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Basic information

Entry
Database: PDB / ID: 5im5
TitleCrystal structure of designed two-component self-assembling icosahedral cage I53-40
Components
  • Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
  • Designed Riboflavin synthase
KeywordsPROTEIN BINDING / icosahedron / designed protein cage / two-component / computational design / protein engineering / Rosetta / self-assembling / co-assembling / multimerization / symmetry / nanomaterial / nanostructure
Function / homology
Function and homology information


riboflavin synthase / riboflavin synthase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / riboflavin synthase complex / riboflavin biosynthetic process
Similarity search - Function
Riboflavin synthase, archaeal / KDPG/KHG aldolase, active site 2 / KDPG and KHG aldolases Schiff-base forming residue. / KDPG/KHG aldolase, active site 1 / KDPG and KHG aldolases active site. / KDPG/KHG aldolase / KDPG and KHG aldolase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily ...Riboflavin synthase, archaeal / KDPG/KHG aldolase, active site 2 / KDPG and KHG aldolases Schiff-base forming residue. / KDPG/KHG aldolase, active site 1 / KDPG and KHG aldolases active site. / KDPG/KHG aldolase / KDPG and KHG aldolase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-dehydro-3-deoxy-phosphogluconate aldolase / Riboflavin synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
Vibrionales bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.699 Å
AuthorsLiu, Y.A. / Cascio, D. / Sawaya, M.R. / Bale, J.B. / Collazo, M.J. / Thomas, C. / Sheffler, W. / King, N.P. / Baker, D. / Yeates, T.O.
CitationJournal: Science / Year: 2016
Title: Accurate design of megadalton-scale two-component icosahedral protein complexes.
Authors: Bale, J.B. / Gonen, S. / Liu, Y. / Sheffler, W. / Ellis, D. / Thomas, C. / Cascio, D. / Yeates, T.O. / Gonen, T. / King, N.P. / Baker, D.
History
DepositionMar 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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Assembly

Deposited unit
K: Designed Riboflavin synthase
M: Designed Riboflavin synthase
O: Designed Riboflavin synthase
Q: Designed Riboflavin synthase
S: Designed Riboflavin synthase
A: Designed Riboflavin synthase
B: Designed Riboflavin synthase
C: Designed Riboflavin synthase
D: Designed Riboflavin synthase
E: Designed Riboflavin synthase
F: Designed Riboflavin synthase
G: Designed Riboflavin synthase
H: Designed Riboflavin synthase
I: Designed Riboflavin synthase
J: Designed Riboflavin synthase
P: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
T: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
N: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
V: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
W: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
U: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Y: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Z: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
X: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
2: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
4: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
1: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
L: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
R: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
3: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase


Theoretical massNumber of molelcules
Total (without water)606,00230
Polymers606,00230
Non-polymers00
Water0
1
K: Designed Riboflavin synthase
M: Designed Riboflavin synthase
O: Designed Riboflavin synthase
Q: Designed Riboflavin synthase
S: Designed Riboflavin synthase
A: Designed Riboflavin synthase
B: Designed Riboflavin synthase
C: Designed Riboflavin synthase
D: Designed Riboflavin synthase
E: Designed Riboflavin synthase
F: Designed Riboflavin synthase
G: Designed Riboflavin synthase
H: Designed Riboflavin synthase
I: Designed Riboflavin synthase
J: Designed Riboflavin synthase
P: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
T: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
N: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
V: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
W: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
U: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Y: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Z: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
X: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
2: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
4: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
1: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
L: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
R: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
3: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase

K: Designed Riboflavin synthase
M: Designed Riboflavin synthase
O: Designed Riboflavin synthase
Q: Designed Riboflavin synthase
S: Designed Riboflavin synthase
A: Designed Riboflavin synthase
B: Designed Riboflavin synthase
C: Designed Riboflavin synthase
D: Designed Riboflavin synthase
E: Designed Riboflavin synthase
F: Designed Riboflavin synthase
G: Designed Riboflavin synthase
H: Designed Riboflavin synthase
I: Designed Riboflavin synthase
J: Designed Riboflavin synthase
P: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
T: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
N: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
V: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
W: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
U: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Y: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Z: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
X: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
2: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
4: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
1: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
L: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
R: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
3: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase

K: Designed Riboflavin synthase
M: Designed Riboflavin synthase
O: Designed Riboflavin synthase
Q: Designed Riboflavin synthase
S: Designed Riboflavin synthase
A: Designed Riboflavin synthase
B: Designed Riboflavin synthase
C: Designed Riboflavin synthase
D: Designed Riboflavin synthase
E: Designed Riboflavin synthase
F: Designed Riboflavin synthase
G: Designed Riboflavin synthase
H: Designed Riboflavin synthase
I: Designed Riboflavin synthase
J: Designed Riboflavin synthase
P: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
T: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
N: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
V: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
W: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
U: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Y: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Z: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
X: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
2: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
4: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
1: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
L: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
R: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
3: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase

K: Designed Riboflavin synthase
M: Designed Riboflavin synthase
O: Designed Riboflavin synthase
Q: Designed Riboflavin synthase
S: Designed Riboflavin synthase
A: Designed Riboflavin synthase
B: Designed Riboflavin synthase
C: Designed Riboflavin synthase
D: Designed Riboflavin synthase
E: Designed Riboflavin synthase
F: Designed Riboflavin synthase
G: Designed Riboflavin synthase
H: Designed Riboflavin synthase
I: Designed Riboflavin synthase
J: Designed Riboflavin synthase
P: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
T: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
N: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
V: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
W: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
U: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Y: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Z: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
X: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
2: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
4: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
1: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
L: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
R: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
3: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase


Theoretical massNumber of molelcules
Total (without water)2,424,006120
Polymers2,424,006120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_757-x+2,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Buried area254070 Å2
ΔGint-2120 kcal/mol
Surface area766940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.620, 279.810, 301.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain 1
21chain 2
31chain 3
41chain 4
51chain L
61chain N
71chain P
81chain R
91chain T
101chain U
111chain V
121chain W
131chain X
141chain Y
151chain Z
12chain A
22chain B
32chain C
42chain D
52chain E
62chain F
72chain G
82chain H
92chain I
102chain J
112chain K
122chain M
132chain O
142chain Q
152chain S

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROchain 11AA2 - 2092 - 209
21SERSERPROPROchain 22Y2 - 2092 - 209
31SERSERPROPROchain 33DA2 - 2092 - 209
41SERSERPROPROchain 44Z2 - 2092 - 209
51SERSERPROPROchain LLBA2 - 2092 - 209
61SERSERPROPROchain NNR2 - 2092 - 209
71SERSERPROPROchain PPP2 - 2092 - 209
81SERSERPROPROchain RRCA2 - 2092 - 209
91SERSERPROPROchain TTQ2 - 2092 - 209
101SERSERPROPROchain UUU2 - 2092 - 209
111SERSERPROPROchain VVS2 - 2092 - 209
121SERSERPROPROchain WWT2 - 2092 - 209
131SERSERPROPROchain XXX2 - 2092 - 209
141SERSERPROPROchain YYV2 - 2092 - 209
151SERSERPROPROchain ZZW2 - 2092 - 209
12THRTHRGLYGLYchain AAF2 - 1432 - 143
22THRTHRGLYGLYchain BBG2 - 1432 - 143
32THRTHRGLYGLYchain CCH2 - 1432 - 143
42THRTHRLYSLYSchain DDI2 - 1422 - 142
52THRTHRGLYGLYchain EEJ2 - 1432 - 143
62THRTHRLYSLYSchain FFK2 - 1422 - 142
72THRTHRGLYGLYchain GGL2 - 1432 - 143
82THRTHRGLYGLYchain HHM2 - 1432 - 143
92THRTHRGLYGLYchain IIN2 - 1432 - 143
102THRTHRLYSLYSchain JJO2 - 1422 - 142
112THRTHRGLYGLYchain KKA2 - 1432 - 143
122THRTHRLYSLYSchain MMB2 - 1422 - 142
132THRTHRLYSLYSchain OOC2 - 1422 - 142
142THRTHRGLYGLYchain QQD2 - 1432 - 143
152THRTHRGLYGLYchain SSE2 - 1432 - 143

NCS ensembles :
ID
1
2
Details120-mer icosahedral cage according to gel filtration, transmission electron microscopy, small-angle X-ray scattering

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Components

#1: Protein
Designed Riboflavin synthase


Mass: 17249.373 Da / Num. of mol.: 15 / Fragment: Riboflavin synthase
Mutation: I20A, K23L, K24T, E27M, L28E, K109A, D112K, W113I, K116A, E120I, E124L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: ribC, MJ1184 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58584, riboflavin synthase
#2: Protein
Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase


Mass: 23150.732 Da / Num. of mol.: 15
Fragment: Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Mutation: D47S, E51K, R54M, Q59S, E74V, E102I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrionales bacterium (strain SWAT-3) (bacteria)
Strain: SWAT-3 / Gene: VSWAT3_13722 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5KUH7, 4-hydroxy-2-oxoglutarate aldolase

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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: 4.64 Å3/Da / Density % sol: 73.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM sodium acetate pH 4.6, 0.4 M calcium chloride, 3.2% (v/v) isoproponal

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.699→199.3 Å / Num. obs: 118064 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 70.7 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.168 / Net I/σ(I): 8.34
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.7-3.80.8441.84195.1
3.8-3.90.6912.56199.7
3.9-4.010.5443.24199.7
4.01-4.140.3954.36199.8
4.14-4.270.3175.35199.7
4.27-4.420.2676.12199.7
4.42-4.590.2426.5199.6
4.59-4.780.2037.43198.8
4.78-4.990.1787.9197.9
4.99-5.230.1987.59199.6
5.23-5.510.2127.23199.9
5.51-5.850.2047.31199.8
5.85-6.250.187.99199.7
6.25-6.750.1658.41199.1
6.75-7.40.10312.01197.5
7.4-8.270.06318.74199.4
8.27-9.550.04525.61199.4
9.55-11.70.0427.83198.7
11.7-16.540.04124.69196.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.54 Å96.35 Å
Translation8.54 Å96.35 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rosetta design generated based on the PDB files 2b98 and 4e38, but with differences

2b98

4e38


Resolution: 3.699→199.257 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.32
RfactorNum. reflection% reflection
Rfree0.2468 11798 10 %
Rwork0.24 --
obs0.2407 118004 98.92 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 163.61 Å2 / Biso mean: 99.5539 Å2 / Biso min: 64.28 Å2
Refinement stepCycle: final / Resolution: 3.699→199.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39198 0 0 0 39198
Num. residues----5245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01139768
X-RAY DIFFRACTIONf_angle_d1.34753922
X-RAY DIFFRACTIONf_chiral_restr0.0846555
X-RAY DIFFRACTIONf_plane_restr0.0086894
X-RAY DIFFRACTIONf_dihedral_angle_d14.43614899
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11114623X-RAY DIFFRACTION9.021TORSIONAL
12214623X-RAY DIFFRACTION9.021TORSIONAL
13314623X-RAY DIFFRACTION9.021TORSIONAL
14414623X-RAY DIFFRACTION9.021TORSIONAL
15L14623X-RAY DIFFRACTION9.021TORSIONAL
16N14623X-RAY DIFFRACTION9.021TORSIONAL
17P14623X-RAY DIFFRACTION9.021TORSIONAL
18R14623X-RAY DIFFRACTION9.021TORSIONAL
19T14623X-RAY DIFFRACTION9.021TORSIONAL
110U14623X-RAY DIFFRACTION9.021TORSIONAL
111V14623X-RAY DIFFRACTION9.021TORSIONAL
112W14623X-RAY DIFFRACTION9.021TORSIONAL
113X14623X-RAY DIFFRACTION9.021TORSIONAL
114Y14623X-RAY DIFFRACTION9.021TORSIONAL
115Z14623X-RAY DIFFRACTION9.021TORSIONAL
21A10299X-RAY DIFFRACTION9.021TORSIONAL
22B10299X-RAY DIFFRACTION9.021TORSIONAL
23C10299X-RAY DIFFRACTION9.021TORSIONAL
24D10299X-RAY DIFFRACTION9.021TORSIONAL
25E10299X-RAY DIFFRACTION9.021TORSIONAL
26F10299X-RAY DIFFRACTION9.021TORSIONAL
27G10299X-RAY DIFFRACTION9.021TORSIONAL
28H10299X-RAY DIFFRACTION9.021TORSIONAL
29I10299X-RAY DIFFRACTION9.021TORSIONAL
210J10299X-RAY DIFFRACTION9.021TORSIONAL
211K10299X-RAY DIFFRACTION9.021TORSIONAL
212M10299X-RAY DIFFRACTION9.021TORSIONAL
213O10299X-RAY DIFFRACTION9.021TORSIONAL
214Q10299X-RAY DIFFRACTION9.021TORSIONAL
215S10299X-RAY DIFFRACTION9.021TORSIONAL
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 (%)
3.6991-3.74110.37483560.38513204356091
3.7411-3.78510.34333910.33883516390799
3.7851-3.83130.36623920.33813524391699
3.8313-3.87980.32663930.312935373930100
3.8798-3.93090.34023900.320735213911100
3.9309-3.98470.28163920.300935313923100
3.9847-4.04160.30973960.283935643960100
4.0416-4.1020.2763930.277435393932100
4.102-4.16610.2783920.283335283920100
4.1661-4.23440.27573990.2635853984100
4.2344-4.30740.23583930.23635433936100
4.3074-4.38570.24343950.235935463941100
4.3857-4.47010.25443900.242235143904100
4.4701-4.56130.24563930.235335413934100
4.5613-4.66050.23833950.234435483943100
4.6605-4.7690.22363900.22033512390298
4.769-4.88820.25173870.22663483387098
4.8882-5.02040.24723900.22533510390098
5.0204-5.16810.23163940.24135463940100
5.1681-5.3350.27283990.25535923991100
5.335-5.52570.29033960.269235573953100
5.5257-5.74690.29273960.268335773973100
5.7469-6.00850.30823950.27935583953100
6.0085-6.32530.26743990.266135923991100
6.3253-6.72160.25833950.27723552394799
6.7216-7.24060.22673910.22633522391398
7.2406-7.96930.19993960.19743561395799
7.9693-9.12240.13624040.140236374041100
9.1224-11.49320.14994010.14323604400598
11.4932-199.54660.26884050.25883662406796
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6993-1.0817-0.38534.5020.15025.5018-0.07070.1533-0.5035-0.27590.03630.170.3234-0.23120.04230.5019-0.0118-0.0380.8260.01910.7864287.563473.078261.656
23.7112-1.35190.01537.3126-2.14214.199-0.09740.4998-0.0513-0.39690.1265-0.00560.41810.0757-0.02510.6087-0.065-0.04760.81660.02530.6151271.357562.6049278.4123
35.06920.5643-0.01724.46370.30165.09850.1318-0.0249-0.5025-0.1686-0.14740.13050.31650.1530.00670.6196-0.0181-0.1240.88020.01130.789249.096281.1717248.9831
45.04980.5421-0.89135.9052-0.54994.2773-0.13480.0631-0.3731-0.2055-0.13920.13570.4216-0.07640.27440.6597-0.09910.00190.93410.04290.8214247.557167.5879270.5584
54.3779-0.61360.01963.7835-0.94156.5593-0.0730.0462-0.2113-0.29080.0482-0.0270.5389-0.0740.03550.5149-0.076-0.00120.6366-0.01060.634273.756584.5395243.4233
64.34870.57121.89686.2421.62255.69220.01110.40140.0906-0.08120.0847-0.296-0.07780.2279-0.08550.47550.0411-0.04580.5485-0.03090.7075288.3737134.6161224.4305
73.03520.27410.75864.5776-1.44446.43620.13070.22240.0391-0.2124-0.0159-0.21580.07580.2526-0.09650.75370.0559-0.03820.5842-0.01350.939296.321158.3715229.1469
86.40940.880.73325.234-0.31494.4849-0.02870.3238-0.004-0.2671-0.13570.04360.07790.44880.18310.7070.1304-0.0960.6029-0.030.8112323.5698132.2056246.0153
96.80972.45580.21955.0314-2.35254.70330.06910.3485-0.171-0.18130.0871-0.0505-0.2250.2457-0.12770.6755-0.0202-0.03590.5663-0.12170.7794318.0667156.9371242.562
105.6398-0.7753-0.15216.49851.34395.3777-0.03390.31240.2963-0.3479-0.0862-0.0972-0.14530.17020.11890.66780.0664-0.00950.403-0.02620.7125305.1123118.4001234.8455
116.76570.5924-2.14395.5445-1.98765.5218-0.0604-0.3727-0.2181-0.0596-0.0534-0.64350.46970.31480.07770.7487-0.0184-0.05380.5352-0.0810.5943342.7099116.9734295.7866
123.0707-0.557-0.65376.213-0.55522.80150.0858-0.2148-0.38730.2726-0.04030.62460.0541-0.5961-0.05920.48820.0429-0.04850.8382-0.04310.7504192.076184.8324363.2576
135.85631.77991.11134.07230.17075.6484-0.0772-0.1245-0.31150.03720.1937-0.44010.33460.3889-0.11030.81070.0347-0.07010.6855-0.06560.5654337.8416109.0665319.5954
146.45520.1997-1.02082.5491-0.31412.7766-0.1306-0.1949-0.94020.02680.1322-0.02640.6809-0.0921-0.01730.79320.1407-0.05050.63070.03930.76319.691163.1799251.7146
153.58130.50560.00455.9008-0.55864.3630.19590.1886-0.48460.1258-0.1816-0.2937-0.10260.1364-0.0340.81120.0169-0.07030.6432-0.05980.6488320.977481.8805293.4928
165.4037-0.62891.96631.90150.85525.7590.05820.02980.01860.06110.0439-0.2381-0.20780.2949-0.11210.672-0.02140.08830.6081-0.05210.6674342.310890.9091247.5482
175.27430.4554-0.92156.6061-1.38467.4023-0.2586-0.0788-0.3154-0.16930.1475-0.11670.01880.55010.09780.71050.0519-0.02990.61430.03660.5156324.332687.4413318.1644
183.652-1.37221.42653.39760.19325.56930.06880.06730.1392-0.45780.0337-0.1026-0.2184-0.2744-0.10.7501-0.01420.11990.6381-0.03310.6455204.421213.8158345.6677
194.42510.0667-0.54745.86830.33048.40260.2120.0639-0.21290.125-0.0354-0.36790.23070.5014-0.17120.6390.0304-0.01370.6457-0.03450.4877332.215100.1803279.7054
202.6338-0.9644-0.26425.3937-1.46195.70640.05670.3527-0.1122-0.3749-0.15750.16560.1371-0.02970.07860.5190.0816-0.06030.5492-0.15540.6983314.873186.3828224.6014
212.15630.7448-0.68423.9772-1.55743.6040.0244-0.1708-0.03270.2101-0.1213-0.65730.10340.85240.11740.734-0.0617-0.05311.173-0.05470.9637370.0489134.8659282.9644
220.9357-0.5925-0.54925.1710.93182.81650.11890.23210.1703-0.321-0.1183-0.603-0.51840.33270.00240.8508-0.07760.15861.00970.03590.7959360.8071159.9868258.8292
234.25930.48391.2332.35760.30524.7365-0.01860.3114-0.4396-0.38290.0013-0.19530.17950.53570.03290.7020.18680.05820.7742-0.10.903357.5685124.9968250.6351
242.5358-0.6247-0.8652.1830.04365.4596-0.0618-0.376-0.36040.21480.1125-0.16240.50430.1692-0.0360.77660.1793-0.08930.84010.04611.0052308.024644.6284321.4675
252.93521.2997-0.16572.33020.51432.2498-0.11590.1696-0.5728-0.29830.0759-0.33710.33420.34230.01811.06480.13210.0440.7292-0.14980.9827316.363147.7146286.5538
263.9595-0.17571.28621.01250.20164.77130.02810.0372-0.70660.09980.00110.12490.7452-0.1844-0.03250.9574-0.08070.04650.60210.09141.027284.022435.1924296.3248
274.27752.01020.87823.63670.18082.7855-0.14680.62340.3157-0.73030.1253-0.01-0.1318-0.11980.01460.97180.1163-0.09290.81690.02640.6964270.7024121.6569197.0133
284.6806-1.0869-0.75683.61950.89253.09220.08140.3743-0.2877-0.2430.02840.38840.3076-0.2759-0.09440.8947-0.0906-0.07840.6493-0.12060.8628245.806697.2386206.2331
294.47590.6934-0.0972.60890.96323.1453-0.0738-0.17880.14950.24620.1789-0.03650.11260.1936-0.10350.70190.15930.0860.76970.01560.6529221.6263201.7227374.9783
302.6358-0.3819-0.05224.0365-1.50893.88190.14410.2252-0.4517-0.5462-0.1342-0.20280.35880.2020.00140.71510.06930.06910.8431-0.12820.7318280.778889.2954209.4245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 143
2X-RAY DIFFRACTION2chain BB2 - 143
3X-RAY DIFFRACTION3chain CC2 - 143
4X-RAY DIFFRACTION4chain DD2 - 142
5X-RAY DIFFRACTION5chain EE2 - 143
6X-RAY DIFFRACTION6chain FF2 - 142
7X-RAY DIFFRACTION7chain GG2 - 143
8X-RAY DIFFRACTION8chain HH2 - 143
9X-RAY DIFFRACTION9chain II2 - 143
10X-RAY DIFFRACTION10chain JJ2 - 142
11X-RAY DIFFRACTION11chain KK2 - 143
12X-RAY DIFFRACTION12chain LL2 - 209
13X-RAY DIFFRACTION13chain MM2 - 142
14X-RAY DIFFRACTION14chain NN2 - 209
15X-RAY DIFFRACTION15chain OO2 - 142
16X-RAY DIFFRACTION16chain PP2 - 209
17X-RAY DIFFRACTION17chain QQ2 - 143
18X-RAY DIFFRACTION18chain RR2 - 209
19X-RAY DIFFRACTION19chain SS2 - 143
20X-RAY DIFFRACTION20chain TT2 - 209
21X-RAY DIFFRACTION21chain UU2 - 209
22X-RAY DIFFRACTION22chain VV2 - 209
23X-RAY DIFFRACTION23chain WW2 - 209
24X-RAY DIFFRACTION24chain XX2 - 209
25X-RAY DIFFRACTION25chain YY2 - 209
26X-RAY DIFFRACTION26chain ZZ2 - 209
27X-RAY DIFFRACTION27chain 112 - 209
28X-RAY DIFFRACTION28chain 222 - 209
29X-RAY DIFFRACTION29chain 332 - 209
30X-RAY DIFFRACTION30chain 442 - 209

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