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- PDB-6war: Crystal structure of the MERS-CoV RBD bound by the neutralizing s... -

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Basic information

Entry
Database: PDB / ID: 6war
TitleCrystal structure of the MERS-CoV RBD bound by the neutralizing single-domain antibody MERS VHH-55
Components
  • Spike protein
  • nanobody MERS VHH-55
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / MERS-CoV / nanobody / coronavirus / RBD / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / ubp-family deubiquitinating enzyme fold / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single Sheet / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily ...ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / ubp-family deubiquitinating enzyme fold / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single Sheet / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Spike glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesMiddle East respiratory syndrome-related coronavirus
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsWrapp, D. / Torres, G.M. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI127521 United States
CitationJournal: Cell / Year: 2020
Title: Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies.
Authors: Wrapp, D. / De Vlieger, D. / Corbett, K.S. / Torres, G.M. / Wang, N. / Van Breedam, W. / Roose, K. / van Schie, L. / Hoffmann, M. / Pohlmann, S. / Graham, B.S. / Callewaert, N. / Schepens, B. ...Authors: Wrapp, D. / De Vlieger, D. / Corbett, K.S. / Torres, G.M. / Wang, N. / Van Breedam, W. / Roose, K. / van Schie, L. / Hoffmann, M. / Pohlmann, S. / Graham, B.S. / Callewaert, N. / Schepens, B. / Saelens, X. / McLellan, J.S.
History
DepositionMar 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 10, 2020Group: Advisory / Database references / Derived calculations
Category: citation / pdbx_validate_close_contact / struct_conn
Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 18, 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: Spike protein
B: nanobody MERS VHH-55
C: Spike protein
D: nanobody MERS VHH-55
E: Spike protein
F: nanobody MERS VHH-55
G: Spike protein
H: nanobody MERS VHH-55
I: Spike protein
J: nanobody MERS VHH-55
K: Spike protein
L: nanobody MERS VHH-55
M: Spike protein
N: nanobody MERS VHH-55
O: Spike protein
P: nanobody MERS VHH-55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,83719
Polymers312,17316
Non-polymers6643
Water00
1
A: Spike protein
B: nanobody MERS VHH-55


Theoretical massNumber of molelcules
Total (without water)39,0222
Polymers39,0222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Spike protein
D: nanobody MERS VHH-55


Theoretical massNumber of molelcules
Total (without water)39,0222
Polymers39,0222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Spike protein
F: nanobody MERS VHH-55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2433
Polymers39,0222
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Spike protein
H: nanobody MERS VHH-55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2433
Polymers39,0222
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Spike protein
J: nanobody MERS VHH-55


Theoretical massNumber of molelcules
Total (without water)39,0222
Polymers39,0222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Spike protein
L: nanobody MERS VHH-55


Theoretical massNumber of molelcules
Total (without water)39,0222
Polymers39,0222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Spike protein
N: nanobody MERS VHH-55


Theoretical massNumber of molelcules
Total (without water)39,0222
Polymers39,0222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: Spike protein
P: nanobody MERS VHH-55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2433
Polymers39,0222
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.047, 283.378, 173.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 378 through 587)
21(chain C and resid 378 through 587)
31(chain E and resid 378 through 587)
41(chain G and (resid 378 through 586 or (resid 587...
51(chain I and (resid 378 through 586 or (resid 587...
61(chain K and (resid 378 through 586 or (resid 587...
71(chain M and resid 378 through 587)
81(chain O and (resid 378 through 586 or (resid 587...
12(chain B and (resid 2 through 39 or resid 45 through 114))
22(chain D and (resid 2 through 39 or resid 45 through 114))
32(chain F and (resid 2 through 39 or resid 45 through 114))
42(chain H and (resid 2 through 39 or resid 45 through 114))
52(chain J and (resid 2 through 39 or resid 45 through 114))
62chain L
72(chain N and (resid 2 through 39 or resid 45 through 114))
82(chain P and (resid 2 through 39 or resid 45 through 114))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 378 through 587)A378 - 587
211(chain C and resid 378 through 587)C378 - 587
311(chain E and resid 378 through 587)E378 - 587
411(chain G and (resid 378 through 586 or (resid 587...G0
511(chain I and (resid 378 through 586 or (resid 587...I0
611(chain K and (resid 378 through 586 or (resid 587...K0
711(chain M and resid 378 through 587)M378 - 587
811(chain O and (resid 378 through 586 or (resid 587...O0
112(chain B and (resid 2 through 39 or resid 45 through 114))B2 - 39
122(chain B and (resid 2 through 39 or resid 45 through 114))B45 - 114
212(chain D and (resid 2 through 39 or resid 45 through 114))D2 - 39
222(chain D and (resid 2 through 39 or resid 45 through 114))D45 - 114
312(chain F and (resid 2 through 39 or resid 45 through 114))F2 - 39
322(chain F and (resid 2 through 39 or resid 45 through 114))F45 - 114
412(chain H and (resid 2 through 39 or resid 45 through 114))H2 - 39
422(chain H and (resid 2 through 39 or resid 45 through 114))H45 - 114
512(chain J and (resid 2 through 39 or resid 45 through 114))J2 - 39
522(chain J and (resid 2 through 39 or resid 45 through 114))J45 - 114
612chain LL2 - 114
712(chain N and (resid 2 through 39 or resid 45 through 114))N2 - 39
722(chain N and (resid 2 through 39 or resid 45 through 114))N45 - 114
812(chain P and (resid 2 through 39 or resid 45 through 114))P2 - 39
822(chain P and (resid 2 through 39 or resid 45 through 114))P45 - 114

NCS ensembles :
ID
1
2

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Components

#1: Protein
Spike protein


Mass: 25337.531 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Production host: Homo sapiens (human) / References: UniProt: A0A0U2MS80, UniProt: K9N5Q8*PLUS
#2: Antibody
nanobody MERS VHH-55


Mass: 13684.109 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)
#3: 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.: 3
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
Has ligand of interestN

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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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 1.0 M Na/K phosphate pH 7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.4→66.3 Å / Num. obs: 50369 / % possible obs: 98.5 % / Redundancy: 5.8 % / CC1/2: 0.485 / Net I/σ(I): 6.2
Reflection shellResolution: 3.4→3.51 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4438 / CC1/2: 0.161

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Processing

Software
NameVersionClassification
PHENIXdev_3758refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L72, 5F1O

4l72

5f1o


Resolution: 3.4→54.9 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 2474 5.19 %
Rwork0.2141 45224 -
obs0.217 47698 93.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 262.8 Å2 / Biso mean: 84.3692 Å2 / Biso min: 22.16 Å2
Refinement stepCycle: final / Resolution: 3.4→54.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20170 0 42 0 20212
Biso mean--115.73 --
Num. residues----2647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720689
X-RAY DIFFRACTIONf_angle_d1.04628170
X-RAY DIFFRACTIONf_dihedral_angle_d16.3732871
X-RAY DIFFRACTIONf_chiral_restr0.0663144
X-RAY DIFFRACTIONf_plane_restr0.0073639
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5048X-RAY DIFFRACTION9.437TORSIONAL
12C5048X-RAY DIFFRACTION9.437TORSIONAL
13E5048X-RAY DIFFRACTION9.437TORSIONAL
14G5048X-RAY DIFFRACTION9.437TORSIONAL
15I5048X-RAY DIFFRACTION9.437TORSIONAL
16K5048X-RAY DIFFRACTION9.437TORSIONAL
17M5048X-RAY DIFFRACTION9.437TORSIONAL
18O5048X-RAY DIFFRACTION9.437TORSIONAL
21B2757X-RAY DIFFRACTION9.437TORSIONAL
22D2757X-RAY DIFFRACTION9.437TORSIONAL
23F2757X-RAY DIFFRACTION9.437TORSIONAL
24H2757X-RAY DIFFRACTION9.437TORSIONAL
25J2757X-RAY DIFFRACTION9.437TORSIONAL
26L2757X-RAY DIFFRACTION9.437TORSIONAL
27N2757X-RAY DIFFRACTION9.437TORSIONAL
28P2757X-RAY DIFFRACTION9.437TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.470.3111140.28942132224680
3.47-3.540.32831050.27762218232382
3.54-3.610.3151420.29652271241386
3.61-3.70.39851230.29012342246588
3.7-3.790.34171240.26562391251590
3.79-3.890.34091140.2672400251489
3.89-4.010.24211210.22842460258191
4.01-4.140.2721400.21852457259793
4.14-4.280.24481300.21232480261092
4.28-4.450.28081620.19682636279898
4.45-4.660.21261580.17422626278499
4.66-4.90.23891470.169926932840100
4.9-5.210.23741490.18832673282299
5.21-5.610.24641420.19492623276597
5.61-6.180.26661210.1992667278897
6.18-7.070.26891600.20742688284899
7.07-8.90.23511530.19672674282797
8.9-54.90.25791690.20192793296298
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)
10.9830.21660.32631.42830.81272.97290.09380.0279-0.036-0.0704-0.0982-0.0355-0.4431-0.16370.01570.25750.04320.00660.25430.05790.3003-46.203-21.71929.181
21.2180.1726-0.29922.20090.15882.27210.14740.7150.5497-0.3901-0.4554-0.1557-0.1677-0.32360.21740.36920.1932-0.08370.67020.03090.3706-45.706-40.519-4.447
31.0928-0.3513-0.27431.9762-0.31710.8279-0.0334-0.20660.12550.09170.0099-0.1445-0.13610.14070.02630.48680.04890.02480.36010.02790.1731-39.797-35.15865.198
40.3307-0.0083-0.44121.742-1.00161.6902-0.0974-0.242-0.13740.25680.0048-0.40570.0098-0.08530.09840.76920.2940.19340.58540.50450.3978-39.397-71.70579.09
51.37750.0072-0.41312.3303-0.61891.7501-0.05560.3522-0.2496-0.1718-0.08060.3650.1677-0.02680.11160.2594-0.0019-0.03240.3775-0.13740.3154-24.561-54.85430.803
60.1967-0.0218-0.43151.30930.06311.4666-0.7533-0.4865-0.82150.337-0.25510.00531.04180.6429-0.92770.89890.51810.72180.57790.55741.6721-23.153-83.51456.562
71.4439-0.24490.13471.8302-0.73570.98650.0111-0.3097-0.26560.31190.21640.6786-0.1046-0.0872-0.14330.64460.00740.24460.28910.01810.615-65.917-25.28265.537
81.41590.21040.40171.8748-0.19641.5822-0.1033-0.05580.12890.0745-0.1145-0.2402-0.16470.02690.1140.40180.01150.05320.26810.0350.5564-64.23110.98252.64
90.74690.40260.34340.9046-0.56262.59190.1574-0.0362-0.0757-0.0132-0.0480.04350.14180.414-0.06630.36640.13340.15510.3792-0.04510.4405-61.087-58.04542.425
100.38010.4109-0.21981.71040.61461.7477-0.00760.3527-0.5539-0.5679-0.45080.3930.2973-0.33080.37620.72550.21420.10790.7267-0.21640.9402-59.016-63.4424.143
111.8655-0.09330.12771.38051.07591.98310.18480.03360.76590.01260.1369-0.2963-0.01240.1842-0.2260.2831-0.0515-0.06250.4526-0.07850.667-19.09-16.77337.264
120.02760.00160.15581.8593-0.0820.8808-0.0917-0.83980.54840.4497-0.1095-0.257-0.4549-0.0791-0.06120.83460.1585-0.28841.3675-0.7281.3073-16.9153.72669.196
132.6326-0.42450.28662.35770.56682.22470.4354-1.0297-0.4350.0831-0.11120.08150.3519-0.5365-0.22840.4193-0.045-0.11970.75740.16970.5018-2.642-46.52562.514
140.2064-0.38120.36230.8011-0.36140.9870.0941-0.13930.39820.3562-0.1935-0.0003-0.1077-0.0287-0.36130.82890.29480.06741.8034-0.93651.2025-3.694-17.71187.664
152.9461-0.22270.16641.4773-0.42592.0314-0.7573-0.41370.1483-0.16770.20140.179-0.7175-0.03690.31260.91970.0077-0.22620.4180.18060.6183-62.9434.80854.349
161.0419-0.0141-0.17780.4815-0.16960.9001-0.04210.229-0.1682-0.2759-0.0901-0.2855-0.17561.01950.03530.7196-0.2334-0.00861.54080.44440.8354-35.25829.77627.471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 378:588 )A378 - 588
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:115 )B2 - 115
3X-RAY DIFFRACTION3( CHAIN C AND RESID 378:588 )C378 - 588
4X-RAY DIFFRACTION4( CHAIN D AND RESID 2:118 )D2 - 118
5X-RAY DIFFRACTION5( CHAIN E AND ( RESID 378:588 OR RESID 601:601 ) )E378 - 588
6X-RAY DIFFRACTION5( CHAIN E AND ( RESID 378:588 OR RESID 601:601 ) )E601
7X-RAY DIFFRACTION6( CHAIN F AND RESID 2:114 )F2 - 114
8X-RAY DIFFRACTION7( CHAIN G AND ( RESID 378:588 OR RESID 601:601 ) )G378 - 588
9X-RAY DIFFRACTION7( CHAIN G AND ( RESID 378:588 OR RESID 601:601 ) )G601
10X-RAY DIFFRACTION8( CHAIN H AND RESID 2:114 )H2 - 114
11X-RAY DIFFRACTION9( CHAIN I AND RESID 378:588 )I378 - 588
12X-RAY DIFFRACTION10( CHAIN J AND RESID 2:114 )J2 - 114
13X-RAY DIFFRACTION11( CHAIN K AND RESID 378:587 )K378 - 587
14X-RAY DIFFRACTION12( CHAIN L AND RESID 2:114 )L2 - 114
15X-RAY DIFFRACTION13( CHAIN M AND RESID 378:588 )M378 - 588
16X-RAY DIFFRACTION14( CHAIN N AND RESID 2:114 )N2 - 114
17X-RAY DIFFRACTION15( CHAIN O AND ( RESID 378:588 OR RESID 601:601 ) )O378 - 588
18X-RAY DIFFRACTION15( CHAIN O AND ( RESID 378:588 OR RESID 601:601 ) )O601
19X-RAY DIFFRACTION16( CHAIN P AND RESID 2:114 )P2 - 114

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