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- PDB-7oay: Nanobody F2 bound to RBD -

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Basic information

Entry
Database: PDB / ID: 7oay
TitleNanobody F2 bound to RBD
Components
  • F2 nanobody
  • Spike protein S1
KeywordsANTIVIRAL PROTEIN / Spike / nanobody / high affinity
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsNaismith, J.H. / Mikolajek, H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust100209/Z/12/Z) United Kingdom
Engineering and Physical Sciences Research CouncilEP/S025243/1 United Kingdom
Citation
Journal: Nat Commun / Year: 2021
Title: A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19.
Authors: Jiandong Huo / Halina Mikolajek / Audrey Le Bas / Jordan J Clark / Parul Sharma / Anja Kipar / Joshua Dormon / Chelsea Norman / Miriam Weckener / Daniel K Clare / Peter J Harrison / Julia A ...Authors: Jiandong Huo / Halina Mikolajek / Audrey Le Bas / Jordan J Clark / Parul Sharma / Anja Kipar / Joshua Dormon / Chelsea Norman / Miriam Weckener / Daniel K Clare / Peter J Harrison / Julia A Tree / Karen R Buttigieg / Francisco J Salguero / Robert Watson / Daniel Knott / Oliver Carnell / Didier Ngabo / Michael J Elmore / Susan Fotheringham / Adam Harding / Lucile Moynié / Philip N Ward / Maud Dumoux / Tessa Prince / Yper Hall / Julian A Hiscox / Andrew Owen / William James / Miles W Carroll / James P Stewart / James H Naismith / Raymond J Owens /
Abstract: SARS-CoV-2 remains a global threat to human health particularly as escape mutants emerge. There is an unmet need for effective treatments against COVID-19 for which neutralizing single domain ...SARS-CoV-2 remains a global threat to human health particularly as escape mutants emerge. There is an unmet need for effective treatments against COVID-19 for which neutralizing single domain antibodies (nanobodies) have significant potential. Their small size and stability mean that nanobodies are compatible with respiratory administration. We report four nanobodies (C5, H3, C1, F2) engineered as homotrimers with pmolar affinity for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Crystal structures show C5 and H3 overlap the ACE2 epitope, whilst C1 and F2 bind to a different epitope. Cryo Electron Microscopy shows C5 binding results in an all down arrangement of the Spike protein. C1, H3 and C5 all neutralize the Victoria strain, and the highly transmissible Alpha (B.1.1.7 first identified in Kent, UK) strain and C1 also neutralizes the Beta (B.1.35, first identified in South Africa). Administration of C5-trimer via the respiratory route showed potent therapeutic efficacy in the Syrian hamster model of COVID-19 and separately, effective prophylaxis. The molecule was similarly potent by intraperitoneal injection.
#1: Journal: Res Sq / Year: 2021
Title: A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19
Authors: Huo, J. / Mikolajek, H. / Le Bas, A. / Clark, J. / Sharma, P. / Kipar, A. / Dormon, J. / Norman, C. / Weckener, M. / Clare, D. / Harrison, P. / Tree, J. / Buttigieg, K. / Salguero, F. / ...Authors: Huo, J. / Mikolajek, H. / Le Bas, A. / Clark, J. / Sharma, P. / Kipar, A. / Dormon, J. / Norman, C. / Weckener, M. / Clare, D. / Harrison, P. / Tree, J. / Buttigieg, K. / Salguero, F. / Watson, R. / Knott, D. / Carnell, O. / Ngabo, D. / Elmore, M. / Fotheringham, S. / Harding, A. / Ward, P. / Moynie, L. / Dumoux, M. / Hall, Y. / Hiscox, J. / Owen, A. / James, W. / Carroll, M. / Stewart, J. / Naismith, J. / Owens, R.
History
DepositionApr 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 2.0Oct 6, 2021Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / diffrn_source / pdbx_database_proc
Item: _atom_site.pdbx_tls_group_id / _diffrn_source.pdbx_synchrotron_site
Revision 2.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Spike protein S1
BBB: F2 nanobody
CCC: Spike protein S1
DDD: F2 nanobody
EEE: Spike protein S1
FFF: F2 nanobody
GGG: Spike protein S1
HHH: F2 nanobody
III: Spike protein S1
JJJ: F2 nanobody
KKK: Spike protein S1
LLL: F2 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,40218
Polymers232,07512
Non-polymers1,3276
Water5,819323
1
AAA: Spike protein S1
BBB: F2 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9003
Polymers38,6792
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CCC: Spike protein S1
DDD: F2 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9003
Polymers38,6792
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
EEE: Spike protein S1
FFF: F2 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9003
Polymers38,6792
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
GGG: Spike protein S1
HHH: F2 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9003
Polymers38,6792
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
III: Spike protein S1
JJJ: F2 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9003
Polymers38,6792
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
KKK: Spike protein S1
LLL: F2 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9003
Polymers38,6792
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.420, 108.420, 165.538
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21CCC
32AAA
42EEE
53AAA
63GGG
74AAA
84III
95AAA
105KKK
116BBB
126DDD
137BBB
147FFF
158BBB
168HHH
179BBB
189JJJ
1910BBB
2010LLL
2111CCC
2211EEE
2312CCC
2412GGG
2513CCC
2613III
2714CCC
2814KKK
2915DDD
3015FFF
3116DDD
3216HHH
3317DDD
3417JJJ
3518DDD
3618LLL
3719EEE
3819GGG
3920EEE
4020III
4121EEE
4221KKK
4322FFF
4422HHH
4523FFF
4623JJJ
4724FFF
4824LLL
4925GGG
5025III
5126GGG
5226KKK
5327HHH
5427JJJ
5528HHH
5628LLL
5729III
5829KKK
5930JJJ
6030LLL

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNLYSLYSAAAA331 - 5282 - 199
211ASNASNLYSLYSCCCC331 - 5282 - 199
322ILEILEPROPROAAAA332 - 5273 - 198
422ILEILEPROPROEEEE332 - 5273 - 198
533THRTHRPROPROAAAA333 - 5274 - 198
633THRTHRPROPROGGGG333 - 5274 - 198
744ASNASNLYSLYSAAAA331 - 5282 - 199
844ASNASNLYSLYSIIII331 - 5282 - 199
955ILEILEPROPROAAAA332 - 5273 - 198
1055ILEILEPROPROKKKK332 - 5273 - 198
1166GLNGLNSERSERBBBB1 - 1251 - 125
1266GLNGLNSERSERDDDD1 - 1251 - 125
1377GLNGLNVALVALBBBB1 - 1231 - 123
1477GLNGLNVALVALFFFF1 - 1231 - 123
1588GLNGLNSERSERBBBB1 - 1251 - 125
1688GLNGLNSERSERHHHH1 - 1251 - 125
1799GLNGLNSERSERBBBB1 - 1251 - 125
1899GLNGLNSERSERJJJJ1 - 1251 - 125
191010GLNGLNSERSERBBBB1 - 1251 - 125
201010GLNGLNSERSERLLLL1 - 1251 - 125
211111ILEILEPROPROCCCC332 - 5273 - 198
221111ILEILEPROPROEEEE332 - 5273 - 198
231212THRTHRPROPROCCCC333 - 5274 - 198
241212THRTHRPROPROGGGG333 - 5274 - 198
251313ASNASNLYSLYSCCCC331 - 5282 - 199
261313ASNASNLYSLYSIIII331 - 5282 - 199
271414ILEILEPROPROCCCC332 - 5273 - 198
281414ILEILEPROPROKKKK332 - 5273 - 198
291515GLNGLNVALVALDDDD1 - 1231 - 123
301515GLNGLNVALVALFFFF1 - 1231 - 123
311616GLNGLNSERSERDDDD1 - 1251 - 125
321616GLNGLNSERSERHHHH1 - 1251 - 125
331717GLNGLNSERSERDDDD1 - 1251 - 125
341717GLNGLNSERSERJJJJ1 - 1251 - 125
351818GLNGLNSERSERDDDD1 - 1251 - 125
361818GLNGLNSERSERLLLL1 - 1251 - 125
371919THRTHRPROPROEEEE333 - 5274 - 198
381919THRTHRPROPROGGGG333 - 5274 - 198
392020ILEILEPROPROEEEE332 - 5273 - 198
402020ILEILEPROPROIIII332 - 5273 - 198
412121ILEILELYSLYSEEEE332 - 5283 - 199
422121ILEILELYSLYSKKKK332 - 5283 - 199
432222GLNGLNVALVALFFFF1 - 1231 - 123
442222GLNGLNVALVALHHHH1 - 1231 - 123
452323GLNGLNVALVALFFFF1 - 1231 - 123
462323GLNGLNVALVALJJJJ1 - 1231 - 123
472424GLNGLNVALVALFFFF1 - 1231 - 123
482424GLNGLNVALVALLLLL1 - 1231 - 123
492525THRTHRPROPROGGGG333 - 5274 - 198
502525THRTHRPROPROIIII333 - 5274 - 198
512626THRTHRPROPROGGGG333 - 5274 - 198
522626THRTHRPROPROKKKK333 - 5274 - 198
532727GLNGLNSERSERHHHH1 - 1251 - 125
542727GLNGLNSERSERJJJJ1 - 1251 - 125
552828GLNGLNSERSERHHHH1 - 1251 - 125
562828GLNGLNSERSERLLLL1 - 1251 - 125
572929ILEILEPROPROIIII332 - 5273 - 198
582929ILEILEPROPROKKKK332 - 5273 - 198
593030GLNGLNSERSERJJJJ1 - 1251 - 125
603030GLNGLNSERSERLLLL1 - 1251 - 125

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56
29Local NCS retraints between domains: 57 58
30Local NCS retraints between domains: 59 60

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Components

#1: Protein
Spike protein S1


Mass: 23716.580 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody
F2 nanobody


Mass: 14962.622 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#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.: 6 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M SPG, pH 8, 25 % Peg 1500,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.34→94 Å / Num. obs: 91842 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 1 / Rpim(I) all: 0.051 / Net I/σ(I): 9.9
Reflection shellResolution: 2.34→2.4 Å / Redundancy: 7 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4643 / CC1/2: 0.5 / Rpim(I) all: 0.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZBP

6zbp


Resolution: 2.34→93.895 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 20.742 / SU ML: 0.216 / Cross valid method: FREE R-VALUE / ESU R: 0.367 / ESU R Free: 0.23
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2275 4643 5.057 %
Rwork0.1919 87174 -
all0.194 --
obs-91817 99.977 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 53.178 Å2
Baniso -1Baniso -2Baniso -3
1-0.024 Å20.012 Å2-0 Å2
2--0.024 Å2-0 Å2
3----0.077 Å2
Refinement stepCycle: LAST / Resolution: 2.34→93.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15292 0 84 323 15699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01215826
X-RAY DIFFRACTIONr_bond_other_d0.0010.01814182
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.6621530
X-RAY DIFFRACTIONr_angle_other_deg1.2871.58332532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.72951921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37821.604879
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.259152358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.13715108
X-RAY DIFFRACTIONr_chiral_restr0.0690.21986
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218331
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024154
X-RAY DIFFRACTIONr_nbd_refined0.1940.22459
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.212959
X-RAY DIFFRACTIONr_nbtor_refined0.1740.27669
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.27675
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2446
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0160.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.229
X-RAY DIFFRACTIONr_nbd_other0.2570.2149
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2750.210
X-RAY DIFFRACTIONr_mcbond_it1.8833.477720
X-RAY DIFFRACTIONr_mcbond_other1.8823.4697719
X-RAY DIFFRACTIONr_mcangle_it3.0865.1949629
X-RAY DIFFRACTIONr_mcangle_other3.0865.1959630
X-RAY DIFFRACTIONr_scbond_it2.1033.6788106
X-RAY DIFFRACTIONr_scbond_other2.1033.6788106
X-RAY DIFFRACTIONr_scangle_it3.3855.43511901
X-RAY DIFFRACTIONr_scangle_other3.3855.43611902
X-RAY DIFFRACTIONr_lrange_it5.50538.72916771
X-RAY DIFFRACTIONr_lrange_other5.50138.69816753
X-RAY DIFFRACTIONr_ncsr_local_group_10.0870.056107
X-RAY DIFFRACTIONr_ncsr_local_group_20.070.056159
X-RAY DIFFRACTIONr_ncsr_local_group_30.0850.056033
X-RAY DIFFRACTIONr_ncsr_local_group_40.0770.056174
X-RAY DIFFRACTIONr_ncsr_local_group_50.0870.056029
X-RAY DIFFRACTIONr_ncsr_local_group_60.0490.053977
X-RAY DIFFRACTIONr_ncsr_local_group_70.0350.053967
X-RAY DIFFRACTIONr_ncsr_local_group_80.060.053934
X-RAY DIFFRACTIONr_ncsr_local_group_90.0510.053946
X-RAY DIFFRACTIONr_ncsr_local_group_100.0450.053992
X-RAY DIFFRACTIONr_ncsr_local_group_110.0880.056002
X-RAY DIFFRACTIONr_ncsr_local_group_120.0720.056097
X-RAY DIFFRACTIONr_ncsr_local_group_130.0910.056067
X-RAY DIFFRACTIONr_ncsr_local_group_140.0760.056134
X-RAY DIFFRACTIONr_ncsr_local_group_150.0530.053940
X-RAY DIFFRACTIONr_ncsr_local_group_160.0630.053933
X-RAY DIFFRACTIONr_ncsr_local_group_170.0670.053929
X-RAY DIFFRACTIONr_ncsr_local_group_180.0440.053987
X-RAY DIFFRACTIONr_ncsr_local_group_190.0890.055970
X-RAY DIFFRACTIONr_ncsr_local_group_200.0760.056070
X-RAY DIFFRACTIONr_ncsr_local_group_210.0910.056002
X-RAY DIFFRACTIONr_ncsr_local_group_220.0640.053898
X-RAY DIFFRACTIONr_ncsr_local_group_230.0560.053909
X-RAY DIFFRACTIONr_ncsr_local_group_240.0420.053953
X-RAY DIFFRACTIONr_ncsr_local_group_250.0790.056026
X-RAY DIFFRACTIONr_ncsr_local_group_260.0590.056147
X-RAY DIFFRACTIONr_ncsr_local_group_270.060.053919
X-RAY DIFFRACTIONr_ncsr_local_group_280.0640.053952
X-RAY DIFFRACTIONr_ncsr_local_group_290.0770.056052
X-RAY DIFFRACTIONr_ncsr_local_group_300.060.053943
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.087310.05009
12CCCX-RAY DIFFRACTIONLocal ncs0.087310.05009
23AAAX-RAY DIFFRACTIONLocal ncs0.070320.05009
24EEEX-RAY DIFFRACTIONLocal ncs0.070320.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.084770.05009
36GGGX-RAY DIFFRACTIONLocal ncs0.084770.05009
47AAAX-RAY DIFFRACTIONLocal ncs0.076560.05009
48IIIX-RAY DIFFRACTIONLocal ncs0.076560.05009
59AAAX-RAY DIFFRACTIONLocal ncs0.086740.05009
510KKKX-RAY DIFFRACTIONLocal ncs0.086740.05009
611BBBX-RAY DIFFRACTIONLocal ncs0.049150.0501
612DDDX-RAY DIFFRACTIONLocal ncs0.049150.0501
713BBBX-RAY DIFFRACTIONLocal ncs0.035050.05011
714FFFX-RAY DIFFRACTIONLocal ncs0.035050.05011
815BBBX-RAY DIFFRACTIONLocal ncs0.059660.0501
816HHHX-RAY DIFFRACTIONLocal ncs0.059660.0501
917BBBX-RAY DIFFRACTIONLocal ncs0.051340.0501
918JJJX-RAY DIFFRACTIONLocal ncs0.051340.0501
1019BBBX-RAY DIFFRACTIONLocal ncs0.04470.05011
1020LLLX-RAY DIFFRACTIONLocal ncs0.04470.05011
1121CCCX-RAY DIFFRACTIONLocal ncs0.087940.05008
1122EEEX-RAY DIFFRACTIONLocal ncs0.087940.05008
1223CCCX-RAY DIFFRACTIONLocal ncs0.072460.05009
1224GGGX-RAY DIFFRACTIONLocal ncs0.072460.05009
1325CCCX-RAY DIFFRACTIONLocal ncs0.090840.05009
1326IIIX-RAY DIFFRACTIONLocal ncs0.090840.05009
1427CCCX-RAY DIFFRACTIONLocal ncs0.075960.05009
1428KKKX-RAY DIFFRACTIONLocal ncs0.075960.05009
1529DDDX-RAY DIFFRACTIONLocal ncs0.053440.0501
1530FFFX-RAY DIFFRACTIONLocal ncs0.053440.0501
1631DDDX-RAY DIFFRACTIONLocal ncs0.062830.0501
1632HHHX-RAY DIFFRACTIONLocal ncs0.062830.0501
1733DDDX-RAY DIFFRACTIONLocal ncs0.067020.0501
1734JJJX-RAY DIFFRACTIONLocal ncs0.067020.0501
1835DDDX-RAY DIFFRACTIONLocal ncs0.043990.0501
1836LLLX-RAY DIFFRACTIONLocal ncs0.043990.0501
1937EEEX-RAY DIFFRACTIONLocal ncs0.089040.05009
1938GGGX-RAY DIFFRACTIONLocal ncs0.089040.05009
2039EEEX-RAY DIFFRACTIONLocal ncs0.076340.05009
2040IIIX-RAY DIFFRACTIONLocal ncs0.076340.05009
2141EEEX-RAY DIFFRACTIONLocal ncs0.090720.05009
2142KKKX-RAY DIFFRACTIONLocal ncs0.090720.05009
2243FFFX-RAY DIFFRACTIONLocal ncs0.064340.0501
2244HHHX-RAY DIFFRACTIONLocal ncs0.064340.0501
2345FFFX-RAY DIFFRACTIONLocal ncs0.055530.0501
2346JJJX-RAY DIFFRACTIONLocal ncs0.055530.0501
2447FFFX-RAY DIFFRACTIONLocal ncs0.042490.0501
2448LLLX-RAY DIFFRACTIONLocal ncs0.042490.0501
2549GGGX-RAY DIFFRACTIONLocal ncs0.079440.05009
2550IIIX-RAY DIFFRACTIONLocal ncs0.079440.05009
2651GGGX-RAY DIFFRACTIONLocal ncs0.058920.05009
2652KKKX-RAY DIFFRACTIONLocal ncs0.058920.05009
2753HHHX-RAY DIFFRACTIONLocal ncs0.060430.0501
2754JJJX-RAY DIFFRACTIONLocal ncs0.060430.0501
2855HHHX-RAY DIFFRACTIONLocal ncs0.063660.0501
2856LLLX-RAY DIFFRACTIONLocal ncs0.063660.0501
2957IIIX-RAY DIFFRACTIONLocal ncs0.0770.05009
2958KKKX-RAY DIFFRACTIONLocal ncs0.0770.05009
3059JJJX-RAY DIFFRACTIONLocal ncs0.059530.0501
3060LLLX-RAY DIFFRACTIONLocal ncs0.059530.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.34-2.4010.2993040.33564730.33367770.520.5251000.336
2.401-2.4660.3473420.31163200.31266620.6720.6921000.308
2.466-2.5380.3413340.361000.30264390.7440.76899.92230.295
2.538-2.6160.3074020.28957730.2961800.8120.81599.91910.278
2.616-2.7020.3093250.2758020.27261300.8410.84599.95110.253
2.702-2.7960.2992830.25455380.25658230.8610.86999.96570.23
2.796-2.9020.2763100.24253850.24456960.8710.88399.98240.216
2.902-3.020.2522680.22751270.22953970.9020.91399.96290.202
3.02-3.1540.2542700.21349250.21551950.9120.9261000.189
3.154-3.3080.2482780.21347150.21549930.920.9311000.193
3.308-3.4870.2222310.20645560.20747880.930.94299.97910.192
3.487-3.6980.2491940.19542650.19744590.9190.941000.179
3.698-3.9530.1921930.17540230.17642160.9480.9561000.162
3.953-4.2690.1991880.14737440.14939320.9570.9671000.135
4.269-4.6760.1451660.11634480.11736150.9770.97999.97230.111
4.676-5.2260.1891280.13231490.13432770.9660.9761000.124
5.226-6.0310.2231370.15627500.15928870.9550.9661000.146
6.031-7.3790.1671460.14522840.14624300.9650.9681000.138
7.379-10.4040.1621040.13917720.1418770.9660.97299.94670.14
10.404-93.8950.171400.19310050.19210450.9810.9551000.203
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)
15.7589-0.1554-2.69760.9922-1.28623.40050.03440.1764-0.2863-0.2131-0.01280.03130.1945-0.0766-0.02160.1651-0.08180.03240.11170.01060.113121.803-15.195-9.298
23.64860.3751-0.94048.8785-0.99227.32820.1420.13630.0495-0.1399-0.0386-0.0549-0.41190.3818-0.10350.0776-0.06930.00050.1006-0.00850.064730.668-6.494-0.875
32.0616-0.27890.04182.1222-0.3472.6050.0781-0.1731-0.08860.0410.11320.30480.1194-0.4398-0.19140.098-0.0806-0.01190.1240.04620.06315.747-16.1662.242
43.34671.0603-0.23123.7894-0.08384.46570.0057-0.13080.24970.17070.028-0.2634-0.22590.6423-0.03370.0412-0.0298-0.01080.202-0.07890.113342.912-12.88416.632
58.08223.3806-1.54388.88553.1722.26560.269-0.00480.187-0.629-0.086-0.3943-0.4102-0.1029-0.18290.146-0.06650.04780.3918-0.04630.353152.984-7.25311.366
61.80620.00760.33130.7345-0.46133.914-0.0693-0.17890.22950.01590.0729-0.2771-0.19150.9282-0.00360.0991-0.04520.01080.3143-0.10950.166545.664-12.87615.885
71.89291.28640.50041.5187-0.11385.80350.1229-0.12120.25080.21880.0933-0.1692-0.35320.3552-0.21620.0818-0.0264-0.02540.1315-0.15880.263838.264-7.80116.176
87.060.4973-9.04413.8962.49914.70080.06740.6669-0.0765-0.4098-0.45850.2791-0.0948-1.21390.39110.32850.0678-0.10270.22160.01420.156820.482-68.023-11.661
95.2979-1.4989-4.17841.39730.35554.59750.18820.1895-0.0829-0.3571-0.2920.0240.0922-0.08470.10370.18980.0055-0.06260.17620.01940.100919.225-73.497-6.766
105.1606-1.3728-2.12725.50371.61979.51540.43070.37890.1189-0.3738-0.0351-0.4884-0.57180.6382-0.39560.1376-0.0548-0.02920.1859-0.02380.178129.501-65.9961.237
112.18650.4212-0.27632.3963-0.03861.39690.1973-0.1646-0.06840.3073-0.19950.3060.0357-0.16930.00220.1631-0.073-0.03330.0747-0.01260.101413.926-73.9445.236
121.75293.4462-1.16237.1595-0.90155.78880.0769-0.0267-0.08160.1510.2235-0.23910.03091.0226-0.30040.12650.0319-0.13240.3665-0.06440.181246.748-75.87924.015
134.1130.71460.06613.50980.09115.24310.06480.02910.2691-0.10490.111-0.2249-0.2460.8109-0.17580.0729-0.0307-0.04780.2943-0.08160.143844.216-73.5815.276
149.0629-1.8768-0.79698.6961-3.82674.65290.21010.0042-0.1083-0.2801-0.1529-0.00870.06130.2466-0.05710.0523-0.021-0.03990.1571-0.03810.066433.594-72.36.043
150.0990.1582-0.55451.9029-0.05365.12050.0808-0.08970.10740.01760.1070.0616-0.25290.5417-0.18780.1469-0.10040.0730.1696-0.1280.338138.741-69.21819.44
167.83891.6539-4.40282.6033-0.60916.87360.1589-1.28460.04540.693-0.39190.1180.10950.48260.23290.3447-0.1048-0.0020.2643-0.05520.15233.919-38.58713.19
174.14490.5582-0.58131.3720.38731.81160.0551-0.2834-0.10460.3548-0.07090.083-0.2117-0.05290.01580.17260.00850.00710.0536-0.0350.108933.353-43.0998.213
184.2480.22970.04343.0188-0.61772.70120.03370.252-0.3493-0.189-0.0765-0.33120.05410.42670.04280.11610.0091-0.01310.1131-0.05190.115740.279-46.372-3.948
191.9561-0.55910.82372.98910.70180.86660.0145-0.01670.0992-0.17580.0374-0.1808-0.03730.1384-0.05190.113-0.0071-0.02110.1811-0.08080.061937.87-42.985-0.172
204.1014-4.3987-2.22067.37061.3893.46690.11170.06630.1168-0.11370.07410.2134-0.1464-0.2954-0.18580.09120.0179-0.09680.1738-0.03940.19898.341-44.416-23.002
211.3442-1.35571.34842.28272.101914.714-0.22350.4215-0.10590.3404-0.3440.23690.39580.81370.56760.2107-0.05560.09570.24280.01430.29419.985-56.234-14.324
223.0871-0.39920.26312.3818-0.50652.7746-0.0013-0.07210.37160.12610.07480.3055-0.319-0.4779-0.07350.08280.0760.01080.1064-0.02360.166110.09-40.669-13.821
231.30830.30621.06260.82250.61185.4284-0.1703-0.01410.04180.05790.19150.2396-0.2902-0.2739-0.02120.0930.0543-0.01630.08510.05380.145117.13-38.074-15.464
249.8026-2.20537.34976.1018-3.292312.2269-0.2703-0.942-0.03720.50310.16360.1873-0.3191-0.55780.10670.1353-0.0680.07550.26110.03550.147714.471-14.95263.37
253.6258-1.46862.86442.6417-3.28664.47910.0399-0.4145-0.2123-0.14640.08940.05040.192-0.2742-0.12920.1403-0.05320.05630.20350.01690.087818.445-12.79258.434
261.76280.13290.06163.3436-0.78051.902-0.02830.09990.332-0.28670.06430.18530.0338-0.1396-0.03590.049-0.02990.00320.1084-0.00680.091116.919-4.31945.752
272.4370.96080.97622.0012-0.30343.3534-0.0905-0.09660.1131-0.10050.14330.2015-0.0712-0.0631-0.05280.0669-0.00860.04990.0856-0.00030.08217.33-11.48751.444
281.27673.0396-0.606710.0909-4.16933.18640.00730.1368-0.3049-0.35050.067-0.37660.44670.1137-0.07440.31730.08450.06380.2669-0.08540.194238.417-30.09828.999
292.92610.6736-0.51395.39041.17334.4277-0.0983-0.0173-0.40540.2067-0.01680.00360.83290.23590.11510.27990.0969-0.0310.1126-0.04190.1134.818-29.89937.552
309.77367.0247-2.562610.9467-2.60674.472-0.0008-0.05320.118-0.04980.18780.3560.51850.2728-0.1870.17570.01550.00980.0501-0.03030.068827.262-22.06846.526
312.71792.183-0.30711.9542-1.15254.1290.05720.1678-0.1224-0.04840.1363-0.05570.4524-0.0253-0.19350.2069-0.0092-0.01750.0602-0.05920.101428.193-28.05733.162
328.5286-5.1943.06598.7831-2.9941.5919-0.2503-0.8050.20620.53160.2844-0.0721-0.3626-0.2222-0.03420.2206-0.05740.14690.5070.09130.305720.129-76.37566.615
333.3057-2.51370.47473.7581-1.1432.88310.0038-0.3837-0.13290.13730.06680.12060.2796-0.5921-0.07070.2593-0.04390.08940.3920.07160.19623.962-74.0561.604
343.1008-1.5478-0.04783.15990.52532.71050.18170.04930.03-0.2496-0.11020.3306-0.2563-0.5993-0.07150.08240.02840.01360.31280.02150.144622.213-66.3649.573
350.9079-0.1242-0.7322.35540.67560.93310.06070.0065-0.0642-0.1245-0.14470.5353-0.0824-0.40360.0840.14550.0080.04690.67240.11570.267520.897-69.83953.109
362.59550.74270.90870.2738-0.26724.87390.00370.225-0.3035-0.03760.0691-0.09220.34910.1007-0.07270.11920.0317-0.11160.1993-0.04670.17738.459-87.74931.162
372.74250.3047-1.02264.06171.07413.61780.1026-0.0466-0.45540.294-0.00430.10640.9177-0.171-0.09830.3212-0.0204-0.14880.1577-0.00220.201434.172-94.20837.484
383.4271-2.6595-1.70037.30590.22125.435-0.020.0449-0.1281-0.0815-0.16030.11080.6554-0.13170.18040.1614-0.1071-0.0840.23430.03830.222929.456-84.45748.042
392.57552.4950.90252.73180.30353.24240.12580.0088-0.06380.0005-0.06290.18040.2285-0.1511-0.0630.1555-0.0523-0.13430.192-0.05770.296928.108-89.27734.162
4012.9191-0.5378-9.76596.0185.262211.3570.02330.6429-0.0534-0.7897-0.22620.1738-0.5267-0.59960.20290.55260.0983-0.03570.34950.04480.1266-31.203-37.842-9.036
414.4366-2.2453-2.35222.58661.28023.6250.24890.599-0.0204-0.6035-0.2504-0.1931-0.22050.03540.00150.2485-0.06970.00340.22770.02660.1535-33.379-43.456-4.687
423.338-1.6878-3.81170.91842.321710.57950.48460.1310.2573-0.3513-0.0481-0.1618-0.55180.3897-0.43650.3972-0.04680.10350.2126-0.02940.2672-22.527-37.9033.82
433.10650.86310.30812.1208-0.21821.69010.0238-0.0419-0.04320.0186-0.04190.20860.0611-0.19590.01810.1304-0.0679-0.03290.09-0.00680.0687-38.954-43.8617.317
443.47143.7501-2.13515.0836-0.78053.5793-0.1291-0.0469-0.1883-0.03420.1732-0.31230.21840.3938-0.04410.12820.0287-0.03310.16530.02950.1218-8.4-50.01127.506
453.92551.09331.13033.5025-0.14674.4373-0.13320.28710.0638-0.14290.0728-0.22-0.06530.49880.06030.04480.00160.0390.1351-0.02790.085-9.961-47.58618.608
467.61691.56222.63939.8921-1.04021.18850.30450.40740.074-0.418-0.3104-0.03130.21740.22540.00590.15990.0311-0.01990.1344-0.0810.0871-19.534-45.1048.508
471.66611.3216-0.66732.7522-1.00363.34480.0402-0.11660.1528-0.02670.024-0.07350.03060.1058-0.06410.0342-0.00450.01290.0241-0.03040.0422-14.942-42.33822.244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA347 - 368
2X-RAY DIFFRACTION2ALLAAA369 - 378
3X-RAY DIFFRACTION3ALLAAA379 - 527
4X-RAY DIFFRACTION4ALLBBB1 - 63
5X-RAY DIFFRACTION5ALLBBB64 - 69
6X-RAY DIFFRACTION6ALLBBB70 - 104
7X-RAY DIFFRACTION7ALLBBB105 - 124
8X-RAY DIFFRACTION8ALLCCC333 - 346
9X-RAY DIFFRACTION9ALLCCC347 - 368
10X-RAY DIFFRACTION10ALLCCC369 - 378
11X-RAY DIFFRACTION11ALLCCC379 - 527
12X-RAY DIFFRACTION12ALLDDD1 - 23
13X-RAY DIFFRACTION13ALLDDD24 - 99
14X-RAY DIFFRACTION14ALLDDD100 - 106
15X-RAY DIFFRACTION15ALLDDD107 - 124
16X-RAY DIFFRACTION16ALLEEE333 - 346
17X-RAY DIFFRACTION17ALLEEE347 - 371
18X-RAY DIFFRACTION18ALLEEE372 - 488
19X-RAY DIFFRACTION19ALLEEE489 - 527
20X-RAY DIFFRACTION20ALLFFF1 - 24
21X-RAY DIFFRACTION21ALLFFF25 - 32
22X-RAY DIFFRACTION22ALLFFF33 - 103
23X-RAY DIFFRACTION23ALLFFF104 - 124
24X-RAY DIFFRACTION24ALLGGG333 - 346
25X-RAY DIFFRACTION25ALLGGG347 - 373
26X-RAY DIFFRACTION26ALLGGG374 - 492
27X-RAY DIFFRACTION27ALLGGG493 - 527
28X-RAY DIFFRACTION28ALLHHH1 - 24
29X-RAY DIFFRACTION29ALLHHH25 - 99
30X-RAY DIFFRACTION30ALLHHH100 - 106
31X-RAY DIFFRACTION31ALLHHH107 - 124
32X-RAY DIFFRACTION32ALLIII333 - 346
33X-RAY DIFFRACTION33ALLIII347 - 371
34X-RAY DIFFRACTION34ALLIII372 - 487
35X-RAY DIFFRACTION35ALLIII488 - 527
36X-RAY DIFFRACTION36ALLJJJ1 - 32
37X-RAY DIFFRACTION37ALLJJJ33 - 99
38X-RAY DIFFRACTION38ALLJJJ100 - 106
39X-RAY DIFFRACTION39ALLJJJ107 - 124
40X-RAY DIFFRACTION40ALLKKK333 - 346
41X-RAY DIFFRACTION41ALLKKK347 - 368
42X-RAY DIFFRACTION42ALLKKK369 - 378
43X-RAY DIFFRACTION43ALLKKK379 - 527
44X-RAY DIFFRACTION44ALLLLL1 - 23
45X-RAY DIFFRACTION45ALLLLL24 - 99
46X-RAY DIFFRACTION46ALLLLL100 - 106
47X-RAY DIFFRACTION47ALLLLL107 - 124

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