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- PDB-3tax: A Neutral Diphosphate Mimic Crosslinks the Active Site of Human O... -

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Basic information

Entry
Database: PDB / ID: 3tax
TitleA Neutral Diphosphate Mimic Crosslinks the Active Site of Human O-GlcNAc Transferase
Components
  • Casein kinase II subunit alpha
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / thiocarbamate crosslink / covalent inhibitor / gylcosyltransferase inhibitor / O-GlcNAc Transferase / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / negative regulation of stem cell population maintenance ...negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / negative regulation of stem cell population maintenance / protein O-linked glycosylation / NSL complex / 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 / regulation of glycolytic process / RIPK1-mediated regulated necrosis / regulation of gluconeogenesis / Receptor Mediated Mitophagy / regulation of synapse assembly / Formation of WDR5-containing histone-modifying complexes / Synthesis of PC / Sin3-type complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / positive regulation of stem cell population maintenance / phosphatidylinositol-3,4,5-trisphosphate binding / hemopoiesis / positive regulation of proteolysis / negative regulation of apoptotic signaling pathway / histone acetyltransferase complex / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / positive regulation of lipid biosynthetic process / mitophagy / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / response to nutrient / positive regulation of TORC1 signaling / negative regulation of cell migration / positive regulation of translation / Signal transduction by L1 / cell projection / cellular response to glucose stimulus / Hsp90 protein binding / circadian regulation of gene expression / negative regulation of transforming growth factor beta receptor signaling pathway / response to insulin / PML body / mitochondrial membrane / protein processing / chromatin DNA binding / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / UCH proteinases / kinase activity / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cold-induced thermogenesis / HATs acetylate histones / chromatin organization / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Glycogen Phosphorylase B; / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMYL GROUP / URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsLazarus, M.B. / Jiang, J. / Pasquina, L. / Sliz, P. / Walker, S.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: A neutral diphosphate mimic crosslinks the active site of human O-GlcNAc transferase.
Authors: Jiang, J. / Lazarus, M.B. / Pasquina, L. / Sliz, P. / Walker, S.
History
DepositionAug 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Sep 13, 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 / struct_conn / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_conn.ptnr2_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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Casein kinase II subunit alpha
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,99912
Polymers164,7464
Non-polymers1,2538
Water18,3391018
1
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Casein kinase II subunit alpha
hetero molecules

A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,99912
Polymers164,7464
Non-polymers1,2538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10510 Å2
ΔGint-122 kcal/mol
Surface area52880 Å2
MethodPISA
2
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9996
Polymers82,3732
Non-polymers6264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-51 kcal/mol
Surface area28870 Å2
MethodPISA
3
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Casein kinase II subunit alpha
hetero molecules

C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,99912
Polymers164,7464
Non-polymers1,2538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10530 Å2
ΔGint-123 kcal/mol
Surface area52690 Å2
MethodPISA
4
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9996
Polymers82,3732
Non-polymers6264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-52 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.600, 136.640, 153.319
Angle α, β, γ (deg.)90.00, 103.02, 90.00
Int Tables number5
Space group name H-MI121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / O-GlcNAc transferase subunit p110 / O-linked N-acetylglucosamine transferase 110 kDa subunit


Mass: 80974.508 Da / Num. of mol.: 2 / Fragment: UNP residues 323-1041
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Production host: Escherichia coli (E. coli)
References: UniProt: O15294, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Protein/peptide Casein kinase II subunit alpha / CK II alpha


Mass: 1398.562 Da / Num. of mol.: 2 / Fragment: UNP residues 340-352 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human)
References: UniProt: P68400, non-specific serine/threonine protein kinase

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Non-polymers , 4 types, 1026 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-FOR / FORMYL GROUP


Mass: 30.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1018 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTHE INHIBITOR, 4-METHOXYPHENYL 6-ACETYL-2-BENZOXAZOLINONE- CARBOXYLATE, CROSSLINKS THE ACTIVE SITE ...THE INHIBITOR, 4-METHOXYPHENYL 6-ACETYL-2-BENZOXAZOLINONE- CARBOXYLATE, CROSSLINKS THE ACTIVE SITE OF OGT. EXPERIMENTAL EVIDENCE SUGGESTS THAT LYSINE 842 REACTS WITH ONE OF THE TWO CARBAMATES OF THE INHIBITOR, RELEASING 6-ACETYL-2-BENZOXAZOLINONE. THEN, THE NEARBY CYSTEINE 917 REACTS AGAIN WITH THE LYSINE ADDUCT TO RELEASE 4-METHOXYPHENOL AND GENERATES A COVALENT THIOCARBAMATE LINKAGE BETWEEN LYSINE 842 AND CYSTEINE 917.

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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: 3.05 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.6M Lithium Sulfate, 0.1M Bis Tris Propane pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.875→45 Å / Num. obs: 160121 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 23.74 Å2
Reflection shellResolution: 1.875→1.98 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.4 / Num. unique all: 22892 / % possible all: 97.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.11.1refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PE4

3pe4


Resolution: 1.88→37.6 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.9068 / SU R Cruickshank DPI: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 7950 5 %RANDOM
Rwork0.2191 ---
all0.22 166942 --
obs0.22 158992 99.2 %-
Displacement parametersBiso mean: 27.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.8602 Å20 Å2-2.4031 Å2
2--3.1149 Å20 Å2
3----2.2547 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: LAST / Resolution: 1.88→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11180 0 74 1018 12272
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00911574HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9815716HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4044SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes302HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1658HARMONIC5
X-RAY DIFFRACTIONt_it11574HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion16.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1514SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies10HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14130SEMIHARMONIC4
LS refinement shellResolution: 1.88→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2332 565 4.95 %
Rwork0.2172 10852 -
all0.218 11417 -
obs--99.2 %
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)
11.7568-1.01060.96732.03531.13170.4491-0.0095-0.02470.0014-0.09710.03210.1039-0.0458-0.0514-0.0225-0.06380.0977-0.09670.0950.108-0.056935.491236.5634-36.2652
20.5215-0.1487-0.3180.80840.86221.70050.0168-0.0023-0.0212-0.18350.04960.06450.0069-0.0144-0.06640.05810.0191-0.0830.03590.0717-0.058943.099832.6335-37.2162
31.9834-0.4522-1.12250.88980.26330.80150.1310.20270.1022-0.04870.01120.1593-0.1337-0.1137-0.1422-0.0630.03990.0786-0.03370.0357-0.043244.188341.265-14.9219
41.1950.63871.20152.42540.54932.27060.09720.18150.1339-0.4607-0.02890.2966-0.0594-0.2167-0.06840.0070.07450.0776-0.05670.0559-0.023724.053644.4691-2.8613
50.4662-0.13570.04780.9764-0.0970.87730.07830.1544-0.0044-0.3157-0.05510.14240.0793-0.0769-0.02320.00840.03930.0186-0.0676-0.0037-0.079723.770616.8801-2.3
6-0.03090.02730.0640.03930.04720.04670.0010.00460.0046-0.0046-0.0003-0.004-0.00750.0082-0.00070.0729-0.0013-0.08260.03030.0030.026433.202730.140143.8203
72.3353-0.7509-0.11621.2191-1.64290.4728-0.0172-0.2828-0.00790.37870.02840.2193-0.1181-0.0532-0.01120.03040.01770.1065-0.0546-0.0119-0.104531.905817.843838.5946
82.5802-0.056-2.48191.1083-2.79751.5774-0.0833-0.24210.21830.51460.17060.0938-0.1441-0.0448-0.08730.07820.0130.03270.0379-0.1029-0.018237.55322.475140.0407
90.4715-0.04870.01380.8168-0.01590.40380.052-0.04210.06030.0694-0.01890.0963-0.0396-0.0178-0.0331-0.02910.01550.1059-0.0631-0.0129-0.033826.645931.222321.9692
102.0671-0.68760.85980.0050.16151.322-0.04030.1231-0.1442-0.12760.00270.21590.1379-0.10590.03770.036-0.0054-0.10320.0082-0.01650.04297.484113.3763-4.7375
110.53820.4521-1.3711.6334-1.01122.4624-0.0701-0.1811-0.11940.1513-0.0726-0.21020.00640.35130.1427-0.04780.02970.0568-0.02750.0329-0.109367.5149-28.65482.8323
122.24350.3521.03471.34240.60160.4118-0.0456-0.1068-0.01970.17720.0116-0.2610.12930.14480.0340.02040.06080.0661-0.03510.0529-0.045555.0936-33.0224.4436
130.8342-0.0319-0.04480.9087-0.06520.4597-0.0013-0.05820.07850.0813-0.0384-0.2766-0.00590.15720.0397-0.05980.00430.0393-0.06660.0318-0.008954.5488-5.281224.9274
140.02520.0727-0.01240.0669-0.052-0.0071-0.00180.0098-0.0034-0.00790.00240.0010.00240.0038-0.00060.0606-0.0019-0.08920.00680.02460.04187.5581-18.563321.0801
151.378-2.47810.3860.09-0.4872.80630.0017-0.13-0.04650.14790.07920.37320.0092-0.3129-0.081-0.0963-0.00910.1155-0.04760.03050.032912.8919-6.271321.7457
160.2116-0.3404-0.171100.1882-0.0225-0.0037-0.00610.00250.02740.00030.0113-0.0083-0.00320.0034-0.00730.00650.09050.1538-0.01130.127315.3806-4.841833.3865
17-0.6208-2.00841.21680.1869-0.1041.08550.0549-0.1045-0.210.00270.06620.52040.1916-0.2781-0.121-0.0772-0.11290.0268-0.02950.02940.04569.8213-12.166412.7742
180.4439-0.09810.03430.70650.01110.5365-0.0369-0.0325-0.02710.1056-0.01040.03530.0555-0.01750.0473-0.0175-0.00820.0954-0.0660.0221-0.054232.7627-17.961926.4582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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