1 / Protein MD-2


Mass: 21304.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ly96, Esop1, Md2 / Cell line (production host): High Five (BTI-Tn-5B1-4) / Production host: Trichoplusia ni / References: UniProt: Q9JHF9

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Sugars , 3 types, 6 molecules

#3: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 4 / Source method: obtained synthetically / 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 , 2 types, 265 molecules

#6: Chemical ChemComp-ZKM / N-[(1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-en-1-yl]-hexadecanamide


Mass: 780.104 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H77NO11S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH8.0, 0.8 M sodium formate, 8% PEG 8000, 8% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 58410 / % possible obs: 94.2 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.029 / Rrim(I) all: 0.105 / Χ2: 0.953 / Net I/σ(I): 6.3 / Num. measured all: 697266
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.146.91.13419990.670.3981.2090.94964.8
2.14-2.1871.03622560.6980.3581.1030.95173.8
2.18-2.227.50.99125050.7320.3391.0540.95582.4
2.22-2.268.10.97427320.7880.3251.0320.96189
2.26-2.319.30.99427710.8130.3211.0490.95489.8
2.31-2.3710.60.98930160.8970.3091.0390.95498.3
2.37-2.4212.10.92230580.9210.2730.9630.93499
2.42-2.49130.78730500.9550.2250.8190.94699.1
2.49-2.5613.40.66130520.9660.1870.6880.96299.1
2.56-2.6513.30.53230350.9780.150.5530.97699.2
2.65-2.74130.42630640.9760.1220.4430.95999.4
2.74-2.8512.50.29229530.9860.0840.3040.98996.1
2.85-2.9813.90.25131050.9910.0690.2610.96999.5
2.98-3.1413.80.1830820.9940.050.1870.99499.7
3.14-3.3313.60.12730850.9960.0360.1320.99299.6
3.33-3.59130.0931000.9960.0260.0941.00499.6
3.59-3.9513.50.0730410.9980.020.0731.04597.3
3.95-4.5213.80.06131450.9980.0170.0640.9999.9
4.52-5.712.90.05530940.9980.0160.0570.87697.9
5.7-50130.04232670.9980.0120.0440.69998.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IJC

5ijc


Resolution: 2.104→46.396 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 2000 4.28 %
Rwork0.2097 44679 -
obs0.2112 46679 75.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.72 Å2 / Biso mean: 37.5477 Å2 / Biso min: 13.34 Å2
Refinement stepCycle: final / Resolution: 2.104→46.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5806 0 285 262 6353
Biso mean--76.03 37.4 -
Num. residues----726
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.104-2.15620.3793430.240397423
2.1562-2.21450.2697550.2364121929
2.2145-2.27960.2764660.2454146635
2.2796-2.35320.3046810.2497181343
2.3532-2.43730.28381080.2536241557
2.4373-2.53490.26111450.2497323377
2.5349-2.65020.30741770.2491394193
2.6502-2.78990.25181840.245414297
2.7899-2.96470.30861860.2414415098
2.9647-3.19360.26121890.22434222100
3.1936-3.51490.25911900.21374224100
3.5149-4.02320.20681880.1694421098
4.0232-5.06780.18091920.16124302100
5.0678-46.3960.23491960.2145436898
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)
10.90340.0027-1.47260.0628-0.07482.48240.08760.00450.19460.0123-0.0021-0.3738-0.1150.6806-0.05820.2034-0.01220.10450.5249-0.09590.642245.31747.57312.06
20.73320.00020.23671.13050.32941.08630.04140.23570.1193-0.0836-0.0720.1056-0.1074-0.04690.01950.15990.03810.10890.2153-0.03060.210917.89946.7658.321
30.8566-0.38450.01710.99340.33220.767-0.12590.0607-0.1890.1461-0.12290.510.5188-0.46720.16260.3794-0.06790.09590.3692-0.14110.35117.72919.6552.163
40.3459-0.2932-0.12190.64580.33170.7694-0.45230.1689-0.13030.41270.1330.17430.4338-0.40860.02190.52630.01040.12790.1047-0.26050.0523.1169.087-10.397
52.263-0.72920.70512.22720.54562.6829-0.2274-0.0204-0.1440.30710.0235-0.23880.2875-0.05750.11940.315-0.01180.04210.1341-0.04670.201537.1573.69-15.402
60.9133-0.0105-0.15190.1768-0.18490.6235-0.2872-0.019-0.04140.2113-0.007-0.51490.04720.18460.08560.31960.0197-0.14080.14420.03030.428152.5349.819-14.764
70.3207-0.2235-0.07620.4426-0.27490.4282-0.1936-0.08650.1690.2053-0.0145-0.4679-0.1390.2799-0.04440.3753-0.174-0.77060.2207-0.08210.891167.60718.781-7.967
80.78641.178-0.29372.8154-0.35750.13350.0223-0.1871-0.080.24510.1015-0.20120.20670.1632-0.11560.77150.0808-0.21370.271-0.21970.302335.07922.73831.554
96.71150.26620.79561.87463.13755.6376-0.1542-0.2881-0.3120.54670.10520.55470.1696-0.21940.02250.44150.01250.06090.1921-0.03370.29724.4616.03431.203
100.6929-0.0502-0.19491.9883-0.35691.1680.15730.0054-0.030.37610.0627-0.05460.12660.0141-0.11260.26460.0291-0.010.1727-0.06130.213929.91224.26220.001
111.2727-1.41650.11492.8483-1.17410.87410.1520.02380.04530.2959-0.0585-0.13690.16180.09-0.07990.26560.0563-0.05750.2299-0.09240.291531.4517.64714.22
120.7703-0.4752-0.2882.9302-1.04790.82370.17560.06030.08130.39610.0478-0.24020.2590.1399-0.03950.35010.0031-0.08520.2045-0.10230.226829.37821.41320.784
131.6095-0.29410.97362.21121.2681.55420.2032-0.13350.01560.37950.0083-0.06390.06740.1213-0.02820.34410.0062-0.15590.234-0.15920.306436.29119.58426.359
140.0008-0.00770.00130.0040.0019-0.00060.04650.0694-0.0095-0.08020.08220.06760.0472-0.08290.00010.51760.0244-0.05740.49730.02740.509625.24212.27817.039
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 27:59 )A27 - 59
2X-RAY DIFFRACTION2( CHAIN A AND RESID 60:260 )A60 - 260
3X-RAY DIFFRACTION3( CHAIN A AND RESID 261:346 )A261 - 346
4X-RAY DIFFRACTION4( CHAIN A AND RESID 347:433 )A347 - 433
5X-RAY DIFFRACTION5( CHAIN A AND RESID 434:466 )A434 - 466
6X-RAY DIFFRACTION6( CHAIN A AND RESID 467:563 )A467 - 563
7X-RAY DIFFRACTION7( CHAIN A AND RESID 564:618 )A564 - 618
8X-RAY DIFFRACTION8( CHAIN C AND RESID 21:44 )C21 - 44
9X-RAY DIFFRACTION9( CHAIN C AND RESID 45:55 )C45 - 55
10X-RAY DIFFRACTION10( CHAIN C AND RESID 56:82 )C56 - 82
11X-RAY DIFFRACTION11( CHAIN C AND RESID 83:102 )C83 - 102
12X-RAY DIFFRACTION12( CHAIN C AND RESID 103:143 )C103 - 143
13X-RAY DIFFRACTION13( CHAIN C AND RESID 144:156 )C144 - 156
14X-RAY DIFFRACTION14( CHAIN A AND RESID 703:704 ) OR ( CHAIN C AND RESID 203:203 )A703 - 704
15X-RAY DIFFRACTION14( CHAIN A AND RESID 703:704 ) OR ( CHAIN C AND RESID 203:203 )C203

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