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- PDB-5cll: Truncated Ran wild type in complex with GDP-BeF and RanBD1 -

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Basic information

Entry
Database: PDB / ID: 5cll
TitleTruncated Ran wild type in complex with GDP-BeF and RanBD1
Components
  • E3 SUMO-protein ligase RanBP2
  • GTP-binding nuclear protein Ran
KeywordsHYDROLASE / GTPase / nuclear transport / Ran binding protein
Function / homology
Function and homology information


cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / nuclear pore cytoplasmic filaments / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / manchette / cellular response to mineralocorticoid stimulus ...cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / nuclear pore cytoplasmic filaments / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / manchette / cellular response to mineralocorticoid stimulus / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Transport of the SLBP independent Mature mRNA / importin-alpha family protein binding / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / NLS-bearing protein import into nucleus / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / nuclear export / SUMOylation of RNA binding proteins / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / Transferases; Acyltransferases; Aminoacyltransferases / kinase activator activity / SUMO transferase activity / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / centrosome localization / MicroRNA (miRNA) biogenesis / regulation of gluconeogenesis / Viral Messenger RNA Synthesis / DNA metabolic process / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / dynein intermediate chain binding / mitotic sister chromatid segregation / SUMOylation of DNA replication proteins / protein sumoylation / ribosomal large subunit export from nucleus / spermatid development / Regulation of HSF1-mediated heat shock response / viral process / positive regulation of protein binding / mRNA transport / sperm flagellum / nuclear pore / SUMOylation of DNA damage response and repair proteins / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / protein export from nucleus / Resolution of Sister Chromatid Cohesion / response to amphetamine / SUMOylation of chromatin organization proteins / HCMV Late Events / mitotic spindle organization / male germ cell nucleus / hippocampus development / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / recycling endosome / positive regulation of protein import into nucleus / ISG15 antiviral mechanism / small GTPase binding / protein import into nucleus / HCMV Early Events / Separation of Sister Chromatids / GDP binding / Signaling by ALK fusions and activated point mutants / nuclear envelope / melanosome / protein folding / mitotic cell cycle / G protein activity / actin cytoskeleton organization / snRNP Assembly / midbody / nuclear membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / intracellular membrane-bounded organelle / GTPase activity / chromatin binding
Similarity search - Function
Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Ran GTPase / Small GTPase Ran-type domain profile. / Zinc finger domain ...Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Ran GTPase / Small GTPase Ran-type domain profile. / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / PH-domain like / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / Roll / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / GUANOSINE-5'-DIPHOSPHATE / E3 SUMO-protein ligase RanBP2 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsVetter, I.R. / Brucker, S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Catalysis of GTP Hydrolysis by Small GTPases at Atomic Detail by Integration of X-ray Crystallography, Experimental, and Theoretical IR Spectroscopy.
Authors: Rudack, T. / Jenrich, S. / Brucker, S. / Vetter, I.R. / Gerwert, K. / Kotting, C.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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
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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: E3 SUMO-protein ligase RanBP2
C: GTP-binding nuclear protein Ran
D: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,44010
Polymers81,3734
Non-polymers1,0676
Water59433
1
A: GTP-binding nuclear protein Ran
B: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2205
Polymers40,6872
Non-polymers5343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: GTP-binding nuclear protein Ran
D: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2205
Polymers40,6872
Non-polymers5343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.600, 55.780, 122.930
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A8 - 187
2111C8 - 187
1121B17 - 152
2121D17 - 152

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999997, -0.000702, 0.002212), (-0.000708, -0.999996, 0.002752), (0.00221, -0.002753, -0.999994)25.21118, -28.38302, 61.44887
3given(1), (1), (1)
4given(0.999998, -0.000485, 0.002079), (-0.000489, -0.999998, 0.002131), (0.002078, -0.002132, -0.999996)25.21675, -28.3504, 61.49931

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 21729.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET3d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62826
#2: Protein E3 SUMO-protein ligase RanBP2 / 358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding ...358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding protein 2 / RanBP2 / p270


Mass: 18957.402 Da / Num. of mol.: 2 / Fragment: Ran binding domain 1, residues 1155-1321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANBP2, NUP358 / Plasmid: pGEX4T1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P49792, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 4 types, 39 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 18 % PEG 4000, 250 mM ammonium sulfate, 100 mM MES pH 6.25, 1 mM BeF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9797 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 21, 2014
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.446→46.806 Å / Num. obs: 24587 / % possible obs: 95.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.17
Reflection shellResolution: 2.446→2.51 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.291 / % possible all: 75.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rrp

1rrp


Resolution: 2.45→46.806 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.89 / SU B: 22.852 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.91 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27225 1230 5 %RANDOM
Rwork0.23466 ---
obs0.23653 23356 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.385 Å2
Baniso -1Baniso -2Baniso -3
1--4.18 Å20 Å20.83 Å2
2--1.77 Å20 Å2
3---2.41 Å2
Refinement stepCycle: 1 / Resolution: 2.45→46.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5168 0 66 33 5267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.025377
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9737267
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52523.625251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79815969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6461537
X-RAY DIFFRACTIONr_chiral_restr0.090.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214033
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 / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A14421
22B11131.05
LS refinement shellResolution: 2.446→2.509 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 68 -
Rwork0.328 1297 -
obs--74.51 %
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)
13.2901-1.4488-0.84933.62890.90443.5579-0.0988-0.17130.14770.2255-0.0567-0.30330.03550.20370.15550.04520.0114-0.01970.0430.01240.044414.6906-11.300813.2065
24.0287-3.08420.50063.27320.63071.7343-0.2159-0.415-0.16870.29810.19250.03370.25760.06560.02330.13040.03040.06170.19620.08460.074612.2568-20.344613.0501
33.29522.8982-1.31917.507-2.46213.3482-0.02510.4518-0.2304-0.2823-0.0335-0.60140.15560.01710.05860.03750.02610.00890.1393-0.03790.033919.3979-17.2751-1.2366
42.2089-0.2284-1.10692.10990.69992.52520.05970.2649-0.0673-0.1221-0.1350.0396-0.006-0.27050.07540.0505-0.0029-0.01720.1141-0.02180.01155.6997-11.63743.4302
55.6715-3.4556-5.85454.3644.278210.5129-0.3666-0.1053-0.19520.43320.38040.51460.7661-0.0425-0.01380.1475-0.04780.01590.1768-0.04810.3771-6.0471-25.25828.514
68.84051.5854-1.43395.08720.52062.234-0.164-0.7463-0.2922-0.03690.1123-0.0318-0.0984-0.13270.05170.07950.00390.01680.1823-0.02460.0538-1.04982.277622.5738
74.5178-0.0931-0.50893.33320.97491.6657-0.08-0.37230.07810.11870.00490.3462-0.2802-0.06270.07510.1070.00880.02080.1173-0.03980.054-3.23082.915724.9729
85.0657-0.67760.49983.6936-1.64245.1663-0.1052-0.24590.5925-0.0692-0.0352-0.2631-0.20290.21620.14040.0580.0043-0.02120.1238-0.12280.1740.16569.718824.8405
93.08571.29010.77212.91590.83144.0939-0.17890.3021-0.062-0.2285-0.0266-0.2672-0.04320.22080.20540.0396-0.01140.01540.07930.00430.0605-10.7684-17.053748.2885
102.24312.25520.01593.0380.76831.0297-0.12890.24780.1128-0.2460.13990.0119-0.26020.0715-0.0110.1281-0.0477-0.06790.18520.03330.0985-12.4907-8.978649.7217
115.7863-4.68240.549227.8107-6.1542.1814-0.1071-0.51010.32740.58570.0184-0.9003-0.35990.17460.08870.1372-0.0228-0.03780.1606-0.08170.0986-5.2622-9.23963.1261
121.62170.35150.72391.99040.64912.65420.0268-0.24630.10340.0872-0.15120.02480.029-0.19740.12430.05540.00090.01740.0765-0.04080.0423-19.6489-16.573858.0248
135.1692.19886.22034.33793.728911.3877-0.27550.06220.1238-0.28830.12960.5241-0.4613-0.010.1460.1060.076-0.01370.1337-0.06070.312-31.2293-3.088753.4199
148.8307-1.24970.53435.0331-0.44732.191-0.29410.33150.07860.05510.21340.1198-0.0602-0.2990.08070.0657-0.016-0.00150.1796-0.09260.0822-28.7401-30.256239.2383
154.45430.19930.59853.45820.9252.2047-0.09060.3732-0.0554-0.18110.04050.21920.23990.06120.05020.0879-0.02410.00110.1316-0.06660.0552-27.1904-31.279436.5244
165.316-0.3559-0.5013.0663-1.46755.409-0.11110.2859-0.6903-0.007-0.0067-0.2650.26230.15280.11780.0594-0.01490.02510.1018-0.11120.1836-25.1375-37.990436.6902
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 44
2X-RAY DIFFRACTION2A45 - 87
3X-RAY DIFFRACTION3A88 - 112
4X-RAY DIFFRACTION4A113 - 186
5X-RAY DIFFRACTION5B16 - 29
6X-RAY DIFFRACTION6B30 - 56
7X-RAY DIFFRACTION7B57 - 102
8X-RAY DIFFRACTION8B103 - 150
9X-RAY DIFFRACTION9C8 - 43
10X-RAY DIFFRACTION10C44 - 92
11X-RAY DIFFRACTION11C93 - 112
12X-RAY DIFFRACTION12C113 - 186
13X-RAY DIFFRACTION13D15 - 29
14X-RAY DIFFRACTION14D30 - 53
15X-RAY DIFFRACTION15D54 - 102
16X-RAY DIFFRACTION16D103 - 150

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