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Basic information

Entry
Database: PDB / ID: 5im4
TitleCrystal structure of designed two-component self-assembling icosahedral cage I52-32
Components
  • 6,7-dimethyl-8-ribityllumazine synthaseLumazine synthase
  • Phosphotransferase system, mannose/fructose-specific component IIAPEP group translocation
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


phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / phosphorylation / membrane
Similarity search - Function
PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. / Lumazine/riboflavin synthase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Phosphotransferase system, mannose/fructose-specific component IIA
Similarity search - Component
Biological speciesCandida albicans P37005 (yeast)
Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 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 1.2Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: 6,7-dimethyl-8-ribityllumazine synthase
E: 6,7-dimethyl-8-ribityllumazine synthase
C: 6,7-dimethyl-8-ribityllumazine synthase
B: 6,7-dimethyl-8-ribityllumazine synthase
D: 6,7-dimethyl-8-ribityllumazine synthase
F: Phosphotransferase system, mannose/fructose-specific component IIA
H: Phosphotransferase system, mannose/fructose-specific component IIA
G: Phosphotransferase system, mannose/fructose-specific component IIA
I: Phosphotransferase system, mannose/fructose-specific component IIA
J: Phosphotransferase system, mannose/fructose-specific component IIA
K: 6,7-dimethyl-8-ribityllumazine synthase
L: 6,7-dimethyl-8-ribityllumazine synthase
N: 6,7-dimethyl-8-ribityllumazine synthase
M: 6,7-dimethyl-8-ribityllumazine synthase
O: 6,7-dimethyl-8-ribityllumazine synthase
P: Phosphotransferase system, mannose/fructose-specific component IIA
Q: Phosphotransferase system, mannose/fructose-specific component IIA
S: Phosphotransferase system, mannose/fructose-specific component IIA
R: Phosphotransferase system, mannose/fructose-specific component IIA
T: Phosphotransferase system, mannose/fructose-specific component IIA
U: 6,7-dimethyl-8-ribityllumazine synthase
V: 6,7-dimethyl-8-ribityllumazine synthase
X: 6,7-dimethyl-8-ribityllumazine synthase
W: 6,7-dimethyl-8-ribityllumazine synthase
Y: 6,7-dimethyl-8-ribityllumazine synthase
b: Phosphotransferase system, mannose/fructose-specific component IIA
d: Phosphotransferase system, mannose/fructose-specific component IIA
c: Phosphotransferase system, mannose/fructose-specific component IIA
Z: Phosphotransferase system, mannose/fructose-specific component IIA
a: Phosphotransferase system, mannose/fructose-specific component IIA
e: 6,7-dimethyl-8-ribityllumazine synthase
f: 6,7-dimethyl-8-ribityllumazine synthase
h: 6,7-dimethyl-8-ribityllumazine synthase
g: 6,7-dimethyl-8-ribityllumazine synthase
i: 6,7-dimethyl-8-ribityllumazine synthase
j: Phosphotransferase system, mannose/fructose-specific component IIA
k: Phosphotransferase system, mannose/fructose-specific component IIA
m: Phosphotransferase system, mannose/fructose-specific component IIA
l: Phosphotransferase system, mannose/fructose-specific component IIA
n: Phosphotransferase system, mannose/fructose-specific component IIA


Theoretical massNumber of molelcules
Total (without water)665,30240
Polymers665,30240
Non-polymers00
Water0
1
A: 6,7-dimethyl-8-ribityllumazine synthase
E: 6,7-dimethyl-8-ribityllumazine synthase
C: 6,7-dimethyl-8-ribityllumazine synthase
B: 6,7-dimethyl-8-ribityllumazine synthase
D: 6,7-dimethyl-8-ribityllumazine synthase
F: Phosphotransferase system, mannose/fructose-specific component IIA
H: Phosphotransferase system, mannose/fructose-specific component IIA
G: Phosphotransferase system, mannose/fructose-specific component IIA
I: Phosphotransferase system, mannose/fructose-specific component IIA
J: Phosphotransferase system, mannose/fructose-specific component IIA
K: 6,7-dimethyl-8-ribityllumazine synthase
L: 6,7-dimethyl-8-ribityllumazine synthase
N: 6,7-dimethyl-8-ribityllumazine synthase
M: 6,7-dimethyl-8-ribityllumazine synthase
O: 6,7-dimethyl-8-ribityllumazine synthase
P: Phosphotransferase system, mannose/fructose-specific component IIA
Q: Phosphotransferase system, mannose/fructose-specific component IIA
S: Phosphotransferase system, mannose/fructose-specific component IIA
R: Phosphotransferase system, mannose/fructose-specific component IIA
T: Phosphotransferase system, mannose/fructose-specific component IIA
U: 6,7-dimethyl-8-ribityllumazine synthase
V: 6,7-dimethyl-8-ribityllumazine synthase
X: 6,7-dimethyl-8-ribityllumazine synthase
W: 6,7-dimethyl-8-ribityllumazine synthase
Y: 6,7-dimethyl-8-ribityllumazine synthase
b: Phosphotransferase system, mannose/fructose-specific component IIA
d: Phosphotransferase system, mannose/fructose-specific component IIA
c: Phosphotransferase system, mannose/fructose-specific component IIA
Z: Phosphotransferase system, mannose/fructose-specific component IIA
a: Phosphotransferase system, mannose/fructose-specific component IIA
e: 6,7-dimethyl-8-ribityllumazine synthase
f: 6,7-dimethyl-8-ribityllumazine synthase
h: 6,7-dimethyl-8-ribityllumazine synthase
g: 6,7-dimethyl-8-ribityllumazine synthase
i: 6,7-dimethyl-8-ribityllumazine synthase
j: Phosphotransferase system, mannose/fructose-specific component IIA
k: Phosphotransferase system, mannose/fructose-specific component IIA
m: Phosphotransferase system, mannose/fructose-specific component IIA
l: Phosphotransferase system, mannose/fructose-specific component IIA
n: Phosphotransferase system, mannose/fructose-specific component IIA

A: 6,7-dimethyl-8-ribityllumazine synthase
E: 6,7-dimethyl-8-ribityllumazine synthase
C: 6,7-dimethyl-8-ribityllumazine synthase
B: 6,7-dimethyl-8-ribityllumazine synthase
D: 6,7-dimethyl-8-ribityllumazine synthase
F: Phosphotransferase system, mannose/fructose-specific component IIA
H: Phosphotransferase system, mannose/fructose-specific component IIA
G: Phosphotransferase system, mannose/fructose-specific component IIA
I: Phosphotransferase system, mannose/fructose-specific component IIA
J: Phosphotransferase system, mannose/fructose-specific component IIA
K: 6,7-dimethyl-8-ribityllumazine synthase
L: 6,7-dimethyl-8-ribityllumazine synthase
N: 6,7-dimethyl-8-ribityllumazine synthase
M: 6,7-dimethyl-8-ribityllumazine synthase
O: 6,7-dimethyl-8-ribityllumazine synthase
P: Phosphotransferase system, mannose/fructose-specific component IIA
Q: Phosphotransferase system, mannose/fructose-specific component IIA
S: Phosphotransferase system, mannose/fructose-specific component IIA
R: Phosphotransferase system, mannose/fructose-specific component IIA
T: Phosphotransferase system, mannose/fructose-specific component IIA
U: 6,7-dimethyl-8-ribityllumazine synthase
V: 6,7-dimethyl-8-ribityllumazine synthase
X: 6,7-dimethyl-8-ribityllumazine synthase
W: 6,7-dimethyl-8-ribityllumazine synthase
Y: 6,7-dimethyl-8-ribityllumazine synthase
b: Phosphotransferase system, mannose/fructose-specific component IIA
d: Phosphotransferase system, mannose/fructose-specific component IIA
c: Phosphotransferase system, mannose/fructose-specific component IIA
Z: Phosphotransferase system, mannose/fructose-specific component IIA
a: Phosphotransferase system, mannose/fructose-specific component IIA
e: 6,7-dimethyl-8-ribityllumazine synthase
f: 6,7-dimethyl-8-ribityllumazine synthase
h: 6,7-dimethyl-8-ribityllumazine synthase
g: 6,7-dimethyl-8-ribityllumazine synthase
i: 6,7-dimethyl-8-ribityllumazine synthase
j: Phosphotransferase system, mannose/fructose-specific component IIA
k: Phosphotransferase system, mannose/fructose-specific component IIA
m: Phosphotransferase system, mannose/fructose-specific component IIA
l: Phosphotransferase system, mannose/fructose-specific component IIA
n: Phosphotransferase system, mannose/fructose-specific component IIA

A: 6,7-dimethyl-8-ribityllumazine synthase
E: 6,7-dimethyl-8-ribityllumazine synthase
C: 6,7-dimethyl-8-ribityllumazine synthase
B: 6,7-dimethyl-8-ribityllumazine synthase
D: 6,7-dimethyl-8-ribityllumazine synthase
F: Phosphotransferase system, mannose/fructose-specific component IIA
H: Phosphotransferase system, mannose/fructose-specific component IIA
G: Phosphotransferase system, mannose/fructose-specific component IIA
I: Phosphotransferase system, mannose/fructose-specific component IIA
J: Phosphotransferase system, mannose/fructose-specific component IIA
K: 6,7-dimethyl-8-ribityllumazine synthase
L: 6,7-dimethyl-8-ribityllumazine synthase
N: 6,7-dimethyl-8-ribityllumazine synthase
M: 6,7-dimethyl-8-ribityllumazine synthase
O: 6,7-dimethyl-8-ribityllumazine synthase
P: Phosphotransferase system, mannose/fructose-specific component IIA
Q: Phosphotransferase system, mannose/fructose-specific component IIA
S: Phosphotransferase system, mannose/fructose-specific component IIA
R: Phosphotransferase system, mannose/fructose-specific component IIA
T: Phosphotransferase system, mannose/fructose-specific component IIA
U: 6,7-dimethyl-8-ribityllumazine synthase
V: 6,7-dimethyl-8-ribityllumazine synthase
X: 6,7-dimethyl-8-ribityllumazine synthase
W: 6,7-dimethyl-8-ribityllumazine synthase
Y: 6,7-dimethyl-8-ribityllumazine synthase
b: Phosphotransferase system, mannose/fructose-specific component IIA
d: Phosphotransferase system, mannose/fructose-specific component IIA
c: Phosphotransferase system, mannose/fructose-specific component IIA
Z: Phosphotransferase system, mannose/fructose-specific component IIA
a: Phosphotransferase system, mannose/fructose-specific component IIA
e: 6,7-dimethyl-8-ribityllumazine synthase
f: 6,7-dimethyl-8-ribityllumazine synthase
h: 6,7-dimethyl-8-ribityllumazine synthase
g: 6,7-dimethyl-8-ribityllumazine synthase
i: 6,7-dimethyl-8-ribityllumazine synthase
j: Phosphotransferase system, mannose/fructose-specific component IIA
k: Phosphotransferase system, mannose/fructose-specific component IIA
m: Phosphotransferase system, mannose/fructose-specific component IIA
l: Phosphotransferase system, mannose/fructose-specific component IIA
n: Phosphotransferase system, mannose/fructose-specific component IIA


Theoretical massNumber of molelcules
Total (without water)1,995,905120
Polymers1,995,905120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area277030 Å2
ΔGint-2400 kcal/mol
Surface area633010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)258.820, 258.820, 641.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain K
71chain L
81chain M
91chain N
101chain O
111chain U
121chain V
131chain W
141chain X
151chain Y
161chain e
171chain f
181chain g
191chain h
201chain i
12chain F
22chain G
32chain H
42chain I
52chain J
62chain P
72chain Q
82chain R
92chain S
102chain T
112chain Z
122chain a
132chain b
142chain c
152chain d
162chain j
172chain k
182chain l
192chain m
202chain n

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
11METMETHISHISchain AAA11 - 1671 - 157
21METMETHISHISchain BBD11 - 1671 - 157
31METMETHISHISchain CCC11 - 1671 - 157
41LYSLYSLEULEUchain DDE12 - 1652 - 155
51METMETLEULEUchain EEB11 - 1651 - 155
61METMETLEULEUchain KKK11 - 1651 - 155
71METMETGLUGLUchain LLL11 - 1661 - 156
81LYSLYSHISHISchain MMN12 - 1672 - 157
91TYRTYRLEULEUchain NNM13 - 1653 - 155
101METMETLEULEUchain OOO11 - 1651 - 155
111METMETLEULEUchain UUU11 - 1651 - 155
121METMETLEULEUchain VVV11 - 1651 - 155
131TYRTYRLEULEUchain WWX13 - 1653 - 155
141LYSLYSLEULEUchain XXW12 - 1652 - 155
151METMETLEULEUchain YYY11 - 1651 - 155
161METMETLEULEUchain eeEA11 - 1651 - 155
171METMETLEULEUchain ffFA11 - 1651 - 155
181METMETLEULEUchain ggHA11 - 1651 - 155
191METMETLEULEUchain hhGA11 - 1651 - 155
201TYRTYRGLUGLUchain iiIA13 - 1663 - 156
12METMETLYSLYSchain FFF1 - 1313 - 133
22METMETLYSLYSchain GGH1 - 1313 - 133
32METMETLYSLYSchain HHG1 - 1313 - 133
42METMETLYSLYSchain III1 - 1313 - 133
52METMETLYSLYSchain JJJ1 - 1313 - 133
62METMETLYSLYSchain PPP1 - 1313 - 133
72METMETLYSLYSchain QQQ1 - 1313 - 133
82METMETLYSLYSchain RRS1 - 1313 - 133
92METMETLYSLYSchain SSR1 - 1313 - 133
102METMETLYSLYSchain TTT1 - 1313 - 133
112METMETLYSLYSchain ZZCA1 - 1313 - 133
122METMETLYSLYSchain aaDA1 - 1313 - 133
132METMETLYSLYSchain bbZ1 - 1313 - 133
142METMETLYSLYSchain ccBA1 - 1313 - 133
152METMETLYSLYSchain ddAA1 - 1313 - 133
162METMETLYSLYSchain jjJA1 - 1313 - 133
172METMETLYSLYSchain kkKA1 - 1313 - 133
182METMETLYSLYSchain llMA1 - 1313 - 133
192METMETLYSLYSchain mmLA1 - 1313 - 133
202METMETLYSLYSchain nnNA1 - 1313 - 133

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
6,7-dimethyl-8-ribityllumazine synthase / Lumazine synthase / DMRL synthase


Mass: 18101.053 Da / Num. of mol.: 20
Fragment: 6,7-dimethyl-8-ribityllumazine synthase residues 12-164
Mutation: R29L, K30E, D33A, V40I, E50A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans P37005 (yeast) / Gene: MEU_00538 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0A3CUI3, 6,7-dimethyl-8-ribityllumazine synthase
#2: Protein
Phosphotransferase system, mannose/fructose-specific component IIA / PEP group translocation


Mass: 15164.035 Da / Num. of mol.: 20
Fragment: Phosphotransferase system, mannose/fructose-specifc component IIA
Mutation: V45K, R47A, E51M, K52R, K55I, E56A, Q59A, S81E, E85T, Y86F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: ManX, TTE0192 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RD55

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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: 6.22 Å3/Da / Density % sol: 80.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.17 M potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.5→213.9 Å / Num. obs: 200420 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 104.79 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.132 / Net I/σ(I): 7.31
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.5-3.590.6741.9197.5
3.59-3.690.5032.54199.5
3.69-3.80.4272.97199.7
3.8-3.910.3343.69199.7
3.91-4.040.2764.26199.2
4.04-4.180.2085.25198.3
4.18-4.340.1826.41199.8
4.34-4.520.157.56199.6
4.52-4.720.1288.66199.5
4.72-4.950.1258.67199.5
4.95-5.220.1218.72199.4
5.22-5.530.1148.83197.7
5.53-5.910.129.17199.8
5.91-6.390.1228.85199.8
6.39-70.10210.63199.5
7-7.820.08312.37198.8
7.82-9.030.06715.96197.6
9.03-11.070.06318.69199.5
11.07-15.650.06117.37198.7
15.65-213.90.05918.96196.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.84 Å84.85 Å
Translation7.84 Å84.85 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 2jfb and 3lfh, but with differences

2jfb

3lfh


Resolution: 3.5→110.724 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 24.59
RfactorNum. reflection% reflection
Rfree0.2334 20026 10 %
Rwork0.2269 --
obs0.2275 200301 99.05 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 267.6 Å2 / Biso mean: 103.0777 Å2 / Biso min: 39.53 Å2
Refinement stepCycle: final / Resolution: 3.5→110.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40538 0 0 0 40538
Num. residues----5302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841060
X-RAY DIFFRACTIONf_angle_d1.07155299
X-RAY DIFFRACTIONf_chiral_restr0.0686734
X-RAY DIFFRACTIONf_plane_restr0.0036845
X-RAY DIFFRACTIONf_dihedral_angle_d13.23715193
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12541X-RAY DIFFRACTION7.85TORSIONAL
12B12541X-RAY DIFFRACTION7.85TORSIONAL
13C12541X-RAY DIFFRACTION7.85TORSIONAL
14D12541X-RAY DIFFRACTION7.85TORSIONAL
15E12541X-RAY DIFFRACTION7.85TORSIONAL
16K12541X-RAY DIFFRACTION7.85TORSIONAL
17L12541X-RAY DIFFRACTION7.85TORSIONAL
18M12541X-RAY DIFFRACTION7.85TORSIONAL
19N12541X-RAY DIFFRACTION7.85TORSIONAL
110O12541X-RAY DIFFRACTION7.85TORSIONAL
111U12541X-RAY DIFFRACTION7.85TORSIONAL
112V12541X-RAY DIFFRACTION7.85TORSIONAL
113W12541X-RAY DIFFRACTION7.85TORSIONAL
114X12541X-RAY DIFFRACTION7.85TORSIONAL
115Y12541X-RAY DIFFRACTION7.85TORSIONAL
116e12541X-RAY DIFFRACTION7.85TORSIONAL
117f12541X-RAY DIFFRACTION7.85TORSIONAL
118g12541X-RAY DIFFRACTION7.85TORSIONAL
119h12541X-RAY DIFFRACTION7.85TORSIONAL
120i12541X-RAY DIFFRACTION7.85TORSIONAL
21F12656X-RAY DIFFRACTION7.85TORSIONAL
22G12656X-RAY DIFFRACTION7.85TORSIONAL
23H12656X-RAY DIFFRACTION7.85TORSIONAL
24I12656X-RAY DIFFRACTION7.85TORSIONAL
25J12656X-RAY DIFFRACTION7.85TORSIONAL
26P12656X-RAY DIFFRACTION7.85TORSIONAL
27Q12656X-RAY DIFFRACTION7.85TORSIONAL
28R12656X-RAY DIFFRACTION7.85TORSIONAL
29S12656X-RAY DIFFRACTION7.85TORSIONAL
210T12656X-RAY DIFFRACTION7.85TORSIONAL
211Z12656X-RAY DIFFRACTION7.85TORSIONAL
212a12656X-RAY DIFFRACTION7.85TORSIONAL
213b12656X-RAY DIFFRACTION7.85TORSIONAL
214c12656X-RAY DIFFRACTION7.85TORSIONAL
215d12656X-RAY DIFFRACTION7.85TORSIONAL
216j12656X-RAY DIFFRACTION7.85TORSIONAL
217k12656X-RAY DIFFRACTION7.85TORSIONAL
218l12656X-RAY DIFFRACTION7.85TORSIONAL
219m12656X-RAY DIFFRACTION7.85TORSIONAL
220n12656X-RAY DIFFRACTION7.85TORSIONAL
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 (%)
3.4992-3.53890.38976370.40245738573895
3.5389-3.58060.3826680.352560136681100
3.5806-3.62430.32476820.316161346816100
3.6243-3.67010.32066600.30325941660199
3.6701-3.71840.31256760.300660886764100
3.7184-3.76940.31256680.295960136681100
3.7694-3.82320.29326690.283860236692100
3.8232-3.88030.26426730.26560516724100
3.8803-3.94090.28026750.2636080675599
3.9409-4.00550.27416690.27256022669199
4.0055-4.07460.2626630.25665967663098
4.0746-4.14870.25996600.24745935659598
4.1487-4.22850.24936750.239360756750100
4.2285-4.31480.22896730.232360596732100
4.3148-4.40860.22886710.206360436714100
4.4086-4.51120.22776660.214559866652100
4.5112-4.6240.22746760.2086088676499
4.624-4.7490.22276660.21435998666499
4.749-4.88880.22336720.20736046671899
4.8888-5.04660.23746720.226960416713100
5.0466-5.2270.23176700.22486032670299
5.227-5.43620.21646550.21895895655097
5.4362-5.68360.22096700.21696035670599
5.6836-5.98330.24016730.22960546727100
5.9833-6.35810.24796720.247160516723100
6.3581-6.8490.22996730.222260506723100
6.849-7.5380.21496670.20786003667099
7.538-8.62850.16796560.16225910656697
8.6285-10.86950.13536730.13526040671399
10.8695-110.77990.24456460.25185864651097
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)
13.9988-1.4771-0.69252.73931.12322.43120.14390.234-0.0096-0.0815-0.09180.2247-0.11720.0434-00.66920.0811-0.22820.6411-0.06590.89-165.1781-145.226874.6009
24.20451.59411.11763.22591.3732.059-0.00040.05720.0611-0.1661-0.12970.1471-0.02790.0989-00.56810.1248-0.06330.4352-0.0040.7308-159.0149-125.088190.4204
33.9116-0.8982-0.91192.44721.4392.0770.05310.13780.3892-0.2482-0.030.0986-0.0068-0.1348-00.6355-0.0391-0.00370.37190.03760.5811-133.1464-125.431694.4577
42.6114-0.198-0.25823.51792.02723.05160.1058-0.03390.0692-0.4097-0.0115-0.1706-0.1817-0.080900.63140.01410.0450.51560.01160.5226-123.3838-145.721880.6977
55.27370.38371.59122.39220.0142.9482-0.00590.3023-0.0354-0.2108-0.02160.249-0.05550.1217-00.6640.0864-0.09390.5628-0.0730.4997-143.1033-157.505568.4099
63.86-1.51492.81011.4434-1.31480.8776-0.1356-0.7465-0.33880.09310.3848-0.0024-0.1036-0.49910.00040.78880.2112-0.20711.1449-0.00210.9442-192.5244-134.851466.8719
71.86230.4901-0.42535.23150.65380.3691-0.0081-0.0097-0.24560.51170.00640.02630.19170.0930.00070.89640.2462-0.1520.5015-0.04760.9655-163.2008-96.9853100.3088
83.24363.75330.07222.43860.4210.89420.175-0.1779-0.39180.0166-0.1152-0.3608-0.07890.01310.00460.6321-0.1351-0.01250.40480.05591.0374-106.72-111.418199.1953
93.396-0.9671-2.44450.33150.89263.0705-0.5972-0.324-0.23780.13480.25380.11430.23460.261-0.0970.77930.05790.35540.6236-0.02750.7388-100.9546-158.354664.5599
100.84760.16741.98491.60311.70124.48650.1639-0.20410.10170.38460.0081-0.19730.5393-0.46640.00060.9721-0.1366-0.07891.0674-0.1420.6945-154.004-172.66444.7862
111.7796-0.93840.14984.6052-0.80472.1890.0492-0.00970.11980.0172-0.0791-0.05860.1617-0.039200.683-0.01840.03860.6504-0.01040.5462-235.2057-112.6276-6.4645
121.4503-0.55270.53054.85351.25283.4588-0.11-0.15510.1926-0.08230.08-0.43180.01760.0317-00.6318-0.0673-0.08040.68520.0010.6614-240.4916-88.88232.8913
132.021-0.59470.73693.3154-0.69765.1075-0.0309-0.08160.08990.0462-0.0805-0.1084-0.03790.437600.66980.0266-0.20110.7513-0.08230.6801-235.1324-88.973428.5814
143.5695-1.050.56134.11820.70441.3709-0.21420.06850.02710.09030.0347-0.15730.0136-0.096500.75210.145-0.12850.8449-0.0430.6796-226.7759-113.160234.8446
151.43810.09721.16862.6161.72563.8850.02430.04730.0187-0.0376-0.0047-0.30390.145-0.0326-00.74320.11410.04420.7484-0.02350.6938-227.3158-127.856413.5469
16-0.02841.6873-0.27061.1492-1.33774.96260.089-0.01690.06010.17870.15260.03970.0546-0.71960.00040.82730.12740.18471.06760.04860.5543-234.7764-105.0006-35.7501
170.22160.70070.43114.9771-2.02910.12010.0523-0.07980.0456-0.12040.15680.6134-0.10450.21260.00070.847-0.07590.04070.75040.05280.9724-241.4411-58.7698-0.3303
182.14751.12912.08381.92362.50692.12260.2319-0.28150.01280.0031-0.32180.04570.2354-0.5491-0.00070.9922-0.1478-0.19951.0283-0.14790.7724-225.7223-74.949253.5626
193.4003-2.31471.55760.1636-0.96930.98670.1157-0.1608-0.3653-0.24010.18070.2131-0.0904-0.34910.00010.89160.0994-0.34940.94940.03121.1036-209.4754-130.940351.7849
201.8568-2.5339-2.89753.21451.45271.8536-0.03450.074-0.00510.1436-0.08430.26680.0027-0.0339-00.72730.1537-0.06670.7384-0.04290.752-214.6689-149.5652-3.5311
213.5864-0.06460.88983.6676-1.34792.15020.0768-0.24220.10740.29050.0337-0.0119-0.1561-0.1054-00.5820.0923-0.0490.6035-0.06850.4784-60.7199-113.3174-86.4542
225.82070.71490.97253.5197-1.02131.8554-0.2097-0.17040.24040.02490.20130.0241-0.165-0.369-0.00010.4280.1002-0.00150.483-0.03130.5597-77.3788-100.2077-101.8125
232.86931.104-0.04724.0935-1.01041.33270.0133-0.08630.04580.0864-0.06190.11180.0737-0.258100.45440.0090.04610.76150.09470.6424-98.3037-115.35-105.6594
242.4044-0.70690.77093.1307-1.5242.67780.0568-0.2381-0.07050.27690.06720.19140.0096-0.077500.6614-0.12890.00710.75650.13510.6931-94.7075-137.6617-92.7987
252.52841.56890.94532.36491.20222.01360.2194-0.33220.02860.2118-0.04350.04090.1028-0.106300.6962-0.0267-0.03130.71150.14360.616-71.8863-136.2203-80.2802
261.1904-1.16022.87890.38160.87534.14250.27790.30750.12550.0449-0.08120.0950.30040.50730.00270.847-0.0056-0.0481.13890.29430.6276-54.0902-142.994-56.8654
272.25422.31781.73133.68752.58371.4922-0.18520.153-0.1979-0.28730.2419-0.0982-0.23590.1369-00.9129-0.0699-0.130.7989-0.10780.6182-43.3896-89.7024-78.7933
281.5423-1.8513-0.04884.077-0.9871-0.05520.3045-0.064-0.0901-0.4616-0.25120.00580.048-0.02860.00010.90280.2223-0.1350.5718-0.07720.8067-89.026-74.3784-111.6983
294.9055-0.37020.1266-0.8083-1.28791.1274-0.04340.4335-0.37840.04170.0310.0597-0.12840.15990.00090.417-0.0055-0.02280.9174-0.05371.0525-128.0269-118.0463-110.5674
300.35882.8246-1.36732.238-1.47041.7351-0.4314-0.1313-0.1637-0.3790.0845-0.16640.24510.0395-0.00290.9537-0.08290.21010.92980.27661.0997-106.3293-160.5701-76.7873
313.12491.8219-0.5562.8544-0.61871.3515-0.027-0.0985-0.24770.09320.05220.06460.06190.114-00.8503-0.0413-0.00380.65240.03360.6135-207.66646.1969-5.6169
322.88421.09311.35792.74780.09923.82910.05680.0236-0.26520.0803-0.1252-0.1228-0.03340.0341-00.8108-0.06360.10350.6417-0.03250.8184-222.9645-12.8974-15.0734
333.50762.0388-1.3691.588-1.11414.6822-0.1040.243-0.04860.0771-0.0203-0.00060.22970.017700.793-0.02130.11940.7116-0.18930.7855-218.9312-14.6479-40.9912
342.82921.55150.81954.04290.9560.8457-0.16740.1524-0.1229-0.01970.1613-0.0480.04090.1732-00.5869-0.00510.12420.817-0.10220.5683-200.20842.715-47.3064
352.41521.3310.55892.6634-0.07784.8776-0.00420.0287-0.19510.06410.1443-0.1093-0.01890.096600.6313-0.02240.01370.7124-0.02680.6328-193.29915.4437-25.407
360.0943-0.0524-0.01291.942-1.02224.911-0.0412-0.0351-0.1605-0.16360.20450.0317-0.4555-0.598300.9175-0.0169-0.03861.0420.20420.6685-210.2586-1.152123.6346
370.92831.2588-1.24595.0744-1.2865-0.11710.01730.08030.1928-0.36350.2620.3592-0.03220.0785-01.033-0.1724-0.10210.81360.08771.0083-237.0466-39.3604-11.4843
380.6185-0.2839-1.15832.15682.98062.71130.2454-0.1359-0.2916-0.4161-0.47240.0285-0.5494-0.4416-0.00291.19260.08930.11950.7396-0.22180.8244-216.0973-31.8357-65.7242
395.22570.4256-2.2893-0.4949-0.23791.90250.13560.09180.4590.27040.02580.1007-0.0513-0.3183-00.7838-0.02720.27950.8533-0.09750.8421-176.37211.0729-63.8662
403.36172.13682.9491.32380.41511.40640.0521-0.34390.0343-0.0334-0.16120.06910.0293-0.2592-00.61240.00010.04290.9821-0.09230.7487-172.850629.8686-8.6659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA11 - 167
2X-RAY DIFFRACTION2chain BB11 - 167
3X-RAY DIFFRACTION3chain CC11 - 167
4X-RAY DIFFRACTION4chain DD12 - 165
5X-RAY DIFFRACTION5chain EE11 - 165
6X-RAY DIFFRACTION6chain FF1 - 131
7X-RAY DIFFRACTION7chain GG1 - 131
8X-RAY DIFFRACTION8chain HH1 - 131
9X-RAY DIFFRACTION9chain II1 - 131
10X-RAY DIFFRACTION10chain JJ1 - 131
11X-RAY DIFFRACTION11chain KK11 - 165
12X-RAY DIFFRACTION12chain LL11 - 166
13X-RAY DIFFRACTION13chain MM12 - 167
14X-RAY DIFFRACTION14chain NN13 - 165
15X-RAY DIFFRACTION15chain OO11 - 165
16X-RAY DIFFRACTION16chain PP1 - 131
17X-RAY DIFFRACTION17chain QQ1 - 131
18X-RAY DIFFRACTION18chain RR1 - 131
19X-RAY DIFFRACTION19chain SS1 - 131
20X-RAY DIFFRACTION20chain TT1 - 131
21X-RAY DIFFRACTION21chain UU11 - 165
22X-RAY DIFFRACTION22chain VV11 - 165
23X-RAY DIFFRACTION23chain WW13 - 165
24X-RAY DIFFRACTION24chain XX12 - 165
25X-RAY DIFFRACTION25chain YY11 - 165
26X-RAY DIFFRACTION26chain ZZ1 - 131
27X-RAY DIFFRACTION27chain aa1 - 131
28X-RAY DIFFRACTION28chain bb1 - 131
29X-RAY DIFFRACTION29chain cc1 - 131
30X-RAY DIFFRACTION30chain dd1 - 131
31X-RAY DIFFRACTION31chain ee11 - 165
32X-RAY DIFFRACTION32chain ff11 - 165
33X-RAY DIFFRACTION33chain gg11 - 165
34X-RAY DIFFRACTION34chain hh11 - 165
35X-RAY DIFFRACTION35chain ii13 - 166
36X-RAY DIFFRACTION36chain jj1 - 131
37X-RAY DIFFRACTION37chain kk1 - 131
38X-RAY DIFFRACTION38chain ll1 - 131
39X-RAY DIFFRACTION39chain mm1 - 131
40X-RAY DIFFRACTION40chain nn1 - 131

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