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- PDB-3b08: Crystal structure of the mouse HOIL1-L-NZF in complex with linear... -

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Basic information

Entry
Database: PDB / ID: 3b08
TitleCrystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin
Components
  • Polyubiquitin-C
  • RanBP-type and C3HC4-type zinc finger-containing protein 1
KeywordsSIGNALING PROTEIN/METAL BINDING PROTEIN / protein complex / SIGNALING PROTEIN-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


TNFR1-induced proapoptotic signaling / TNFR1-induced NF-kappa-B signaling pathway / protein linear polyubiquitination / Regulation of TNFR1 signaling / LUBAC complex / RBR-type E3 ubiquitin transferase / ubiquitin ligase activator activity / negative regulation of necroptotic process / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of extrinsic apoptotic signaling pathway ...TNFR1-induced proapoptotic signaling / TNFR1-induced NF-kappa-B signaling pathway / protein linear polyubiquitination / Regulation of TNFR1 signaling / LUBAC complex / RBR-type E3 ubiquitin transferase / ubiquitin ligase activator activity / negative regulation of necroptotic process / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of extrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Pexophagy / VLDLR internalisation and degradation / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / ubiquitin binding / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Deactivation of the beta-catenin transactivating complex / Regulation of signaling by CBL / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / protein kinase C binding / Peroxisomal protein import / Hh mutants are degraded by ERAD / Degradation of AXIN / Stabilization of p53 / Recognition of DNA damage by PCNA-containing replication complex / Activation of NF-kappaB in B cells
Similarity search - Function
: / : / : / : / Zn-finger domain of Sec23/24 / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain ...: / : / : / : / Zn-finger domain of Sec23/24 / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH3 type barrels. / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
trehalose / Polyubiquitin-C / RanBP-type and C3HC4-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsSato, Y. / Fujita, H. / Yoshikawa, A. / Yamashita, M. / Yamagata, A. / Kaiser, S.E. / Iwai, K. / Fukai, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex
Authors: Sato, Y. / Fujita, H. / Yoshikawa, A. / Yamashita, M. / Yamagata, A. / Kaiser, S.E. / Iwai, K. / Fukai, S.
History
DepositionJun 7, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Polyubiquitin-C
B: RanBP-type and C3HC4-type zinc finger-containing protein 1
D: Polyubiquitin-C
E: RanBP-type and C3HC4-type zinc finger-containing protein 1
G: Polyubiquitin-C
H: RanBP-type and C3HC4-type zinc finger-containing protein 1
J: Polyubiquitin-C
K: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,59714
Polymers97,6518
Non-polymers9466
Water14,952830
1
A: Polyubiquitin-C
B: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4783
Polymers24,4132
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-11 kcal/mol
Surface area12200 Å2
MethodPISA
2
D: Polyubiquitin-C
E: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4783
Polymers24,4132
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-11 kcal/mol
Surface area12340 Å2
MethodPISA
3
G: Polyubiquitin-C
H: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8214
Polymers24,4132
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-13 kcal/mol
Surface area11720 Å2
MethodPISA
4
J: Polyubiquitin-C
K: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8214
Polymers24,4132
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-16 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.938, 104.938, 170.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Polyubiquitin-C / Ubiquitin


Mass: 17135.654 Da / Num. of mol.: 4 / Fragment: linear di ubiquitin, UNP residues 1-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P0CG48
#2: Protein
RanBP-type and C3HC4-type zinc finger-containing protein 1 / Heme-oxidized IRP2 ubiquitin ligase 1 homolog / HOIL-1 / UbcM4-interacting protein 28 / Ubiquitin- ...Heme-oxidized IRP2 ubiquitin ligase 1 homolog / HOIL-1 / UbcM4-interacting protein 28 / Ubiquitin-conjugating enzyme 7-interacting protein 3


Mass: 7277.155 Da / Num. of mol.: 4 / Fragment: UNP residues 192-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rbck1, Rbck, Ubce7ip3, Uip28 / Plasmid: pCold GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9WUB0
#3: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.3M tri-sodium citrate, 90mM HEPES-NaOH buffer, 100mM potassium sodium tartrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.2826 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2010 / Details: mirros
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2826 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 125184 / Num. obs: 125184 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.57 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 36.2
Reflection shellResolution: 1.6→1.62 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.75 / % possible all: 89.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.1_743refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3a9j

3a9j


Resolution: 1.701→46.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8866 / SU ML: 0.42 / σ(F): 2.1 / Phase error: 18.66 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2112 5102 5 %
Rwork0.1735 --
obs0.1754 101984 97.47 %
all-125184 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.057 Å2 / ksol: 0.401 e/Å3
Displacement parametersBiso max: 107.41 Å2 / Biso mean: 24.7385 Å2 / Biso min: 6.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.301 Å2-0 Å20 Å2
2--0.301 Å20 Å2
3----0.6019 Å2
Refinement stepCycle: LAST / Resolution: 1.701→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6649 0 50 830 7529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076816
X-RAY DIFFRACTIONf_angle_d1.0799199
X-RAY DIFFRACTIONf_dihedral_angle_d14.3452725
X-RAY DIFFRACTIONf_chiral_restr0.0771048
X-RAY DIFFRACTIONf_plane_restr0.0051202
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7012-1.72050.26011770.20552967314491
1.7205-1.74080.26171490.2053046319593
1.7408-1.7620.26121420.20733068321093
1.762-1.78430.25761650.19353066323194
1.7843-1.80780.22111610.17493108326994
1.8078-1.83250.21941660.18083104327095
1.8325-1.85870.25931670.17753108327595
1.8587-1.88650.20131580.16993159331796
1.8865-1.91590.231570.17043156331396
1.9159-1.94740.20371770.1623181335897
1.9474-1.98090.2081610.1663228338998
1.9809-2.0170.23251760.16713204338098
2.017-2.05580.20281560.16433258341499
2.0558-2.09770.21771730.16683231340499
2.0977-2.14330.19811550.16463270342599
2.1433-2.19320.20951730.16493263343699
2.1932-2.2480.20341810.16583231341298
2.248-2.30880.20441630.16433235339899
2.3088-2.37670.241910.17233282347399
2.3767-2.45350.22251800.18232703450100
2.4535-2.54110.2111670.18693290345799
2.5411-2.64290.24121730.188233123485100
2.6429-2.76310.24811760.193433253501100
2.7631-2.90880.22931810.185833113492100
2.9088-3.0910.20111920.171333233515100
3.091-3.32960.21461960.167433153511100
3.3296-3.66460.16741670.154733673534100
3.6646-4.19460.17431860.14843380356699
4.1946-5.28360.1771840.16193301348596
5.2836-46.94750.25641520.21193523367596
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)
10.8232-0.7628-0.78841.83491.48591.67830.00860.01510.0503-0.06180.0149-0.0143-0.03210.0525-0.02180.10540.0223-0.00190.09290.03790.108329.458244.242430.8375
21.51380.68060.06081.98791.17423.58950.06020.16290.038-0.1655-0.01690.16180.0561-0.2017-0.03960.11590.0234-0.01660.08650.03020.136617.397433.889128.2409
31.0303-0.7881-0.73222.1011.52311.924-0.0035-0.004-0.0092-0.0452-0.00780.0115-0.03380.06270.010.09020.0043-0.00910.07380.04360.101381.93396.449831.5992
41.67410.2599-0.06721.54841.03393.15110.0290.1017-0.0114-0.189-0.05130.13670.1619-0.25570.0240.1196-0.0033-0.01890.06640.01860.115569.579986.41428.6768
51.3749-0.39730.77751.1704-0.91761.8209-0.0188-0.0462-0.1065-0.05930.00210.04440.0981-0.12140.0180.12720.01960.03170.0634-0.03310.096323.51516.046934.8732
61.53060.3484-0.20221.1702-0.09741.3664-0.02960.35730.0159-0.4074-0.0749-0.11310.14240.0987-0.01190.14370.04980.04190.0590.02610.036934.69915.505229.1013
71.4657-0.8521.13991.5123-1.35122.54570.0118-0.039-0.0605-0.0266-0.0080.07550.0995-0.0954-0.01290.1123-0.00630.01460.0707-0.02010.111575.255157.934834.7442
81.74380.5102-0.09621.42170.00462.329-0.01080.2365-0.0782-0.27160.0512-0.1418-0.04020.0085-0.02210.10850.0260.02610.06150.00050.064486.146567.036829.0096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 151
2X-RAY DIFFRACTION2chain BB191 - 248
3X-RAY DIFFRACTION3chain DD1 - 151
4X-RAY DIFFRACTION4chain EE191 - 249
5X-RAY DIFFRACTION5chain GG1 - 150
6X-RAY DIFFRACTION6chain HH191 - 249
7X-RAY DIFFRACTION7chain JJ1 - 149
8X-RAY DIFFRACTION8chain KK190 - 248

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