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- PDB-6d88: Tubulin-RB3_SLD-TTL in complex with compound 13f -

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Basic information

Entry
Database: PDB / ID: 6d88
TitleTubulin-RB3_SLD-TTL in complex with compound 13f
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta chain
  • Tubulin tyrosine ligase
KeywordsCELL CYCLE / Microtubule Inhibitor / Colchicine / Cancer
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / microtubule depolymerization / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / ATP-grasp fold, A domain / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Dna Ligase; domain 1 / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chem-G9K / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin tyrosine ligase / Tubulin beta chain / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.853 Å
AuthorsKumar, G. / Wang, Y. / Li, W. / White, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA148706 United States
CitationJournal: J. Med. Chem. / Year: 2018
Title: Structural Modification of the 3,4,5-Trimethoxyphenyl Moiety in the Tubulin Inhibitor VERU-111 Leads to Improved Antiproliferative Activities.
Authors: Wang, Q. / Arnst, K.E. / Wang, Y. / Kumar, G. / Ma, D. / Chen, H. / Wu, Z. / Yang, J. / White, S.W. / Miller, D.D. / Li, W.
History
DepositionApr 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
E: Stathmin-4
F: Tubulin tyrosine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,03320
Polymers261,3056
Non-polymers3,72814
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.536, 157.894, 182.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 2 through 273 or resid 284...
21(chain D and (resid 2 through 121 or (resid 122...
12(chain A and (resid 1 through 279 or (resid 280...
22(chain C and (resid 1 through 162 or (resid 163...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGLEULEU(chain B and (resid 2 through 273 or resid 284...BB2 - 2732 - 273
121LEULEUPROPRO(chain B and (resid 2 through 273 or resid 284...BB284 - 358284 - 358
131ARGARGARGARG(chain B and (resid 2 through 273 or resid 284...BB359359
141ARGARGALAALA(chain B and (resid 2 through 273 or resid 284...BB2 - 4282 - 428
151ARGARGALAALA(chain B and (resid 2 through 273 or resid 284...BB2 - 4282 - 428
161ARGARGALAALA(chain B and (resid 2 through 273 or resid 284...BB2 - 4282 - 428
171ARGARGALAALA(chain B and (resid 2 through 273 or resid 284...BB2 - 4282 - 428
211ARGARGARGARG(chain D and (resid 2 through 121 or (resid 122...DD2 - 1212 - 121
221LYSLYSLYSLYS(chain D and (resid 2 through 121 or (resid 122...DD122122
231METMETASPASP(chain D and (resid 2 through 121 or (resid 122...DD1 - 4311 - 431
241METMETASPASP(chain D and (resid 2 through 121 or (resid 122...DD1 - 4311 - 431
251METMETASPASP(chain D and (resid 2 through 121 or (resid 122...DD1 - 4311 - 431
261METMETASPASP(chain D and (resid 2 through 121 or (resid 122...DD1 - 4311 - 431
112METMETGLUGLU(chain A and (resid 1 through 279 or (resid 280...AA1 - 2791 - 279
122LYSLYSALAALA(chain A and (resid 1 through 279 or (resid 280...AA280 - 281280 - 281
132METMETVALVAL(chain A and (resid 1 through 279 or (resid 280...AA1 - 4371 - 437
142METMETVALVAL(chain A and (resid 1 through 279 or (resid 280...AA1 - 4371 - 437
152METMETVALVAL(chain A and (resid 1 through 279 or (resid 280...AA1 - 4371 - 437
162METMETVALVAL(chain A and (resid 1 through 279 or (resid 280...AA1 - 4371 - 437
212METMETGLYGLY(chain C and (resid 1 through 162 or (resid 163...CC1 - 1621 - 162
222LYSLYSLYSLYS(chain C and (resid 1 through 162 or (resid 163...CC163163
232METMETVALVAL(chain C and (resid 1 through 162 or (resid 163...CC1 - 4401 - 440
242METMETVALVAL(chain C and (resid 1 through 162 or (resid 163...CC1 - 4401 - 440
252METMETVALVAL(chain C and (resid 1 through 162 or (resid 163...CC1 - 4401 - 440
262METMETVALVAL(chain C and (resid 1 through 162 or (resid 163...CC1 - 4401 - 440

NCS ensembles :
ID
1
2

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Components

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Protein , 4 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50041.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AGU7, UniProt: P02554*PLUS
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16844.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043
#4: Protein Tubulin tyrosine ligase


Mass: 44378.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

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Non-polymers , 8 types, 106 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: 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
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-G9K / [2-(1H-indol-3-yl)-1H-imidazol-4-yl](8-methoxy-1,4-benzodioxin-6-yl)methanone


Mass: 373.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H15N3O4 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% PEG 4000, 5% Glycerol, 0.1 M MES, 30 mM CaCl2, 30 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 71390 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 51.35 Å2 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.095 / Rrim(I) all: 0.246 / Χ2: 0.974 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.927.10.83647110.7380.3380.9020.992100
2.92-2.9970.72446670.8030.2950.7830.985100
2.99-3.0770.58646810.8430.2380.6331.01100
3.07-3.166.90.48147340.8820.1970.521.034100
3.16-3.266.80.42346880.8740.1750.4591.028100
3.26-3.386.60.35247120.9250.1480.3821.007100
3.38-3.516.30.29847580.9360.1280.3251.021100
3.51-3.6770.26247040.9480.1060.2831.014100
3.67-3.8770.23347500.960.0950.2520.967100
3.87-4.116.90.21347290.9580.0870.230.937100
4.11-4.436.60.19447600.9560.0810.2110.9100
4.43-4.876.60.18147760.9590.0760.1970.859100
4.87-5.5870.18248230.9640.0740.1960.829100
5.58-7.026.40.17248620.9620.0730.1870.808100
7.02-506.50.2150350.9180.0890.2291.21499.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.853→45.65 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.89
RfactorNum. reflection% reflection
Rfree0.2461 4083 5.88 %
Rwork0.1919 --
obs0.1952 69423 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 183.89 Å2 / Biso mean: 59.2183 Å2 / Biso min: 19.4 Å2
Refinement stepCycle: final / Resolution: 2.853→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17202 0 250 92 17544
Biso mean--62.22 43.29 -
Num. residues----2178
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B3950X-RAY DIFFRACTION11.459TORSIONAL
12D3950X-RAY DIFFRACTION11.459TORSIONAL
21A3871X-RAY DIFFRACTION11.459TORSIONAL
22C3871X-RAY DIFFRACTION11.459TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8531-2.88670.3592950.28831679177473
2.8867-2.92190.32751320.26742011214387
2.9219-2.95890.33851220.27032102222492
2.9589-2.99780.32621190.26492200231995
2.9978-3.03890.33291440.25632237238198
3.0389-3.08230.34181410.25012254239598
3.0823-3.12830.331410.24642261240299
3.1283-3.17710.27411470.23882264241199
3.1771-3.22920.30511380.23892268240699
3.2292-3.28490.32721510.2332303245499
3.2849-3.34460.26861370.22462262239999
3.3446-3.40890.29041380.21832281241999
3.4089-3.47850.28771540.20842264241899
3.4785-3.55410.30431350.20382288242399
3.5541-3.63670.27171570.19642284244199
3.6367-3.72760.25321330.183422972430100
3.7276-3.82840.22171370.18362292242999
3.8284-3.9410.24531570.17242271242899
3.941-4.06810.21031460.16632303244999
4.0681-4.21340.24861350.161123262461100
4.2134-4.38190.19811590.15722285244499
4.3819-4.58120.21831390.14412288242798
4.5812-4.82250.17271300.14562301243199
4.8225-5.12420.18671470.14762322246999
5.1242-5.51930.20631420.169223492491100
5.5193-6.07360.21891370.182623432480100
6.0736-6.94980.23451490.18912363251299
6.9498-8.74590.19961570.17952351250899
8.7459-45.6560.24221640.21042291245592
Refinement TLS params.Method: refined / Origin x: 17.2047 Å / Origin y: -44.289 Å / Origin z: -26.6618 Å
111213212223313233
T0.1436 Å2-0.0281 Å2-0.002 Å2-0.2706 Å2-0.0106 Å2--0.3166 Å2
L0.225 °20.0295 °20.1791 °2-0.7413 °20.6571 °2--1.182 °2
S-0.064 Å °-0.0141 Å °-0.0161 Å °-0.0516 Å °0.1073 Å °0.0076 Å °-0.0476 Å °0.0686 Å °-0.0361 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 437
2X-RAY DIFFRACTION1allA501
3X-RAY DIFFRACTION1allB2 - 428
4X-RAY DIFFRACTION1allB501
5X-RAY DIFFRACTION1allC1 - 440
6X-RAY DIFFRACTION1allC501
7X-RAY DIFFRACTION1allD1 - 431
8X-RAY DIFFRACTION1allE6 - 141
9X-RAY DIFFRACTION1allF1 - 380
10X-RAY DIFFRACTION1allL1
11X-RAY DIFFRACTION1allM1 - 2
12X-RAY DIFFRACTION1allN1 - 2
13X-RAY DIFFRACTION1allH1 - 3
14X-RAY DIFFRACTION1allW1 - 126
15X-RAY DIFFRACTION1allO1 - 2
16X-RAY DIFFRACTION1allG1

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