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- PDB-5o7x: CRYSTAL STRUCTURE OF S. CEREVISIAE CORE FACTOR AT 3.2A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 5o7x
TitleCRYSTAL STRUCTURE OF S. CEREVISIAE CORE FACTOR AT 3.2A RESOLUTION
Components
  • RNA polymerase I-specific transcription initiation factor RRN11
  • RNA polymerase I-specific transcription initiation factor RRN6
  • RNA polymerase I-specific transcription initiation factor RRN7
KeywordsTRANSCRIPTION / RNA POLYMERASE I INITIATION / CORE FACTOR
Function / homology
Function and homology information


RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I general transcription initiation factor activity / RNA polymerase I general transcription initiation factor binding / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / TBP-class protein binding / nucleolus ...RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I general transcription initiation factor activity / RNA polymerase I general transcription initiation factor binding / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / TBP-class protein binding / nucleolus / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Transcription initiation factor Rrn11 / RNA polymerase I-specific transcription initiation factor Rrn6 / Transcription initiation factor Rrn11, budding yeast / RNA polymerase I-specific transcription initiation factor RRN6-like / : / : / : / : / RNA polymerase I-specific transcription initiation factor Rrn11 / Rrn6, beta-propeller ...Transcription initiation factor Rrn11 / RNA polymerase I-specific transcription initiation factor Rrn6 / Transcription initiation factor Rrn11, budding yeast / RNA polymerase I-specific transcription initiation factor RRN6-like / : / : / : / : / RNA polymerase I-specific transcription initiation factor Rrn11 / Rrn6, beta-propeller / RRN6, K-rich C-terminal domain / Rrn6, helical bundle domain / Transcription initiation factor Rrn7, Zinc-finger / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / : / : / Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 / Rrn7/TAF1B, N-terminal cyclin domain / Rrn7/TAF1B, C-terminal cyclin domain
Similarity search - Domain/homology
RNA polymerase I-specific transcription initiation factor RRN6 / RNA polymerase I-specific transcription initiation factor RRN7 / RNA polymerase I-specific transcription initiation factor RRN11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsEngel, C. / Gubbey, T. / Neyer, S. / Sainsbury, S. / Oberthuer, C. / Baejen, C. / Bernecky, C. / Cramer, P.
CitationJournal: Cell / Year: 2017
Title: Structural Basis of RNA Polymerase I Transcription Initiation.
Authors: Christoph Engel / Tobias Gubbey / Simon Neyer / Sarah Sainsbury / Christiane Oberthuer / Carlo Baejen / Carrie Bernecky / Patrick Cramer /
Abstract: Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron ...Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. The three-subunit CF binds upstream promoter DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp domains enables cleft contraction, resulting in an active Pol I conformation and RNA synthesis. Comparison with the Pol II system suggests that promoter specificity relies on a distinct "bendability" and "meltability" of the promoter sequence that enables contacts between initiation factors, DNA, and polymerase.
History
DepositionJun 9, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionAug 2, 2017ID: 5N5X
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Structure summary / Category: pdbx_entry_details
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase I-specific transcription initiation factor RRN6
B: RNA polymerase I-specific transcription initiation factor RRN7
C: RNA polymerase I-specific transcription initiation factor RRN11
D: RNA polymerase I-specific transcription initiation factor RRN6
E: RNA polymerase I-specific transcription initiation factor RRN7
F: RNA polymerase I-specific transcription initiation factor RRN11
G: RNA polymerase I-specific transcription initiation factor RRN6
H: RNA polymerase I-specific transcription initiation factor RRN7
I: RNA polymerase I-specific transcription initiation factor RRN11
J: RNA polymerase I-specific transcription initiation factor RRN6
K: RNA polymerase I-specific transcription initiation factor RRN7
L: RNA polymerase I-specific transcription initiation factor RRN11
M: RNA polymerase I-specific transcription initiation factor RRN6
N: RNA polymerase I-specific transcription initiation factor RRN7
O: RNA polymerase I-specific transcription initiation factor RRN11
P: RNA polymerase I-specific transcription initiation factor RRN6
Q: RNA polymerase I-specific transcription initiation factor RRN7
R: RNA polymerase I-specific transcription initiation factor RRN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,334,62454
Polymers1,331,59618
Non-polymers3,02836
Water00
1
A: RNA polymerase I-specific transcription initiation factor RRN6
B: RNA polymerase I-specific transcription initiation factor RRN7
C: RNA polymerase I-specific transcription initiation factor RRN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4379
Polymers221,9333
Non-polymers5056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20060 Å2
ΔGint-223 kcal/mol
Surface area61620 Å2
MethodPISA
2
D: RNA polymerase I-specific transcription initiation factor RRN6
E: RNA polymerase I-specific transcription initiation factor RRN7
F: RNA polymerase I-specific transcription initiation factor RRN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4379
Polymers221,9333
Non-polymers5056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20060 Å2
ΔGint-222 kcal/mol
Surface area61620 Å2
MethodPISA
3
G: RNA polymerase I-specific transcription initiation factor RRN6
H: RNA polymerase I-specific transcription initiation factor RRN7
I: RNA polymerase I-specific transcription initiation factor RRN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4379
Polymers221,9333
Non-polymers5056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20070 Å2
ΔGint-222 kcal/mol
Surface area61540 Å2
MethodPISA
4
J: RNA polymerase I-specific transcription initiation factor RRN6
K: RNA polymerase I-specific transcription initiation factor RRN7
L: RNA polymerase I-specific transcription initiation factor RRN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4379
Polymers221,9333
Non-polymers5056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20030 Å2
ΔGint-221 kcal/mol
Surface area61570 Å2
MethodPISA
5
M: RNA polymerase I-specific transcription initiation factor RRN6
N: RNA polymerase I-specific transcription initiation factor RRN7
O: RNA polymerase I-specific transcription initiation factor RRN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4379
Polymers221,9333
Non-polymers5056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20060 Å2
ΔGint-222 kcal/mol
Surface area61580 Å2
MethodPISA
6
P: RNA polymerase I-specific transcription initiation factor RRN6
Q: RNA polymerase I-specific transcription initiation factor RRN7
R: RNA polymerase I-specific transcription initiation factor RRN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4379
Polymers221,9333
Non-polymers5056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20060 Å2
ΔGint-222 kcal/mol
Surface area61570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.070, 109.140, 385.640
Angle α, β, γ (deg.)90.02, 90.01, 59.98
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
12
22
32
42
52
62
13
23
33
43
53
63
14
24
34
44
54
64
15
25
35
45
55
65
16
26
36
46
56
66
17
27
37
47
57
67

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain A and resid 20 through 558)
211(chain D and resid 20 through 558)
311(chain G and resid 20 through 558)
411(chain J and resid 20 through 558)
511(chain M and resid 20 through 558)
611(chain P and resid 20 through 558)
112(chain A and resid 567 through 650)
212(chain D and resid 567 through 650)
312(chain G and resid 567 through 650)
412(chain J and resid 567 through 650)
512(chain M and resid 567 through 650)
612(chain P and resid 567 through 650)
113(chain A and resid 651 through 779)
213(chain D and resid 651 through 779)
313(chain G and resid 651 through 779)
413(chain J and resid 651 through 779)
513(chain M and resid 651 through 779)
613(chain P and resid 651 through 779)
114(chain B and resid 245 through 513)
214(chain E and resid 245 through 513)
314(chain H and resid 245 through 513)
414(chain K and resid 245 through 513)
514(chain N and resid 245 through 513)
614(chain Q and resid 245 through 513)
115(chain B and resid 94 through 244)
215(chain E and resid 94 through 244)
315(chain H and resid 94 through 244)
415(chain K and resid 94 through 244)
515(chain N and resid 94 through 244)
615(chain Q and resid 94 through 244)
116(chain C and resid 1 through 197)
216(chain F and resid 1 through 197)
316(chain I and resid 1 through 197)
416(chain L and resid 1 through 197)
516(chain O and resid 1 through 197)
616(chain R and resid 1 through 197)
117(chain C and resid 198 through 440)
217(chain F and resid 198 through 440)
317(chain I and resid 198 through 440)
417(chain L and resid 198 through 440)
517(chain O and resid 198 through 440)
617(chain R and resid 198 through 440)

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein
RNA polymerase I-specific transcription initiation factor RRN6


Mass: 102163.227 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RRN6, YBL014C, YBL0311, YBL0312 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32786
#2: Protein
RNA polymerase I-specific transcription initiation factor RRN7


Mass: 60435.195 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RRN7, YJL025W, J1273 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40992
#3: Protein
RNA polymerase I-specific transcription initiation factor RRN11


Mass: 59334.262 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RRN11, YML043C, YM9827.09C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04712
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 30
Source method: isolated from a genetically manipulated source
Formula: SO4
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RRN6, YBL014C, YBL0311, YBL0312 / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Mg
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RRN6, YBL014C, YBL0311, YBL0312 / Production host: Escherichia coli BL21(DE3) (bacteria)
Sequence detailsFollowing the original deposition 5N5X, a frameshift was detected in blades I and II of the Rrn6 ...Following the original deposition 5N5X, a frameshift was detected in blades I and II of the Rrn6 beta-propeller domain using a new algorithm by T. Croll. The mistake in chains A, D, G, J, M and P (residues 169-281) has now been corrected and the structure was refined again as described in Engel et al., 2017.

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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: 4.41 Å3/Da / Density % sol: 72.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 12% PEG 4000 , 500mM Ammonium sulfate, 100mM MES pH=6.0, 1mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 3.2→54.57 Å / Num. obs: 251223 / % possible obs: 98.9 % / Redundancy: 8.283 % / Net I/σ(I): 14.83

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→54.57 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 34.2
RfactorNum. reflection% reflection
Rfree0.2828 7453 2.97 %
Rwork0.2544 --
obs0.2553 251066 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→54.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms63438 0 0 0 63438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764782
X-RAY DIFFRACTIONf_angle_d1.07487510
X-RAY DIFFRACTIONf_dihedral_angle_d21.21439024
X-RAY DIFFRACTIONf_chiral_restr0.0549780
X-RAY DIFFRACTIONf_plane_restr0.00810914
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3105X-RAY DIFFRACTIONPOSITIONAL
12D3105X-RAY DIFFRACTIONPOSITIONAL0.018
13G3105X-RAY DIFFRACTIONPOSITIONAL0.019
14J3105X-RAY DIFFRACTIONPOSITIONAL0.011
15M3105X-RAY DIFFRACTIONPOSITIONAL0.019
16P3105X-RAY DIFFRACTIONPOSITIONAL0.018
21A696X-RAY DIFFRACTIONPOSITIONAL
22D696X-RAY DIFFRACTIONPOSITIONAL0.009
23G696X-RAY DIFFRACTIONPOSITIONAL0.009
24J696X-RAY DIFFRACTIONPOSITIONAL0.008
25M696X-RAY DIFFRACTIONPOSITIONAL0.009
26P696X-RAY DIFFRACTIONPOSITIONAL0.008
31A1055X-RAY DIFFRACTIONPOSITIONAL
32D1055X-RAY DIFFRACTIONPOSITIONAL0.01
33G1055X-RAY DIFFRACTIONPOSITIONAL0.01
34J1055X-RAY DIFFRACTIONPOSITIONAL0.01
35M1055X-RAY DIFFRACTIONPOSITIONAL0.01
36P1055X-RAY DIFFRACTIONPOSITIONAL0.011
41B1919X-RAY DIFFRACTIONPOSITIONAL
42E1919X-RAY DIFFRACTIONPOSITIONAL0.012
43H1919X-RAY DIFFRACTIONPOSITIONAL0.012
44K1919X-RAY DIFFRACTIONPOSITIONAL0.011
45N1919X-RAY DIFFRACTIONPOSITIONAL0.012
46Q1919X-RAY DIFFRACTIONPOSITIONAL0.012
51B1229X-RAY DIFFRACTIONPOSITIONAL
52E1229X-RAY DIFFRACTIONPOSITIONAL0.01
53H1229X-RAY DIFFRACTIONPOSITIONAL0.01
54K1229X-RAY DIFFRACTIONPOSITIONAL0.01
55N1229X-RAY DIFFRACTIONPOSITIONAL0.01
56Q1229X-RAY DIFFRACTIONPOSITIONAL0.01
61C978X-RAY DIFFRACTIONPOSITIONAL
62F978X-RAY DIFFRACTIONPOSITIONAL0.011
63I978X-RAY DIFFRACTIONPOSITIONAL0.012
64L978X-RAY DIFFRACTIONPOSITIONAL0.011
65O978X-RAY DIFFRACTIONPOSITIONAL0.012
66R978X-RAY DIFFRACTIONPOSITIONAL0.011
71C1557X-RAY DIFFRACTIONPOSITIONAL
72F1557X-RAY DIFFRACTIONPOSITIONAL0.008
73I1557X-RAY DIFFRACTIONPOSITIONAL0.009
74L1557X-RAY DIFFRACTIONPOSITIONAL0.009
75O1557X-RAY DIFFRACTIONPOSITIONAL0.009
76R1557X-RAY DIFFRACTIONPOSITIONAL0.009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1999-3.23620.38232280.38378046X-RAY DIFFRACTION99
3.2362-3.27430.38872380.37818133X-RAY DIFFRACTION99
3.2743-3.31420.39262580.38858330X-RAY DIFFRACTION99
3.3142-3.35620.45692460.3968035X-RAY DIFFRACTION99
3.3562-3.40030.37472490.37778267X-RAY DIFFRACTION100
3.4003-3.44690.40641990.36558125X-RAY DIFFRACTION99
3.4469-3.49610.33662510.34448140X-RAY DIFFRACTION100
3.4961-3.54830.34912530.3458299X-RAY DIFFRACTION100
3.5483-3.60380.37612420.35518131X-RAY DIFFRACTION100
3.6038-3.66280.36132570.33518120X-RAY DIFFRACTION100
3.6628-3.7260.36782580.32858252X-RAY DIFFRACTION100
3.726-3.79370.3722530.32388199X-RAY DIFFRACTION100
3.7937-3.86670.38262620.32378140X-RAY DIFFRACTION100
3.8667-3.94560.35262510.32718148X-RAY DIFFRACTION99
3.9456-4.03130.38282460.327657X-RAY DIFFRACTION92
4.0313-4.12510.34352370.30697919X-RAY DIFFRACTION97
4.1251-4.22820.30542510.27588189X-RAY DIFFRACTION100
4.2282-4.34250.30332560.26468236X-RAY DIFFRACTION100
4.3425-4.47020.28152470.24268118X-RAY DIFFRACTION100
4.4702-4.61440.27522540.23998218X-RAY DIFFRACTION100
4.6144-4.77920.26922590.22598252X-RAY DIFFRACTION100
4.7792-4.97050.27072590.21768325X-RAY DIFFRACTION100
4.9705-5.19650.23712500.21548148X-RAY DIFFRACTION100
5.1965-5.47030.26732590.24468199X-RAY DIFFRACTION100
5.4703-5.81260.30272550.25418071X-RAY DIFFRACTION99
5.8126-6.26080.30022390.24347652X-RAY DIFFRACTION93
6.2608-6.88980.28742600.26258202X-RAY DIFFRACTION100
6.8898-7.88420.24182510.21378217X-RAY DIFFRACTION100
7.8842-9.92350.19832570.17248242X-RAY DIFFRACTION100
9.9235-54.57790.23232280.22747603X-RAY DIFFRACTION93
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4364-0.53480.2592.1701-0.9522.47630.17830.18040.0283-0.036-0.3424-0.0262-0.28970.3943-0.03611.16260.0443-0.1510.7724-0.05711.060922.371768.8427-124.7966
20.4491-0.5432-0.30252.12991.01792.49080.17760.1843-0.0293-0.0397-0.35440.01090.2798-0.3792-0.04031.2110.03930.14790.75220.05231.0599-35.41066.186968.028
32.3444-0.4039-0.98890.40450.20692.4123-0.27470.2546-0.03310.07360.1199-0.02970.45960.0859-0.03750.86040.16250.02281.10450.14291.04566.1031-3.13353.7542
41.23431.0621-0.68681.413-0.75782.3665-0.1501-0.1248-0.0072-0.36250.0048-0.03180.18910.4063-0.03820.9102-0.2092-0.11251.0640.08741.049934.985928.1736-60.5245
52.2744-0.39050.98880.3866-0.23962.5152-0.27680.29410.03510.08650.1120.0262-0.4732-0.0634-0.03760.840.1503-0.02871.1167-0.14421.0561-19.123978.2104-189.0708
61.23981.05620.70961.4390.7662.4337-0.1422-0.14890.0124-0.3527-0.02260.0544-0.1682-0.451-0.04310.8919-0.22140.11811.0764-0.09371.05-47.995846.9379-253.3429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or chain B or chain C
2X-RAY DIFFRACTION2chain D or chain E or chain F
3X-RAY DIFFRACTION3chain G or chain H or chain I
4X-RAY DIFFRACTION4chain J or chain K or chain L
5X-RAY DIFFRACTION5chain M or chain N or chain O
6X-RAY DIFFRACTION6chain P or chain Q or chain R

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