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- PDB-4md9: Crystal Structure of symmetric CK2 holoenzyme with mutated alpha ... -

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Basic information

Entry
Database: PDB / ID: 4md9
TitleCrystal Structure of symmetric CK2 holoenzyme with mutated alpha subunit (F121E truncated at aa 336)
Components
  • Casein kinase II subunit alpha
  • Casein kinase II subunit beta
KeywordsTRANSFERASE / protein serine/threonine kinase
Function / homology
Function and homology information


regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / UTP-C complex / endothelial tube morphogenesis / negative regulation of viral life cycle / regulation of transcription by RNA polymerase III / protein kinase regulator activity / regulation of chromosome separation / positive regulation of aggrephagy ...regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / UTP-C complex / endothelial tube morphogenesis / negative regulation of viral life cycle / regulation of transcription by RNA polymerase III / protein kinase regulator activity / regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / positive regulation of SMAD protein signal transduction / negative regulation of apoptotic signaling pathway / negative regulation of blood vessel endothelial cell migration / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / protein-macromolecule adaptor activity / kinase activity / positive regulation of cell growth / protein-containing complex assembly / peptidyl-serine phosphorylation / secretory granule lumen / RNA polymerase II-specific DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / negative regulation of cell population proliferation / protein domain specific binding / protein phosphorylation / protein serine kinase activity / signaling receptor binding / protein serine/threonine kinase activity / apoptotic process / DNA damage response / chromatin binding / positive regulation of cell population proliferation / Neutrophil degranulation / chromatin / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, domain 1 / Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / N-terminal domain of TfIIb - #20 / Casein Kinase 2, subunit alpha ...protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, domain 1 / Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / N-terminal domain of TfIIb - #20 / Casein Kinase 2, subunit alpha / N-terminal domain of TfIIb / Single Sheet / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Casein kinase II subunit beta / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsLolli, G. / Ranchio, A. / Battistutta, R.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Active Form of the Protein Kinase CK2 alpha 2 beta 2 Holoenzyme Is a Strong Complex with Symmetric Architecture.
Authors: Lolli, G. / Ranchio, A. / Battistutta, R.
History
DepositionAug 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Sep 20, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Casein kinase II subunit beta
B: Casein kinase II subunit beta
C: Casein kinase II subunit beta
D: Casein kinase II subunit beta
E: Casein kinase II subunit alpha
F: Casein kinase II subunit alpha
G: Casein kinase II subunit alpha
H: Casein kinase II subunit alpha
I: Casein kinase II subunit beta
J: Casein kinase II subunit beta
K: Casein kinase II subunit alpha
L: Casein kinase II subunit alpha
M: Casein kinase II subunit alpha
N: Casein kinase II subunit beta
O: Casein kinase II subunit beta
P: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)521,36524
Polymers520,84116
Non-polymers5238
Water00
1
A: Casein kinase II subunit beta
B: Casein kinase II subunit beta
E: Casein kinase II subunit alpha
F: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3416
Polymers130,2104
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-62 kcal/mol
Surface area49980 Å2
MethodPISA
2
C: Casein kinase II subunit beta
D: Casein kinase II subunit beta
H: Casein kinase II subunit alpha
K: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3416
Polymers130,2104
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-61 kcal/mol
Surface area49650 Å2
MethodPISA
3
G: Casein kinase II subunit alpha
N: Casein kinase II subunit beta
O: Casein kinase II subunit beta
P: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3416
Polymers130,2104
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-64 kcal/mol
Surface area50010 Å2
MethodPISA
4
I: Casein kinase II subunit beta
J: Casein kinase II subunit beta
L: Casein kinase II subunit alpha
M: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3416
Polymers130,2104
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-61 kcal/mol
Surface area49930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)283.924, 115.707, 208.223
Angle α, β, γ (deg.)90.00, 119.22, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51I
61J
71N
81O
12E
22F
32G
42H
52K
62L
72M
82P

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERPROPROAA8 - 588 - 58
211SERSERPROPROBB8 - 588 - 58
311SERSERPROPROCC8 - 588 - 58
411SERSERPROPRODD8 - 588 - 58
511SERSERPROPROII8 - 588 - 58
611SERSERPROPROJJ8 - 588 - 58
711SERSERPROPRONN8 - 588 - 58
811SERSERPROPROOO8 - 588 - 58
121GLNGLNTYRTYRAA68 - 18868 - 188
221GLNGLNTYRTYRBB68 - 18868 - 188
321GLNGLNTYRTYRCC68 - 18868 - 188
421GLNGLNTYRTYRDD68 - 18868 - 188
521GLNGLNTYRTYRII68 - 18868 - 188
621GLNGLNTYRTYRJJ68 - 18868 - 188
721GLNGLNTYRTYRNN68 - 18868 - 188
821GLNGLNTYRTYROO68 - 18868 - 188
112PROPROLEULEUEE4 - 414 - 41
212PROPROLEULEUFF4 - 414 - 41
312PROPROLEULEUGG4 - 414 - 41
412PROPROLEULEUHH4 - 414 - 41
512PROPROLEULEUKK4 - 414 - 41
612PROPROLEULEULL4 - 414 - 41
712PROPROLEULEUMM4 - 414 - 41
812PROPROLEULEUPP4 - 414 - 41
122TYRTYRLYSLYSEE50 - 7150 - 71
222TYRTYRLYSLYSFF50 - 7150 - 71
322TYRTYRLYSLYSGG50 - 7150 - 71
422TYRTYRLYSLYSHH50 - 7150 - 71
522TYRTYRLYSLYSKK50 - 7150 - 71
622TYRTYRLYSLYSLL50 - 7150 - 71
722TYRTYRLYSLYSMM50 - 7150 - 71
822TYRTYRLYSLYSPP50 - 7150 - 71
132VALVALLYSLYSEE73 - 10273 - 102
232VALVALLYSLYSFF73 - 10273 - 102
332VALVALLYSLYSGG73 - 10273 - 102
432VALVALLYSLYSHH73 - 10273 - 102
532VALVALLYSLYSKK73 - 10273 - 102
632VALVALLYSLYSLL73 - 10273 - 102
732VALVALLYSLYSMM73 - 10273 - 102
832VALVALLYSLYSPP73 - 10273 - 102
142THRTHRPHEPHEEE108 - 113108 - 113
242THRTHRPHEPHEFF108 - 113108 - 113
342THRTHRPHEPHEGG108 - 113108 - 113
442THRTHRPHEPHEHH108 - 113108 - 113
542THRTHRPHEPHEKK108 - 113108 - 113
642THRTHRPHEPHELL108 - 113108 - 113
742THRTHRPHEPHEMM108 - 113108 - 113
842THRTHRPHEPHEPP108 - 113108 - 113
152THRTHRILEILEEE127 - 263127 - 263
252THRTHRILEILEFF127 - 263127 - 263
352THRTHRILEILEGG127 - 263127 - 263
452THRTHRILEILEHH127 - 263127 - 263
552THRTHRILEILEKK127 - 263127 - 263
652THRTHRILEILELL127 - 263127 - 263
752THRTHRILEILEMM127 - 263127 - 263
852THRTHRILEILEPP127 - 263127 - 263
162GLYGLYHISHISEE274 - 286274 - 286
262GLYGLYHISHISFF274 - 286274 - 286
362GLYGLYHISHISGG274 - 286274 - 286
462GLYGLYHISHISHH274 - 286274 - 286
562GLYGLYHISHISKK274 - 286274 - 286
662GLYGLYHISHISLL274 - 286274 - 286
762GLYGLYHISHISMM274 - 286274 - 286
862GLYGLYHISHISPP274 - 286274 - 286
172GLNGLNVALVALEE290 - 327290 - 327
272GLNGLNVALVALFF290 - 327290 - 327
372GLNGLNVALVALGG290 - 327290 - 327
472GLNGLNVALVALHH290 - 327290 - 327
572GLNGLNVALVALKK290 - 327290 - 327
672GLNGLNVALVALLL290 - 327290 - 327
772GLNGLNVALVALMM290 - 327290 - 327
872GLNGLNVALVALPP290 - 327290 - 327

NCS ensembles :
ID
1
2

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Components

#1: Protein
Casein kinase II subunit beta / CK2 subunit beta / CK II beta / Phosvitin / Protein G5a


Mass: 24969.412 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2B, CK2N, G5A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P67870
#2: Protein
Casein kinase II subunit alpha / CK2 subunit alpha / CK II alpha


Mass: 40135.758 Da / Num. of mol.: 8 / Fragment: kinase domain (UNP residues 1-336) / Mutation: F121E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P68400, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 9, 2011
RadiationMonochromator: horizontally diffracting Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.5→181.725 Å / Num. all: 74256 / Num. obs: 74256 / % possible obs: 99.7 % / Redundancy: 3.3 % / Rsym value: 0.172 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.5-3.693.20.6211.20.621199.9
3.69-3.913.20.4291.80.4291100
3.91-4.183.30.2962.60.296199.9
4.18-4.523.40.1983.90.198199.9
4.52-4.953.40.1644.70.164199.9
4.95-5.533.40.15650.156199.8
5.53-6.393.40.1465.20.146199.8
6.39-7.833.30.1057.10.105199.6
7.83-11.073.30.05510.20.055199.1
11.07-48.3063.20.03912.50.039197.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4DGL AND 4KWP

4dgl

4kwp


Resolution: 3.5→181.725 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.879 / Occupancy max: 1 / Occupancy min: 1 / SU B: 55.068 / SU ML: 0.379 / SU R Cruickshank DPI: 0.1441 / Cross valid method: THROUGHOUT / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25897 3736 5 %RANDOM
Rwork0.22888 ---
obs0.23038 70519 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.224 Å2
Baniso -1Baniso -2Baniso -3
1--24.26 Å2-0 Å26.04 Å2
2--16.99 Å20 Å2
3---7.26 Å2
Refinement stepCycle: LAST / Resolution: 3.5→181.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35065 0 8 0 35073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0236042
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.94848781
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.47654180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22423.4951943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95156194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.98815272
X-RAY DIFFRACTIONr_chiral_restr0.0830.25005
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02128092
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A688MEDIUM POSITIONAL0.230.5
12B688MEDIUM POSITIONAL0.210.5
13C688MEDIUM POSITIONAL0.190.5
14D688MEDIUM POSITIONAL0.180.5
15I688MEDIUM POSITIONAL0.20.5
16J688MEDIUM POSITIONAL0.20.5
17N688MEDIUM POSITIONAL0.210.5
18O688MEDIUM POSITIONAL0.210.5
11A722LOOSE POSITIONAL0.535
12B722LOOSE POSITIONAL0.55
13C722LOOSE POSITIONAL0.495
14D722LOOSE POSITIONAL0.55
15I722LOOSE POSITIONAL0.55
16J722LOOSE POSITIONAL0.475
17N722LOOSE POSITIONAL0.495
18O722LOOSE POSITIONAL0.535
11A688MEDIUM THERMAL5.432
12B688MEDIUM THERMAL4.992
13C688MEDIUM THERMAL5.042
14D688MEDIUM THERMAL5.212
15I688MEDIUM THERMAL5.632
16J688MEDIUM THERMAL6.512
17N688MEDIUM THERMAL5.392
18O688MEDIUM THERMAL10.12
11A722LOOSE THERMAL6.210
12B722LOOSE THERMAL6.5110
13C722LOOSE THERMAL6.5310
14D722LOOSE THERMAL6.8510
15I722LOOSE THERMAL7.2710
16J722LOOSE THERMAL7.2710
17N722LOOSE THERMAL6.8710
18O722LOOSE THERMAL10.6210
21E1136MEDIUM POSITIONAL0.20.5
22F1136MEDIUM POSITIONAL0.230.5
23G1136MEDIUM POSITIONAL0.210.5
24H1136MEDIUM POSITIONAL0.260.5
25K1136MEDIUM POSITIONAL0.260.5
26L1136MEDIUM POSITIONAL0.220.5
27M1136MEDIUM POSITIONAL0.220.5
28P1136MEDIUM POSITIONAL0.240.5
21E1276LOOSE POSITIONAL0.475
22F1276LOOSE POSITIONAL0.435
23G1276LOOSE POSITIONAL0.455
24H1276LOOSE POSITIONAL0.485
25K1276LOOSE POSITIONAL0.465
26L1276LOOSE POSITIONAL0.485
27M1276LOOSE POSITIONAL0.495
28P1276LOOSE POSITIONAL0.55
21E1136MEDIUM THERMAL5.862
22F1136MEDIUM THERMAL5.152
23G1136MEDIUM THERMAL5.442
24H1136MEDIUM THERMAL5.342
25K1136MEDIUM THERMAL5.72
26L1136MEDIUM THERMAL5.552
27M1136MEDIUM THERMAL6.262
28P1136MEDIUM THERMAL5.472
21E1276LOOSE THERMAL6.7410
22F1276LOOSE THERMAL6.9310
23G1276LOOSE THERMAL6.7110
24H1276LOOSE THERMAL7.2310
25K1276LOOSE THERMAL6.8610
26L1276LOOSE THERMAL7.410
27M1276LOOSE THERMAL7.5910
28P1276LOOSE THERMAL7.1810
LS refinement shellResolution: 3.498→3.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 255 -
Rwork0.291 5045 -
obs--96.86 %
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)
10.3320.3061-1.07490.5403-2.04867.85570.0777-0.31180.08680.06960.02750.0289-0.3701-0.2045-0.10520.3507-0.07640.09390.6659-0.03170.5992-98.5945-3.0472-43.0705
23.7626-0.3398-2.27376.8875-5.08557.54780.07350.0352-0.1440.20950.03610.3920.6204-0.8147-0.10960.3745-0.1883-0.01720.6649-0.03520.6605-113.0738-10.2149-45.2348
32.18240.4201-0.731.0140.42781.5569-0.0229-0.3490.0399-0.1046-0.00850.0750.0702-0.04250.03140.11320.0312-0.01460.2673-0.00120.5204-89.994-2.6874-56.6607
46.158716.591-0.857745.45190.404111.6862-0.5177-0.0543-0.112-1.5623-0.1304-0.05160.94190.47280.64810.25610.2244-0.05050.40210.04380.7936-62.4603-14.5564-74.3491
57.083-7.28834.339741.5587-13.80175.22650.9106-0.2956-0.2493-0.457-0.67170.29270.48610.1523-0.23890.40620.21480.0321.0301-0.19310.4724-53.0189-10.272-38.0542
60.5659-0.3596-0.36751.40782.12834.538-0.0352-0.25430.10610.36710.2354-0.07370.0960.7695-0.20010.304-0.08990.02710.5590.0380.6039-46.5133-5.2569-45.7151
72.6555-0.20591.07680.8554-0.34831.57460.1451-0.2323-0.12140.01730.01350.01750.1837-0.058-0.15860.06730.0370.04640.26260.02420.4691-64.4602-8.0542-56.3421
85.11495.5365-0.245720.289210.54948.6220.2018-0.05580.4019-0.6894-0.44520.6744-1.0124-0.22790.24340.33380.1046-0.12610.56930.04590.4769-90.90526.6998-73.6608
97.85280.0623-4.78013.9985.18089.7315-0.66390.06540.2324-0.45130.20330.505-0.17930.33690.46060.28760.22910.12760.47190.15040.571810.899430.1466-49.2774
100.2035-0.7854-1.37916.96664.030811.69250.06190.0237-0.0264-0.60920.07710.44390.01670.9759-0.1390.25710.18830.0010.79080.03580.62325.267822.5982-46.2996
113.70190.0738-0.74671.25640.15261.74360.20210.22990.0576-0.2753-0.16240.07040.06540.0399-0.03970.1159-0.0277-0.00520.31770.04730.46073.537728.3305-35.0237
120.81770.3995-0.1551.75484.384612.87810.35330.0577-0.2750.78840.2031-0.29871.72290.173-0.55640.5604-0.07850.12060.730.02960.7219-25.470215.9845-18.0861
134.3461-1.0765-0.35551.4716-0.47460.70570.26350.22260.3559-0.21620.06760.08410.1846-0.4411-0.33110.1958-0.0462-0.00650.53420.0420.5558-40.21527.6966-45.0018
143.7536-0.20061.04890.32960.55321.5104-0.03740.03360.03290.003-0.05660.0065-0.04890.01960.0940.0689-0.13760.06350.3092-0.02210.4907-23.109623.7624-34.5191
150.6949-2.6882-2.867115.33598.602113.3809-0.06150.05780.15571.44920.0028-1.4679-0.4933-0.71390.05870.37270.0216-0.16450.6746-0.08860.81444.892134.9167-16.7314
162.6894-0.8826-0.46080.63430.03440.83480.193-0.03890.5068-0.0195-0.0345-0.278-0.460.3816-0.15850.3358-0.07210.04630.47930.00180.5824-29.3747-0.7814-75.5945
175.6472-0.5704-1.01511.6411-0.34441.9767-0.1715-0.05220.27240.17120.1403-0.01490.01420.11180.03110.16430.0040.05520.3081-0.02380.4488-41.412-5.6104-74.9567
180.71260.03360.82593.40991.42781.57890.13640.0024-0.24390.8355-0.2340.48010.4824-0.07260.09750.26240.07290.07920.5132-0.00340.6452-44.3422-12.276-76.7972
193.5261-0.1760.99033.1903-0.25023.95310.2697-0.0589-0.05540.1104-0.21890.02120.1470.2947-0.05080.10690.06-0.00180.4039-0.03250.4786-27.3792-16.5789-76.325
201.5920.1075-0.04022.6189-0.80380.69840.2031-0.1191-0.35360.3083-0.1387-0.22750.32340.1232-0.06440.48040.0524-0.06380.64440.0250.6521-19.0578-28.5673-72.6429
212.8263-0.8486-0.51491.81640.15920.17720.01650.0608-0.37460.1957-0.0840.24340.1795-0.07140.06750.4611-0.01850.07540.5574-0.07010.6492-127.2682-7.0013-82.0951
223.8022-0.66041.9742.4658-1.19391.34330.0921-0.2506-0.13750.19-0.07440.00370.0081-0.122-0.01770.23840.02370.0910.4684-0.04460.5033-109.4942-2.8919-77.1705
232.22431.0173-0.88950.4908-0.42040.37520.0164-0.1933-0.08380.12380.0041-0.1129-0.1119-0.0038-0.02050.89210.2205-0.21780.8789-0.02690.7528-108.933613.7878-79.0861
241.5805-0.2559-0.64271.3910.68712.2034-0.0128-0.08340.01680.3168-0.04880.16210.0648-0.19980.06160.23250.05310.06230.4930.00030.4886-129.126813.3714-73.1857
252.05320.4668-0.59162.1721-1.89225.304-0.12850.34650.2288-0.22390.13090.2284-0.1426-0.3052-0.00240.19610.103-0.02890.568-0.05070.5308-130.14723.8194-82.489
260.83690.7391-0.21262.8722-0.0530.304-0.24510.09050.46050.14720.14740.374-0.1535-0.01130.09760.52530.0061-0.16370.5131-0.01190.6923-61.8453-27.3132-12.2913
274.0108-0.7966-2.02582.27880.02872.39-0.32680.47930.2586-0.27680.065-0.2070.0023-0.27660.26180.2051-0.0661-0.01810.40210.05480.467-40.6371-32.9857-15.1321
282.87735.9461-3.196312.48-6.67313.5748-0.01850.170.2007-0.0740.36480.81420.0354-0.1998-0.34620.4672-0.0104-0.02160.5617-0.00730.8456-42.3919-50.2709-10.2106
291.85510.54230.80712.30380.66042.4906-0.0080.0011-0.1896-0.01450.05450.10520.0902-0.144-0.04650.05230.02390.07960.424-0.02330.461-62.7093-50.3654-14.7824
300.5075-0.64330.13331.4508-0.18440.0376-0.33330.17640.31390.45860.2382-0.0096-0.09990.00750.09510.5593-0.1355-0.00690.83270.00270.8348-60.286831.2525-12.242
316.37060.6301-0.99172.9602-0.24220.8982-0.3337-0.07630.2226-0.06480.15550.0325-0.16610.0360.17830.2531-0.14570.07840.4159-0.08930.3094-42.918824.4094-14.2993
320.52621.4986-0.283417.8282-2.82720.9441-0.2293-0.101-0.2573-0.4772-0.0443-0.21250.3457-0.0090.27370.3512-0.04250.04690.6752-0.00530.5426-42.57413.6864-14.2339
332.41090.74351.00772.6527-0.53.09880.0991-0.0602-0.1011-0.2375-0.05310.29390.22670.1367-0.0460.18160.0010.12340.4591-0.09670.4825-63.99118.5063-17.9593
346.7689-5.59890.18824.6637-0.19390.05110.1776-0.0756-0.2032-0.3584-0.04130.2230.17690.0066-0.13640.6738-0.1035-0.06260.6868-0.05850.6732-61.6725-63.445-40.8029
355.5054-0.03042.16556.58832.02213.1509-0.1251-0.20240.49690.30010.2861-0.4479-0.1833-0.3933-0.1610.0361-0.03270.03590.60420.00840.5613-47.278-57.3705-45.1902
361.79371.20091.73912.0210.81053.34020.1137-0.52310.0725-0.1478-0.26110.0475-0.0765-0.10620.14730.19230.03510.06120.4826-0.0190.5443-67.4507-61.7906-52.3592
370.7904-0.68831.04430.7311-1.18052.06070.08440.26270.20490.0119-0.0334-0.1374-0.17830.0171-0.0510.42150.090.00830.4558-0.02740.7572-91.2034-60.7033-68.1964
381.52340.26410.00391.2784-1.05890.915-0.1545-0.4287-0.45120.0760.2950.1065-0.1272-0.2864-0.14050.46870.04370.04160.72-0.03240.7975-113.1068-60.2303-42.7966
392.7031-0.121-0.96510.62430.14491.4716-0.0135-0.0790.1652-0.00870.00990.11790.0829-0.07040.00360.26680.1199-0.0790.4418-0.05250.5937-92.6206-59.4951-56.3034
400.9677-0.23591.00020.1017-0.11871.45740.0316-0.2252-0.082-0.08660.132-0.03770.04660.2487-0.16360.5888-0.00620.11380.62630.11990.713250.527520.1712-14.5769
413.8231-0.98011.00742.21080.70491.84820.1207-0.0187-0.119-0.0781-0.1607-0.08830.45850.03840.040.252-0.09940.07010.39190.02450.424623.855922.1152-16.8301
420.17360.03070.05011.87332.77444.1094-0.0979-0.18580.2832-0.7052-0.13770.1629-1.0486-0.16380.23560.4154-0.0716-0.15620.7806-0.00040.799224.676440.011-11.7503
432.1283-0.0031-0.13292.3566-0.40512.4514-0.095-0.04050.2426-0.07070.01780.0504-0.0170.21610.07720.1099-0.05290.03270.48280.04220.425140.264235.0203-15.5395
442.0901-1.2134-0.73412.29930.57935.08750.1602-0.1150.2713-0.1936-0.1259-0.1303-0.3830.267-0.03430.2091-0.1873-0.06130.45590.03440.580749.307346.2304-19.7881
450.71670.1152-0.4580.67260.08962.30860.0447-0.0286-0.20660.158-0.11610.14210.3573-0.35040.07140.29330.0447-0.01090.4009-0.07050.6268-129.7954-63.3337-76.9207
464.14040.83741.08893.5202-0.18693.27770.1772-0.1858-0.10850.4502-0.10810.0255-0.0799-0.0989-0.0690.20560.15130.00050.35440.01880.5598-117.3894-60.3551-73.682
470.03470.00360.00330.00210.0010.0029-0.1244-0.05430.0704-0.02270.09330.0142-0.03580.0090.03111.13610.2195-0.09510.84930.02010.8875-115.8386-42.588-78.8009
481.6135-0.3989-0.46612.34360.22711.75150.0562-0.03590.09510.1631-0.17690.0005-0.34370.00350.12060.34710.0997-0.02680.47780.01340.6012-136.4737-41.1049-74.9959
490.29690.08120.18750.2366-0.22261.0705-0.04140.17290.2830.08130.0121-0.0895-0.57950.11570.02930.4272-0.01230.08510.47630.00770.7994-37.0857-58.4798-78.0824
501.8201-0.4615-0.23073.19472.02033.28060.1216-0.08110.4343-0.0563-0.052-0.1134-0.41480.0384-0.06960.34180.09350.00410.44920.00580.6065-49.8806-61.1994-74.6952
512.5278-1.999-1.92411.62531.46211.6647-0.34320.14270.09550.44810.0573-0.22640.3012-0.47830.28590.45460.0184-0.16250.8991-0.15420.8714-51.2083-78.9676-78.0058
521.4507-0.3958-0.62121.4563-0.48721.56520.0584-0.07380.08450.21160.0133-0.0757-0.2774-0.0241-0.07170.2146-0.008-0.00850.4153-0.02140.5352-31.0876-77.5738-71.5393
534.5670.94870.75050.84381.65223.7281-0.00660.1948-0.2348-0.01480.0575-0.13370.06850.2773-0.05090.23870.10690.04410.46440.01370.5931-30.0408-87.5548-82.0159
543.03650.83281.76452.9426-0.02828.28690.1836-0.0836-0.0691-0.1292-0.0077-0.18210.00940.4609-0.17590.2935-0.00590.24650.53480.08150.482919.7062-34.6977-44.3178
554.7197-1.543-4.40651.10411.70174.2393-0.1566-0.20950.1003-0.06390.5046-0.69130.14240.4616-0.3480.71410.14120.00690.8475-0.21510.952728.1193-40.188-52.2686
562.1160.22080.2990.6813-0.6980.91380.16930.15890.2154-0.0204-0.1661-0.0247-0.02430.1257-0.00330.4108-0.08140.11550.41740.02840.6315.5099-32.2691-35.1662
570.60692.45331.335212.26878.94148.69570.03720.2292-0.25071.01150.8319-0.85841.13240.2133-0.86910.3105-0.08780.19710.56360.02160.7925-23.8461-43.1057-17.7491
581.0575-0.72060.62490.5318-0.43451.21230.05010.1378-0.0109-0.0989-0.00270.1189-0.2286-0.3072-0.04740.58530.1037-0.06460.8064-0.05250.6199-36.4818-35.8343-43.813
596.42390.02025.2724.7671-2.10895.27730.019-0.29940.3609-0.3163-0.4296-0.35650.1441-0.09390.41070.78340.12270.01920.9005-0.0540.8389-45.0725-31.2547-51.5094
602.0773-0.06460.58480.9967-0.07910.93890.00190.26540.064-0.01550.00020.0725-0.4163-0.0356-0.00210.3553-0.01630.12480.4845-0.03460.5706-17.7884-35.6522-32.554
613.14330.75-0.07971.15840.54790.54620.1206-0.0719-0.48850.2801-0.1503-0.23980.42250.030.02980.532-0.11070.04950.5130.10340.561138.645-36.5558-12.5279
623.9388-0.52752.2751.9722-0.25591.33880.17150.10810.0839-0.0451-0.2116-0.0239-0.01190.14150.04010.4385-0.32880.13560.5129-0.00850.544225.9497-34.1967-15.3844
632.43680.28750.277812.19411.50650.2406-0.0054-0.26820.2683-1.7118-0.1337-0.2702-0.2087-0.1490.13910.6878-0.25390.15730.7309-0.12720.652423.7985-17.5112-10.5094
641.04480.80780.24463.2792-0.61562.73690.15760.21960.133-0.01-0.2391-0.05430.0552-0.10960.08160.2417-0.10140.02970.43210.07330.537443.4815-16.1441-16.8994
652.9655-1.6346-0.45771.46680.53174.43370.1608-0.28950.57220.3893-0.0781-0.5391-0.30540.0751-0.08280.4989-0.2154-0.05270.52190.03310.66444.707-7.5341-5.7584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 26
2X-RAY DIFFRACTION2A27 - 65
3X-RAY DIFFRACTION3A66 - 189
4X-RAY DIFFRACTION4A190 - 207
5X-RAY DIFFRACTION5B6 - 15
6X-RAY DIFFRACTION6B16 - 58
7X-RAY DIFFRACTION7B66 - 189
8X-RAY DIFFRACTION8B190 - 207
9X-RAY DIFFRACTION9C6 - 26
10X-RAY DIFFRACTION10C27 - 61
11X-RAY DIFFRACTION11C66 - 186
12X-RAY DIFFRACTION12C187 - 207
13X-RAY DIFFRACTION13D6 - 58
14X-RAY DIFFRACTION14D65 - 189
15X-RAY DIFFRACTION15D190 - 207
16X-RAY DIFFRACTION16E2 - 44
17X-RAY DIFFRACTION17E45 - 96
18X-RAY DIFFRACTION18E97 - 129
19X-RAY DIFFRACTION19E130 - 226
20X-RAY DIFFRACTION20E227 - 330
21X-RAY DIFFRACTION21F4 - 38
22X-RAY DIFFRACTION22F39 - 108
23X-RAY DIFFRACTION23F109 - 129
24X-RAY DIFFRACTION24F130 - 280
25X-RAY DIFFRACTION25F281 - 330
26X-RAY DIFFRACTION26G2 - 35
27X-RAY DIFFRACTION27G36 - 109
28X-RAY DIFFRACTION28G110 - 129
29X-RAY DIFFRACTION29G130 - 330
30X-RAY DIFFRACTION30H3 - 38
31X-RAY DIFFRACTION31H39 - 103
32X-RAY DIFFRACTION32H104 - 129
33X-RAY DIFFRACTION33H130 - 330
34X-RAY DIFFRACTION34I7 - 26
35X-RAY DIFFRACTION35I27 - 60
36X-RAY DIFFRACTION36I66 - 170
37X-RAY DIFFRACTION37I171 - 207
38X-RAY DIFFRACTION38J7 - 58
39X-RAY DIFFRACTION39J66 - 207
40X-RAY DIFFRACTION40K3 - 24
41X-RAY DIFFRACTION41K25 - 108
42X-RAY DIFFRACTION42K109 - 129
43X-RAY DIFFRACTION43K130 - 226
44X-RAY DIFFRACTION44K227 - 330
45X-RAY DIFFRACTION45L3 - 44
46X-RAY DIFFRACTION46L45 - 109
47X-RAY DIFFRACTION47L110 - 129
48X-RAY DIFFRACTION48L130 - 330
49X-RAY DIFFRACTION49M2 - 44
50X-RAY DIFFRACTION50M45 - 109
51X-RAY DIFFRACTION51M110 - 129
52X-RAY DIFFRACTION52M130 - 280
53X-RAY DIFFRACTION53M281 - 332
54X-RAY DIFFRACTION54N7 - 45
55X-RAY DIFFRACTION55N46 - 61
56X-RAY DIFFRACTION56N66 - 186
57X-RAY DIFFRACTION57N187 - 207
58X-RAY DIFFRACTION58O7 - 45
59X-RAY DIFFRACTION59O46 - 61
60X-RAY DIFFRACTION60O65 - 207
61X-RAY DIFFRACTION61P3 - 44
62X-RAY DIFFRACTION62P45 - 108
63X-RAY DIFFRACTION63P109 - 129
64X-RAY DIFFRACTION64P130 - 280
65X-RAY DIFFRACTION65P281 - 330

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