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- PDB-3eq5: Crystal structure of fragment 137 to 238 of the human Ski-like protein -

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Basic information

Entry
Database: PDB / ID: 3eq5
TitleCrystal structure of fragment 137 to 238 of the human Ski-like protein
ComponentsSki-like protein
KeywordsSIGNALING PROTEIN / SKIL / SKI-LIKE PROTEIN / SNO / RECEPTOR SIGNALLING / TGF-BETA / Structural Genomics / SGC Stockholm / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


lymphocyte homeostasis / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / lens fiber cell differentiation / response to growth factor / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / blastocyst formation / positive regulation of axonogenesis / SMAD binding / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of cell differentiation ...lymphocyte homeostasis / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / lens fiber cell differentiation / response to growth factor / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / blastocyst formation / positive regulation of axonogenesis / SMAD binding / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of cell differentiation / negative regulation of BMP signaling pathway / skeletal muscle tissue development / response to cytokine / acrosomal vesicle / transforming growth factor beta receptor signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / negative regulation of transforming growth factor beta receptor signaling pathway / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / response to antibiotic / chromatin binding / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Ski / c-SKI SMAD4-binding domain / Transcription regulator SKI/SnoN / c-SKI Smad4 binding domain / c-SKI Smad4 binding domain / SKI/SNO/DAC domain / Ski-like, DNA-binding domain superfamily / SKI/SNO/DAC Dachshund homology domain / Mlu1-box Binding Protein; DNA-binding Domain / SAND-like domain superfamily ...Ski / c-SKI SMAD4-binding domain / Transcription regulator SKI/SnoN / c-SKI Smad4 binding domain / c-SKI Smad4 binding domain / SKI/SNO/DAC domain / Ski-like, DNA-binding domain superfamily / SKI/SNO/DAC Dachshund homology domain / Mlu1-box Binding Protein; DNA-binding Domain / SAND-like domain superfamily / Putative DNA-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsTresaugues, L. / Wisniewska, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. ...Tresaugues, L. / Wisniewska, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Schueler, H. / Thorsell, A.G. / Van Den Berg, S. / Welin, M. / Wikstrom, M. / Weigelt, J. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of fragment 137 to 238 of the human Ski-like protein.
Authors: Tresaugues, L. / Wisniewska, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / ...Authors: Tresaugues, L. / Wisniewska, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Schueler, H. / Thorsell, A.G. / Van Den Berg, S. / Welin, M. / Wikstrom, M. / Weigelt, J. / Nordlund, P.
History
DepositionSep 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ski-like protein
B: Ski-like protein
C: Ski-like protein
D: Ski-like protein
E: Ski-like protein
F: Ski-like protein
G: Ski-like protein
H: Ski-like protein
I: Ski-like protein
J: Ski-like protein
K: Ski-like protein
L: Ski-like protein


Theoretical massNumber of molelcules
Total (without water)168,01112
Polymers168,01112
Non-polymers00
Water6,179343
1
A: Ski-like protein


Theoretical massNumber of molelcules
Total (without water)14,0011
Polymers14,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ski-like protein


Theoretical massNumber of molelcules
Total (without water)14,0011
Polymers14,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ski-like protein


Theoretical massNumber of molelcules
Total (without water)14,0011
Polymers14,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ski-like protein


Theoretical massNumber of molelcules
Total (without water)14,0011
Polymers14,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Ski-like protein


Theoretical massNumber of molelcules
Total (without water)14,0011
Polymers14,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Ski-like protein


Theoretical massNumber of molelcules
Total (without water)14,0011
Polymers14,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Ski-like protein


Theoretical massNumber of molelcules
Total (without water)14,0011
Polymers14,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Ski-like protein


Theoretical massNumber of molelcules
Total (without water)14,0011
Polymers14,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Ski-like protein


Theoretical massNumber of molelcules
Total (without water)14,0011
Polymers14,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Ski-like protein


Theoretical massNumber of molelcules
Total (without water)14,0011
Polymers14,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: Ski-like protein


Theoretical massNumber of molelcules
Total (without water)14,0011
Polymers14,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: Ski-like protein


Theoretical massNumber of molelcules
Total (without water)14,0011
Polymers14,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)210.820, 70.120, 116.280
Angle α, β, γ (deg.)90.00, 100.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ski-like protein / Ski-related protein / Ski-related oncogene


Mass: 14000.952 Da / Num. of mol.: 12 / Fragment: UNP Residues 137-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKIL / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: P12757
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2M Ammonium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97623 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2008 / Details: MIRRORS
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.45→19.83 Å / Num. all: 61694 / Num. obs: 60345 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 12
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 2.63 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.26 / Num. unique all: 4488 / Rsym value: 0.597 / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0035refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SBX

1sbx


Resolution: 2.45→19.83 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.906 / SU B: 25.769 / SU ML: 0.244 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.402 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27428 3018 5 %RANDOM
Rwork0.23239 ---
obs0.23449 57326 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 3.018 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å2-0.15 Å2
2---0.46 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.45→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8968 0 0 343 9311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0229224
X-RAY DIFFRACTIONr_bond_other_d0.0010.026219
X-RAY DIFFRACTIONr_angle_refined_deg0.8081.99812552
X-RAY DIFFRACTIONr_angle_other_deg1.278315324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.23351184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.03124.422389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.034151689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6891572
X-RAY DIFFRACTIONr_chiral_restr0.0440.21564
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02110106
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021714
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0781.55837
X-RAY DIFFRACTIONr_mcbond_other0.0211.52338
X-RAY DIFFRACTIONr_mcangle_it0.16229539
X-RAY DIFFRACTIONr_scbond_it0.31833387
X-RAY DIFFRACTIONr_scangle_it0.4994.52997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 222 -
Rwork0.344 4203 -
obs--100 %
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)
11.7406-0.28350.39366.77370.62253.85290.3670.1915-0.0094-0.4017-0.1209-0.31640.67740.755-0.24610.23380.19870.08590.56780.00410.4015-1.171-28.22247.791
20.5391-2.12911.315211.4893-7.30064.65990.45390.0613-0.5379-1.57290.33481.44961.0138-0.2131-0.78880.64950.0803-0.23890.6377-0.09940.8984-11.076-38.45643.284
31.4461-0.22120.6531.9944-2.30422.98360.35940.2362-0.141-0.3481-0.2960.05430.52130.2163-0.06340.17490.10160.0750.4907-0.0120.3465-5.172-27.54644.76
44.2281-0.58443.2486.7444-0.369410.24180.32530.11550.2995-0.5023-0.31770.1042-0.01510.0875-0.00760.19770.14630.15990.5610.01770.3355-7.595-18.02420.81
51.3944-0.2092-0.00475.07742.61922.38040.16330.27-0.1749-0.56840.0384-0.51230.40180.3647-0.20160.54770.1830.12320.70940.0440.408-0.118-24.73323.113
61.81090.58051.26152.54051.86478.17280.29640.2163-0.3627-0.35170.0932-0.34630.79160.027-0.38970.32210.1330.12690.64190.07350.4041-4.531-25.64921.03
77.87540.1568-9.311310.5527-9.274719.3266-0.2669-0.3557-0.6181-0.3688-0.5981-0.48540.25461.01530.8650.4740.0072-0.00830.5757-0.01750.5938-27.414-1.06316.683
83.4121-0.49690.57611.68231.33763.9335-0.03-0.25660.32410.0879-0.0312-0.0234-0.3766-0.06010.06120.36450.0662-0.02410.62550.02160.5876-33.7338.2315.317
91.06610.02480.94821.81471.09142.0503-0.0822-0.12480.05920.218-0.08810.0797-0.1719-0.28460.17040.32610.0785-0.0240.60310.01610.5611-34.5715.54816.67
1011.8269-8.1308-2.432624.19014.55098.52750.42260.52580.1979-1.5528-0.0167-0.5129-0.51160.0144-0.4060.4872-0.0049-0.16660.66860.09260.44-47.9352.057-7.892
114.6551-1.3297-0.61342.56571.34625.4645-0.0607-0.3082-0.22370.0884-0.0290.28890.427-0.62120.08970.29260.0406-0.04210.81070.01970.6454-51.896-3.5792.342
124.9425-1.84321.24131.3555-1.26891.4472-0.2425-0.3799-0.13040.0950.1680.11210.0767-0.26370.07450.32190.0884-0.02420.7331-0.10070.5515-47.445-2.531-0.531
1313.11562.27974.868949.9502-3.825732.0426-0.9888-0.2288-0.04350.7925-0.9641-3.9026-0.16151.50151.95290.8566-0.3222-0.11541.04920.04430.6953-57.979-30.80529.433
141.60351.31330.131210.64129.78039.92830.2958-0.30160.36490.095-0.52440.3871-0.0327-0.10050.22860.7953-0.4466-0.36760.98750.17871.0196-63.796-21.12935.486
150.1031-0.4488-1.02352.61525.987613.8183-0.0138-0.14830.13580.49650.15430.01491.2498-0.0369-0.14050.7537-0.7974-0.23161.68590.12131.3273-68.492-22.70246.233
163.2004-0.293-0.02961.04271.85333.53720.2561-0.20840.04410.111-0.29460.19810.2132-0.47480.03850.6282-0.4136-0.17180.77260.05320.8278-61.605-23.32938.334
176.6456-3.8365-0.69155.67380.45113.7471-0.02180.2145-0.265-0.2972-0.1266-0.04290.28570.12370.14840.27540.06960.10390.72680.02130.436-13.157-15.611-0.298
182.4914-0.88882.48292.055-2.01073.37130.2677-0.4069-0.2082-0.32590.03580.64230.512-0.4538-0.30350.49650.10710.07720.827-0.04220.6545-16.442-24.8980.506
1910.16681.4023-3.74190.51161.161110.33880.16620.21430.5853-0.14020.01660.0949-0.73140.0163-0.18290.42240.1686-0.00420.63860.06980.4819-14.562-3.616-3.824
203.9897-2.79010.08615.73773.12655.9719-0.1169-0.50550.6618-0.19130.1427-0.26670.36360.1209-0.02580.4681-0.40050.02470.9569-0.0860.7048-41.235-10.66748.931
219.93981.67591.11580.31940.31631.923-0.1910.04561.1617-0.1645-0.04530.3182-0.4934-0.31410.23630.8839-0.3247-0.2440.8782-0.1061.1186-51.621-1.8643.342
224.6039-1.20791.28684.51283.66084.25990.2788-0.43930.5705-0.1581-0.2007-0.12960.1101-0.5019-0.07810.5669-0.4562-0.01220.8261-0.02340.8061-44.751-10.18344.026
237.89725.7911-0.662216.1313-6.50712.95250.61890.2046-0.6980.6694-1.3757-1.31530.32932.01790.75680.5165-0.2213-0.0580.9647-0.00360.5018-19.841-39.55847.519
246.6122-2.73592.95337.5769-3.38533.6393-0.26660.06850.02780.11660.10720.1147-0.55830.48460.15940.4572-0.3153-0.02530.82190.07050.4748-31.856-35.13246.213
253.61370.52883.05924.9422-1.02155.9639-0.12990.2625-0.1882-0.22270.44030.6565-0.0669-0.1712-0.31050.2912-0.11240.01010.61290.00170.5672-29.808-39.07249.494
2612.2648-0.07322.15799.10142.16810.9261-0.3085-0.8221.27140.5525-0.04450.2585-0.0344-0.21570.3530.63210.2268-0.13580.6671-0.08530.7181-18.88811.79937.859
276.2131-1.75723.3493.4901-0.61381.8929-0.01-0.5912-0.0571-0.2266-0.00330.6089-0.0456-0.52850.01320.11050.06540.13370.78620.04310.5443-21.850.49435.932
287.6795-2.8451-6.22854.66992.998111.2281-0.0992-0.38130.4234-0.26170.1055-0.2425-0.430.6778-0.00640.12020.01440.11830.44580.02470.3953-7.2593.68935.788
294.93240.87993.986610.05822.36128.2198-0.297-0.06480.41530.45210.0684-1.3065-0.34750.32610.22870.08760.01890.01780.56450.0810.61626.7910.02751.766
3013.39660.24436.37340.84731.54535.7227-0.60542.26050.88790.34410.2968-0.29860.29471.89890.30860.2286-0.0745-0.04481.10970.50981.314115.4513.16847.493
3112.04511.2043-3.506220.7904-0.7249.7851-0.2524-0.28110.7347-0.21840.1150.96310.0813-1.08920.13740.03570.02380.08730.53980.02240.4052-4.864-3.37950.847
321.43392.93640.221511.4951-0.82641.4213-0.08530.64750.2132-0.3763-0.0917-0.5753-0.04050.85570.17710.65610.2222-0.04771.21910.21810.6446-21.0882.223-26.734
330.9339-0.3226-0.44290.9905-2.30187.24410.08440.3060.5470.0144-0.3412-0.2631-0.38260.41070.25680.60120.1477-0.1940.91770.16950.9509-24.8547.026-20.13
3411.2341-4.6507-0.58142.63962.52399.1868-0.31540.0749-0.5890.3142-0.00260.09681.64130.13860.3180.84340.15840.14070.80040.00110.7263-28.957-9.646-14.646
355.49093.3837-0.15823.8902-1.262110.9243-0.28560.78880.1085-0.30490.1783-0.4720.30251.00330.10730.57050.0618-0.1870.77790.02540.7708-33.963-40.25516.212
361.3865-0.06511.80470.03-0.12349.71170.09190.36160.04820.1116-0.0427-0.0696-0.50.628-0.04920.5753-0.2239-0.15570.76370.06270.7057-40.141-30.45117.361
376.9481.93242.42223.60471.97881.43030.4877-0.0662-0.40550.4093-0.2217-0.33010.22910.056-0.26590.5574-0.2512-0.23210.85690.07270.6486-39.894-34.9624.262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A135 - 179
2X-RAY DIFFRACTION2A180 - 197
3X-RAY DIFFRACTION3A198 - 236
4X-RAY DIFFRACTION4B141 - 172
5X-RAY DIFFRACTION5B173 - 209
6X-RAY DIFFRACTION6B210 - 237
7X-RAY DIFFRACTION7C141 - 152
8X-RAY DIFFRACTION8C153 - 205
9X-RAY DIFFRACTION9C206 - 237
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