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- PDB-4j2x: CSL (RBP-Jk) with corepressor KyoT2 bound to DNA -

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Basic information

Entry
Database: PDB / ID: 4j2x
TitleCSL (RBP-Jk) with corepressor KyoT2 bound to DNA
Components
  • 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'
  • 5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'
  • Four and a half LIM domains protein 1
  • Recombining binding protein suppressor of hairless
KeywordsTRANSCRIPTION/DNA BINDING PROTEIN/DNA / LIM domain containing protein / transcription factor corepressor / DNA binding / nucleus / TRANSCRIPTION-DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


determination of heart left/right asymmetry / blood vessel endothelial cell fate specification / positive regulation of ERBB signaling pathway / regulation of generation of precursor metabolites and energy / club cell differentiation / arterial endothelial cell fate commitment / blood vessel lumenization / regulation of timing of cell differentiation / positive regulation of ephrin receptor signaling pathway / secondary heart field specification ...determination of heart left/right asymmetry / blood vessel endothelial cell fate specification / positive regulation of ERBB signaling pathway / regulation of generation of precursor metabolites and energy / club cell differentiation / arterial endothelial cell fate commitment / blood vessel lumenization / regulation of timing of cell differentiation / positive regulation of ephrin receptor signaling pathway / secondary heart field specification / pulmonary valve development / positive regulation of cell proliferation involved in heart morphogenesis / dorsal aorta morphogenesis / sebaceous gland development / endocardium morphogenesis / regulation of cell adhesion involved in heart morphogenesis / MAML1-RBP-Jkappa- ICN1 complex / aortic valve development / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / auditory receptor cell fate commitment / positive regulation of transcription of Notch receptor target / Notch-HLH transcription pathway / heart induction / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac left ventricle morphogenesis / epidermal cell fate specification / pituitary gland development / endocardium development / atrioventricular canal development / hair follicle maturation / cardiac muscle cell myoblast differentiation / myeloid dendritic cell differentiation / ventricular trabecula myocardium morphogenesis / positive regulation of BMP signaling pathway / regulation of epithelial cell proliferation / inflammatory response to antigenic stimulus / negative regulation of ossification / negative regulation of cold-induced thermogenesis / artery morphogenesis / labyrinthine layer blood vessel development / muscle organ development / ventricular septum morphogenesis / heart looping / outflow tract morphogenesis / somatic stem cell population maintenance / negative regulation of cell differentiation / hemopoiesis / humoral immune response / blood vessel remodeling / epithelial to mesenchymal transition / cell fate commitment / somitogenesis / negative regulation of stem cell proliferation / positive regulation of cardiac muscle cell proliferation / keratinocyte differentiation / Notch signaling pathway / transcription repressor complex / B cell differentiation / positive regulation of epithelial cell proliferation / stem cell proliferation / epithelial cell proliferation / protein-DNA complex / neuron differentiation / positive regulation of canonical Wnt signaling pathway / heart development / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / transmembrane transporter binding / cell population proliferation / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / protein-containing complex binding / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Four and a half LIM domains protein 1 / LAG1, DNA binding domain / Beta-trefoil DNA-binding domain / RBP-J/Cbf11/Cbf12, DNA binding / Beta-trefoil domain superfamily / RBP-J/Cbf11, DNA binding domain superfamily / RBP-Jkappa, IPT domain / Suppressor of hairless-like / Beta-trefoil DNA-binding domain / LAG1, DNA binding ...Four and a half LIM domains protein 1 / LAG1, DNA binding domain / Beta-trefoil DNA-binding domain / RBP-J/Cbf11/Cbf12, DNA binding / Beta-trefoil domain superfamily / RBP-J/Cbf11, DNA binding domain superfamily / RBP-Jkappa, IPT domain / Suppressor of hairless-like / Beta-trefoil DNA-binding domain / LAG1, DNA binding / TIG domain / LAG1, DNA binding / Beta-trefoil DNA-binding domain / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / p53-like transcription factor, DNA-binding / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Recombining binding protein suppressor of hairless / Four and a half LIM domains protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsCollins, K.J. / Kovall, R.A.
CitationJournal: Structure / Year: 2014
Title: Structure and Function of the CSL-KyoT2 Corepressor Complex: A Negative Regulator of Notch Signaling.
Authors: Collins, K.J. / Yuan, Z. / Kovall, R.A.
History
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Sep 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 / 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_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: Recombining binding protein suppressor of hairless
B: Four and a half LIM domains protein 1
C: Recombining binding protein suppressor of hairless
D: Four and a half LIM domains protein 1
E: 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'
F: 5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'
G: 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'
H: 5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7259
Polymers120,6638
Non-polymers621
Water1448
1
A: Recombining binding protein suppressor of hairless
B: Four and a half LIM domains protein 1
G: 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'
H: 5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3935
Polymers60,3314
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-28 kcal/mol
Surface area25540 Å2
MethodPISA
2
C: Recombining binding protein suppressor of hairless
D: Four and a half LIM domains protein 1
E: 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'
F: 5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'


Theoretical massNumber of molelcules
Total (without water)60,3314
Polymers60,3314
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-29 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.157, 97.293, 144.102
Angle α, β, γ (deg.)90.00, 93.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 4 molecules EGFH

#3: DNA chain 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'


Mass: 4503.949 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain 5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'


Mass: 4673.059 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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

#1: Protein Recombining binding protein suppressor of hairless / CSL / CBF-1 / Supressor of Hairless / Lag-1 / J kappa-recombination signal-binding protein / RBP-J kappa


Mass: 48224.992 Da / Num. of mol.: 2 / Fragment: Core domain (UNP residues 53-474) / Mutation: R115T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igkjrb1, Igkrsbp, RBP-Jk, Rbpj, Rbpsuh / Plasmid: PGEX-6P1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31266
#2: Protein/peptide Four and a half LIM domains protein 1 / FHL-1 / KyoT / RBP-associated molecule 14-1 / RAM14-1 / Skeletal muscle LIM-protein 1 / SLIM / SLIM-1


Mass: 2929.327 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fhl1 / Plasmid: Pet28B+ / Production host: Escherichia coli (E. coli) / References: UniProt: P97447

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Non-polymers , 2 types, 9 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPEPTIDE COMPRISES THE CSL-INTERACTION DOMAIN (UNP RESIDUES 168-194) OF ISOFORM 2 OF KYOT (UNP ...PEPTIDE COMPRISES THE CSL-INTERACTION DOMAIN (UNP RESIDUES 168-194) OF ISOFORM 2 OF KYOT (UNP P97447-2). ONLY RESIDUES 168-181 ARE ORDERED.

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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: 3.71 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 7.1
Details: 21% PEG3350, 0.1 M HEPES, pH 7.1, 0.25 M ammonium acetate, MICROBATCH, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2011
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.85→40.3 Å / Num. all: 37773 / Num. obs: 37773 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 105.45 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 13.9
Reflection shellResolution: 2.85→2.93 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.82 / Rsym value: 0.375 / % possible all: 93.96

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IAG

3iag


Resolution: 2.85→40.3 Å / Cor.coef. Fo:Fc: 0.9485 / Cor.coef. Fo:Fc free: 0.9198 / SU R Cruickshank DPI: 0.687 / σ(F): 0 / SU R Blow DPI: 0.611 / SU Rfree Blow DPI: 0.301 / SU Rfree Cruickshank DPI: 0.31 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 1898 5.02 %RANDOM
Rwork0.1884 ---
all0.1905 37773 --
obs0.1905 37773 93.96 %-
Displacement parametersBiso mean: 108.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.6996 Å20 Å29.2332 Å2
2--13.7749 Å20 Å2
3----12.0753 Å2
Refine analyzeLuzzati coordinate error obs: 0.56 Å
Refinement stepCycle: LAST / Resolution: 2.85→40.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6913 1218 4 8 8143
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3205SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes178HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1075HARMONIC5
X-RAY DIFFRACTIONt_it8456HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1084SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8795SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8456HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11688HARMONIC21.29
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion21.52
LS refinement shellResolution: 2.85→2.93 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.4375 63 4.18 %
Rwork0.3816 1444 -
all0.384 1507 -
obs--93.96 %
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)
12.2287-0.1052-2.05593.2318-0.54294.8038-0.0761-0.3578-0.14910.81420.1023-0.7160.42830.7597-0.0263-0.2417-0.0151-0.316-0.18740.0427-0.01412.0625-17.778543.7834
22.8673-0.5759-1.32122.36950.26734.34830.092-0.39360.02910.9724-0.02980.1897-0.3435-0.712-0.0622-0.0028-0.00150.0804-0.0970.0482-0.186-13.3279-11.021147.9644
33.6522-1.5431-0.08177.8413-1.43889.17310.54980.29340.6442-0.0586-0.2243-0.5632-1.5442-0.1194-0.3256-0.2256-0.05730.1117-0.26050.10990.144415.29011.549723.556
46.8331-2.8508-2.06901.6589-0.19480.01710.15270.19470.2684-0.1023-0.1335-0.78290.09740.0852-0.17090.13020.04910.09310.1689-0.0146-14.4513-1.578331.1199
55.03645.8738-3.24832.9862-0.9479-0.3753-0.0118-0.253-0.32870.1481-0.16360.54850.1274-0.9680.1753-0.3508-0.19380.11360.36490.08410.2648-24.3707-19.326339.2223
65.3986-0.5904-3.23662.76640.61613.27130.51310.90260.9096-0.9853-0.2044-0.0293-0.2771-0.437-0.30870.0330.2381-0.0205-0.23140.0591-0.1944-4.2164-14.5178-18.4153
71.4366-0.1250.01671.89970.35785.26940.21090.0106-0.0939-0.1567-0.2903-0.075-0.00090.19940.0795-0.2306-0.053-0.0241-0.1298-0.03280.0066-5.6869-19.87039.8126
812.0889-4.49440.55296.6304-0.61793.3849-0.17980.5237-0.6824-0.10870.18590.041-0.0029-0.1222-0.00610.4040.20370.3376-0.0919-0.0895-0.151215.6041-31.527-24.7253
97.061-6.34561.29770.7514-0.64421.0087-0.0244-0.029-0.14870.05590.041-0.1135-0.04990.2556-0.0166-0.20980.14860.04110.36670.03440.347112.672-27.62437.1463
10-0.63944.52955.68120.46390.4538.914-0.081-0.29990.16760.533-0.013-0.385-0.345-0.08710.094-0.2911-0.238-0.0417-0.0016-0.06610.02294.7416-9.596216.4452
117.1414-2.4482-5.12893.6391-8.66224.67340.1484-1.0521-0.67750.6932-0.48210.41870.20310.34410.33380.2632-0.3141-0.2264-0.3288-0.19880.2468-29.1617-37.76683.8379
128.20252.7293.33388.07480.80476.2936-0.0339-0.59960.17580.295-0.57971.1066-0.3334-0.86650.6137-0.36920.2094-0.032-0.4212-0.0920.6065-29.8846-11.84271.7749
1312.1285-0.38492.13783.36091.11982.81490.12371.0416-0.11880.587-0.05160.4681-0.3516-1.0206-0.0721-0.27940.3581-0.2149-0.5181-0.01550.7419-34.17332.2073-2.337
1416.5433-2.1546-6.01788.7172-1.40927.6070.1567-0.4918-0.29060.4254-0.9571.34120.0482-0.29840.8003-0.32070.1491-0.0741-0.6534-0.28460.0522-26.2576-14.47112.1964
1515.27292.76054.33770.60338.366310.84290.34650.19820.2959-0.0518-0.03761.0450.2705-0.8836-0.3089-0.1444-0.20080.0006-0.4225-0.1410.8156-33.8498-30.77470.6242
163.7296-4.8685-3.44730.09761.271313.8871-0.02720.46280.85410.02-0.26961.008-0.2199-0.50710.29680.7098-0.1361-0.1664-0.759-0.2390.0668-5.17310.827270.5165
179.89944.97515.49078.9173-2.739110.09760.1143-0.1754-0.84790.0905-0.1318-0.12670.6586-0.30510.01750.9215-0.0834-0.0483-0.7280.0933-0.4732-5.7431-24.858870.5696
18-0.57473.34467.24574.3862-1.02914.05690.0892-1.03840.04210.2482-0.35110.1893-0.35480.12620.26190.91180.05510.0031-0.91040.29660.5235-5.2721-39.298473.9895
191.132-2.811-8.01651.1487-0.82316.15960.1031-0.63140.25890.6954-0.51270.45730.01690.2060.40960.5681-0.1218-0.2842-0.90650.1074-0.1769-4.367-21.947367.6397
207.35313.545-1.5242.1848-4.067915.7458-0.0606-1.0237-0.2940.6335-0.21590.7483-0.2147-0.04620.27650.9018-0.05090.0851-0.5129-0.3327-0.2526-5.5713-5.913476.2836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|53 - 192}A53 - 192
2X-RAY DIFFRACTION2{A|193 - 378}A193 - 378
3X-RAY DIFFRACTION3{A|379 - 472}A379 - 472
4X-RAY DIFFRACTION4{B|183 - 187}B183 - 187
5X-RAY DIFFRACTION5{B|188 - 197}B188 - 197
6X-RAY DIFFRACTION6{C|53 - 192}C53 - 192
7X-RAY DIFFRACTION7{C|193 - 366}C193 - 366
8X-RAY DIFFRACTION8{C|367 - 473}C367 - 473
9X-RAY DIFFRACTION9{D|183 - 187}D183 - 187
10X-RAY DIFFRACTION10{D|188 - 197}D188 - 197
11X-RAY DIFFRACTION11{E|1 - 6}E1 - 6
12X-RAY DIFFRACTION12{E|7 - 15}E7 - 15
13X-RAY DIFFRACTION13{F|1 - 4}F1 - 4
14X-RAY DIFFRACTION14{F|5 - 10}F5 - 10
15X-RAY DIFFRACTION15{F|11 - 15}F11 - 15
16X-RAY DIFFRACTION16{G|1 - 6}G1 - 6
17X-RAY DIFFRACTION17{G|7 - 15}G7 - 15
18X-RAY DIFFRACTION18{H|1 - 4}H1 - 4
19X-RAY DIFFRACTION19{H|5 - 10}H5 - 10
20X-RAY DIFFRACTION20{H|11 - 15}H11 - 15

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