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- PDB-2j0q: The crystal structure of the Exon Junction Complex at 3.2 A resolution -

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Basic information

Entry
Database: PDB / ID: 2j0q
TitleThe crystal structure of the Exon Junction Complex at 3.2 A resolution
Components
  • 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
  • ATP-DEPENDENT RNA HELICASE DDX48
  • PROTEIN CASC3
  • PROTEIN MAGO NASHI HOMOLOG
  • RNA-BINDING PROTEIN 8A
KeywordsHYDROLASE / MRNA PROCESSING / MRNA SPLICING / MRNA TRANSPORT / NUCLEAR PROTEIN / DEAD-BOX HELICASE / RNA-BINDING
Function / homology
Function and homology information


exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / intracellular mRNA localization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / regulation of mRNA processing ...exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / intracellular mRNA localization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / regulation of mRNA processing / negative regulation of excitatory postsynaptic potential / Deadenylation of mRNA / embryonic cranial skeleton morphogenesis / poly(A) binding / mRNA 3'-end processing / M-decay: degradation of maternal mRNAs by maternally stored factors / U2-type catalytic step 1 spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of alternative mRNA splicing, via spliceosome / exploration behavior / associative learning / ribonucleoprotein complex binding / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cellular response to brain-derived neurotrophic factor stimulus / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of translation / mRNA splicing, via spliceosome / ISG15 antiviral mechanism / Regulation of expression of SLITs and ROBOs / RNA stem-loop binding / cytoplasmic stress granule / rRNA processing / regulation of translation / nuclear membrane / RNA helicase activity / postsynapse / negative regulation of translation / nuclear speck / RNA helicase / neuronal cell body / mRNA binding / dendrite / ubiquitin protein ligase binding / nucleolus / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Mago nashi protein / Mago nashi / Protein CASC3 / CASC3/Barentsz eIF4AIII binding / CASC3/Barentsz eIF4AIII binding / Btz domain / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily ...Mago nashi protein / Mago nashi / Protein CASC3 / CASC3/Barentsz eIF4AIII binding / CASC3/Barentsz eIF4AIII binding / Btz domain / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily / Mago nashi protein / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / RRM (RNA recognition motif) domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / RNA (> 10) / Protein CASC3 / Eukaryotic initiation factor 4A-III / Protein mago nashi homolog / RNA-binding protein 8A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBono, F. / Ebert, J. / Lorentzen, E. / Conti, E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: The Crystal Structure of the Exon Junction Complex Reveals How It Maintains a Stable Grip on Mrna.
Authors: Bono, F. / Ebert, J. / Lorentzen, E. / Conti, E.
History
DepositionAug 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: ATP-DEPENDENT RNA HELICASE DDX48
B: ATP-DEPENDENT RNA HELICASE DDX48
C: PROTEIN MAGO NASHI HOMOLOG
D: RNA-BINDING PROTEIN 8A
E: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
F: PROTEIN MAGO NASHI HOMOLOG
G: RNA-BINDING PROTEIN 8A
H: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
I: PROTEIN CASC3
T: PROTEIN CASC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,96414
Polymers197,90310
Non-polymers1,0614
Water181
1
A: ATP-DEPENDENT RNA HELICASE DDX48
C: PROTEIN MAGO NASHI HOMOLOG
D: RNA-BINDING PROTEIN 8A
E: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
T: PROTEIN CASC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4827
Polymers98,9525
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12990 Å2
ΔGint-57.8 kcal/mol
Surface area28310 Å2
MethodPISA
2
B: ATP-DEPENDENT RNA HELICASE DDX48
F: PROTEIN MAGO NASHI HOMOLOG
G: RNA-BINDING PROTEIN 8A
H: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
I: PROTEIN CASC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4827
Polymers98,9525
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12830 Å2
ΔGint-59.3 kcal/mol
Surface area27880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.150, 161.240, 193.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22F
13D
23G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 440
2111B1 - 440
1121C1 - 300
2121F1 - 300
1131D1 - 300
2131G1 - 300

NCS ensembles :
ID
1
2
3

NCS oper: (Code: given
Matrix: (0.99741, -0.00966, 0.07122), (-0.00979, -0.99995, 0.00152), (0.07121, -0.00221, -0.99746)
Vector: -2.9803, 58.15499, 96.91725)

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Components

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Protein , 4 types, 8 molecules ABCFDGIT

#1: Protein ATP-DEPENDENT RNA HELICASE DDX48 / EIF4AIII RNA-HELICASE / DEAD BOX PROTEIN 48 / EUKARYOTIC INITIATION FACTOR 4A-LIKE NUK-34 / HNMP ...EIF4AIII RNA-HELICASE / DEAD BOX PROTEIN 48 / EUKARYOTIC INITIATION FACTOR 4A-LIKE NUK-34 / HNMP 265 / NUCLEAR MATRIX PROTEIN 265 / EUKARYOTIC TRANSLATION INITIATION FACTOR 4A ISOFORM 3


Mass: 46799.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38919
#2: Protein PROTEIN MAGO NASHI HOMOLOG / MGN


Mass: 17189.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61326
#3: Protein RNA-BINDING PROTEIN 8A / Y14 / RNA-BINDING MOTIF PROTEIN 8A / RIBONUCLEOPROTEIN RBM8A / RNA-BINDING PROTEIN Y14 / BINDER OF ...Y14 / RNA-BINDING MOTIF PROTEIN 8A / RIBONUCLEOPROTEIN RBM8A / RNA-BINDING PROTEIN Y14 / BINDER OF OVCA1-1 / BOV-1


Mass: 12701.285 Da / Num. of mol.: 2 / Fragment: RESIDUES 66-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5S9
#5: Protein PROTEIN CASC3 / BARENTSZ / CANCER SUSCEPTIBILITY CANDIDATE GENE 3 PROTEIN / METASTATIC LYMPH NODE PROTEIN 51 MLN 51 ...BARENTSZ / CANCER SUSCEPTIBILITY CANDIDATE GENE 3 PROTEIN / METASTATIC LYMPH NODE PROTEIN 51 MLN 51 PROTEIN BARENTSZ PROTEIN / BTZ


Mass: 17713.482 Da / Num. of mol.: 2 / Fragment: RESIDUES 137-286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15234

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RNA chain , 1 types, 2 molecules EH

#4: RNA chain 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'


Mass: 4547.529 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 3 types, 5 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 55.5 %
Crystal growDetails: 10% PEG 4000, 200 MM AMMONIUM ACETATE, 10 MM CACL2, NA CACODYLATE PH 6.5 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 34926 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.24 / Rsym value: 0.24 / Net I/σ(I): 4.8
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / Rsym value: 0.68 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1FUU, 1FUK, AND 1P27

1fuu

1fuk

1p27


Resolution: 3.2→46.98 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.843 / SU B: 49.443 / SU ML: 0.416 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.525 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1747 5 %RANDOM
Rwork0.232 ---
obs0.235 33179 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: 66.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2---0.81 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 3.2→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10919 242 64 1 11226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211464
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210334
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.98915561
X-RAY DIFFRACTIONr_angle_other_deg0.815323952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77251362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34523.681546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.051151934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6571591
X-RAY DIFFRACTIONr_chiral_restr0.0780.21730
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212551
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022352
X-RAY DIFFRACTIONr_nbd_refined0.2060.22472
X-RAY DIFFRACTIONr_nbd_other0.1810.210715
X-RAY DIFFRACTIONr_nbtor_refined0.1780.25436
X-RAY DIFFRACTIONr_nbtor_other0.0840.26528
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1440.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3871.57400
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.631210958
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.58835140
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0784.54603
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
11A5989tight positional0.020.05
12B5989tight positional0.020.05
21C2274tight positional0.020.05
22F2274tight positional0.020.05
31D1309tight positional0.010.05
32G1309tight positional0.010.05
11A5989tight thermal0.030.5
12B5989tight thermal0.030.5
21C2274tight thermal0.030.5
22F2274tight thermal0.030.5
31D1309tight thermal0.020.5
32G1309tight thermal0.020.5
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 130 -
Rwork0.37 2455 -
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)
11.11990.5747-0.05371.3495-0.40241.39-0.018-0.0789-0.1610.0947-0.04460.09080.1767-0.0940.0625-0.25360.02390.0483-0.170.0315-0.1564-0.95122.2925.807
22.0382-0.7681-1.01132.64221.18493.22240.04560.1575-0.0277-0.14810.0152-0.331-0.03270.2932-0.0607-0.344-0.00480.0206-0.19950.0524-0.213515.40536.54110.133
30.923-0.2755-0.17571.7361-0.31541.46580.0294-0.00680.17080.091-0.0344-0.1849-0.24430.14940.0049-0.2828-0.00130.0583-0.22920.0294-0.22529.3760.37627.319
41.49381.321-0.64333.7946-0.7344.82440.181-0.103-0.22250.3985-0.1934-1.0908-0.07180.59610.0124-0.0817-0.0021-0.13260.00170.06940.132822.87448.88542.544
50.7237-0.4298-0.19432.4235-0.04151.17540.0740.00930.11670.0851-0.10380.2648-0.1853-0.13960.0299-0.1361-0.03840.0043-0.1578-0.0193-0.196-2.30635.88671.067
61.62770.61620.58982.49050.40372.48870.0011-0.11070.01690.56570.0433-0.4733-0.09320.2768-0.04450.0134-0.0704-0.0778-0.13890.0498-0.154712.74521.4787.879
71.6941-0.12130.35012.5198-0.80821.51130.10350.0543-0.08520.0587-0.1042-0.23380.26940.12520.0007-0.2475-0.0464-0.0379-0.21670.0337-0.25677.756-2.22870.173
80.3054-1.1303-0.31194.5965-0.06343.90160.1735-0.01940.3116-0.4057-0.3445-1.05070.30540.5550.1709-0.13550.02880.07910.01680.0730.113722.3329.14555.881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 257
2X-RAY DIFFRACTION2A258 - 411
3X-RAY DIFFRACTION3C4 - 146
4X-RAY DIFFRACTION4D66 - 154
5X-RAY DIFFRACTION5B20 - 257
6X-RAY DIFFRACTION6B258 - 411
7X-RAY DIFFRACTION7F4 - 146
8X-RAY DIFFRACTION8G66 - 154

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