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- PDB-7tvf: Crystal structure of the SHOC2-MRAS-PP1CA (SMP) complex to a reso... -

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Basic information

Entry
Database: PDB / ID: 7tvf
TitleCrystal structure of the SHOC2-MRAS-PP1CA (SMP) complex to a resolution of 2.17 Angstrom
Components
  • Leucine-rich repeat protein SHOC-2
  • Ras-related protein M-Ras
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsSIGNALING PROTEIN / Oncoprotein Phosphatase Scaffold protein Adaptor RAS Leucine rich repeat
Function / homology
Function and homology information


cellular response to growth hormone stimulus / regulation of glycogen catabolic process / negative regulation of neural precursor cell proliferation / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / volume-sensitive anion channel activity / glycogen granule / nerve growth factor signaling pathway / GTP-dependent protein binding / cyclic-GMP-AMP transmembrane import across plasma membrane ...cellular response to growth hormone stimulus / regulation of glycogen catabolic process / negative regulation of neural precursor cell proliferation / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / volume-sensitive anion channel activity / glycogen granule / nerve growth factor signaling pathway / GTP-dependent protein binding / cyclic-GMP-AMP transmembrane import across plasma membrane / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress / protein phosphatase regulator activity / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of Ras protein signal transduction / regulation of canonical Wnt signaling pathway / dephosphorylation / protein serine/threonine phosphatase activity / branching morphogenesis of an epithelial tube / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / glycogen metabolic process / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / phosphatase activity / telomere maintenance in response to DNA damage / regulation of MAPK cascade / phosphoprotein phosphatase activity / DARPP-32 events / transition metal ion binding / negative regulation of neuron differentiation / fibroblast growth factor receptor signaling pathway / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / positive regulation of neuron differentiation / cellular response to leukemia inhibitory factor / Downregulation of TGF-beta receptor signaling / small monomeric GTPase / adherens junction / lung development / RAF activation / circadian regulation of gene expression / response to lead ion / regulation of circadian rhythm / positive regulation of neuron projection development / GDP binding / : / presynapse / G protein activity / actin cytoskeleton organization / protein phosphatase binding / dendritic spine / perikaryon / Ras protein signal transduction / intracellular signal transduction / iron ion binding / cell division / GTPase activity / GTP binding / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / : / Leucine-rich repeat region / Metallo-dependent phosphatases ...Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / : / Leucine-rich repeat region / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Small GTPase, Ras-type / small GTPase Ras family profile. / Leucine rich repeat / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich 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 / Leucine-rich repeat domain superfamily / 4-Layer Sandwich / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / PHOSPHATE ION / Ras-related protein M-Ras / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Leucine-rich repeat protein SHOC-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsBonsor, D.A. / Simanshu, D.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2022
Title: Structure of the SHOC2-MRAS-PP1C complex provides insights into RAF activation and Noonan syndrome.
Authors: Bonsor, D.A. / Alexander, P. / Snead, K. / Hartig, N. / Drew, M. / Messing, S. / Finci, L.I. / Nissley, D.V. / McCormick, F. / Esposito, D. / Rodriguez-Viciana, P. / Stephen, A.G. / Simanshu, D.K.
History
DepositionFeb 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 12, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 26, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
E: Ras-related protein M-Ras
B: Ras-related protein M-Ras
A: Leucine-rich repeat protein SHOC-2
D: Leucine-rich repeat protein SHOC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,10143
Polymers245,5046
Non-polymers3,59737
Water18,8441046
1
F: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
E: Ras-related protein M-Ras
D: Leucine-rich repeat protein SHOC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,74524
Polymers122,7523
Non-polymers1,99321
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10810 Å2
ΔGint-150 kcal/mol
Surface area38560 Å2
MethodPISA
2
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Ras-related protein M-Ras
A: Leucine-rich repeat protein SHOC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,35519
Polymers122,7523
Non-polymers1,60316
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint-109 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.938, 129.938, 326.795
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 25 or (resid 26...
21(chain D and (resid 7 through 35 or resid 37...
12(chain B and (resid 6 through 115 or resid 117 through 178 or resid 1201 through 1202))
22(chain E and (resid 6 through 115 or resid 117...
13(chain C and (resid 62 through 76 or resid 86...
23(chain F and (resid 62 through 76 or resid 86...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 7 through 25 or (resid 26...A7 - 25
121(chain A and (resid 7 through 25 or (resid 26...A26
131(chain A and (resid 7 through 25 or (resid 26...A62 - 582
141(chain A and (resid 7 through 25 or (resid 26...A62 - 582
151(chain A and (resid 7 through 25 or (resid 26...A62 - 582
161(chain A and (resid 7 through 25 or (resid 26...A62 - 582
211(chain D and (resid 7 through 35 or resid 37...D7 - 35
221(chain D and (resid 7 through 35 or resid 37...D37 - 40
231(chain D and (resid 7 through 35 or resid 37...D60 - 578
241(chain D and (resid 7 through 35 or resid 37...D27
251(chain D and (resid 7 through 35 or resid 37...D60 - 578
261(chain D and (resid 7 through 35 or resid 37...D60 - 578
271(chain D and (resid 7 through 35 or resid 37...D60 - 578
281(chain D and (resid 7 through 35 or resid 37...D60 - 578
291(chain D and (resid 7 through 35 or resid 37...D60 - 578
2101(chain D and (resid 7 through 35 or resid 37...D60 - 578
112(chain B and (resid 6 through 115 or resid 117 through 178 or resid 1201 through 1202))B6 - 115
122(chain B and (resid 6 through 115 or resid 117 through 178 or resid 1201 through 1202))B117 - 178
132(chain B and (resid 6 through 115 or resid 117 through 178 or resid 1201 through 1202))B1201 - 1202
212(chain E and (resid 6 through 115 or resid 117...E6 - 115
222(chain E and (resid 6 through 115 or resid 117...E117 - 130
232(chain E and (resid 6 through 115 or resid 117...E6 - 178
242(chain E and (resid 6 through 115 or resid 117...E6 - 178
252(chain E and (resid 6 through 115 or resid 117...E6 - 178
262(chain E and (resid 6 through 115 or resid 117...E6 - 178
272(chain E and (resid 6 through 115 or resid 117...E6 - 178
282(chain E and (resid 6 through 115 or resid 117...E6 - 178
292(chain E and (resid 6 through 115 or resid 117...E6 - 178
2102(chain E and (resid 6 through 115 or resid 117...E6 - 178
113(chain C and (resid 62 through 76 or resid 86...C62 - 76
123(chain C and (resid 62 through 76 or resid 86...C86 - 237
133(chain C and (resid 62 through 76 or resid 86...C239 - 261
143(chain C and (resid 62 through 76 or resid 86...C263 - 264
153(chain C and (resid 62 through 76 or resid 86...C266 - 271
163(chain C and (resid 62 through 76 or resid 86...C273 - 341
173(chain C and (resid 62 through 76 or resid 86...C343 - 4566
183(chain C and (resid 62 through 76 or resid 86...C567
193(chain C and (resid 62 through 76 or resid 86...C6 - 401
1103(chain C and (resid 62 through 76 or resid 86...C6 - 401
1113(chain C and (resid 62 through 76 or resid 86...C6 - 401
1123(chain C and (resid 62 through 76 or resid 86...C6 - 401
1133(chain C and (resid 62 through 76 or resid 86...C6 - 401
213(chain F and (resid 62 through 76 or resid 86...F62 - 76
223(chain F and (resid 62 through 76 or resid 86...F86 - 237
233(chain F and (resid 62 through 76 or resid 86...F239 - 261
243(chain F and (resid 62 through 76 or resid 86...F273 - 341
253(chain F and (resid 62 through 76 or resid 86...F7 - 402
263(chain F and (resid 62 through 76 or resid 86...F455 - 558
273(chain F and (resid 62 through 76 or resid 86...F7 - 402
283(chain F and (resid 62 through 76 or resid 86...F5
293(chain F and (resid 62 through 76 or resid 86...F7 - 402
2103(chain F and (resid 62 through 76 or resid 86...F7 - 402
2113(chain F and (resid 62 through 76 or resid 86...F7 - 402
2123(chain F and (resid 62 through 76 or resid 86...F7 - 402
2133(chain F and (resid 62 through 76 or resid 86...F7 - 402

NCS ensembles :
ID
1
2
3

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Components

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Protein , 3 types, 6 molecules FCEBAD

#1: Protein Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / PP-1A


Mass: 37426.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein Ras-related protein M-Ras / Ras-related protein R-Ras3


Mass: 20426.330 Da / Num. of mol.: 2 / Mutation: Q71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRAS, RRAS3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O14807, small monomeric GTPase
#3: Protein Leucine-rich repeat protein SHOC-2 / Protein soc-2 homolog / Protein sur-8 homolog


Mass: 64898.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHOC2, KIAA0862 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UQ13

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Non-polymers , 9 types, 1083 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#11: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1046 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Crystals originally grown in 15% PEG 1500, 0.1M MIB pH 4.2 (15mg/ml of SMP) were used to make seeds. Microseeded into a condition with a reservoir consisting of 17.8% PEG 3350, 136mM sodium ...Details: Crystals originally grown in 15% PEG 1500, 0.1M MIB pH 4.2 (15mg/ml of SMP) were used to make seeds. Microseeded into a condition with a reservoir consisting of 17.8% PEG 3350, 136mM sodium sulfate with 1:10 dilution of seeds (7.5mg/ml of SMP) using a ratio of 200nl protein:133nl reservoir:67nl diluted seeds

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.17→163.4 Å / Num. obs: 148476 / % possible obs: 99.9 % / Redundancy: 7.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.077 / Net I/σ(I): 8.5
Reflection shellResolution: 2.17→2.2 Å / Rmerge(I) obs: 2.007 / Num. unique obs: 7129 / CC1/2: 0.34 / Rpim(I) all: 1.228

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X1S, 6DNO

1x1s

6dno


Resolution: 2.17→101.7 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 7489 5.05 %
Rwork0.1988 140808 -
obs0.2002 148297 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.28 Å2 / Biso mean: 52.4903 Å2 / Biso min: 23.77 Å2
Refinement stepCycle: final / Resolution: 2.17→101.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15598 0 200 1046 16844
Biso mean--68.07 52.84 -
Num. residues----1968
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2741X-RAY DIFFRACTION7.339TORSIONAL
12D2741X-RAY DIFFRACTION7.339TORSIONAL
21B1673X-RAY DIFFRACTION7.339TORSIONAL
22E1673X-RAY DIFFRACTION7.339TORSIONAL
31C0X-RAY DIFFRACTION7.339TORSIONAL
32F0X-RAY DIFFRACTION7.339TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.17-2.190.35562380.36044476471497
2.19-2.220.37932340.333446554889100
2.22-2.250.33122530.322746484901100
2.25-2.270.33272450.303646334878100
2.27-2.30.31362790.279745784857100
2.3-2.340.31042470.281146054852100
2.34-2.370.292380.264346734911100
2.37-2.40.28382490.259346694918100
2.4-2.440.28522330.255946764909100
2.44-2.480.31762730.253646034876100
2.48-2.520.30342160.256946664882100
2.52-2.570.28732530.252746584911100
2.57-2.620.2822530.25546574910100
2.62-2.670.31212640.265746234887100
2.67-2.730.31492520.273746594911100
2.73-2.790.31742310.277146954926100
2.79-2.860.27762510.247746604911100
2.86-2.940.25312440.218646794923100
2.94-3.030.24232580.214247054963100
3.03-3.130.24142630.211546454908100
3.13-3.240.22082530.20947214974100
3.24-3.370.25682420.209146964938100
3.37-3.520.26252620.22247054967100
3.52-3.710.20362580.179947284986100
3.71-3.940.1892520.159647434995100
3.94-4.240.17842580.145447224980100
4.24-4.670.16132330.138647905023100
4.67-5.350.16482350.145348405075100
5.35-6.730.19182470.175748815128100
6.74-101.70.17062750.170851195394100
Refinement TLS params.Method: refined / Origin x: -27.1395 Å / Origin y: 53.7873 Å / Origin z: -25.1531 Å
111213212223313233
T0.3042 Å20.018 Å2-0.0243 Å2-0.2879 Å2-0.03 Å2--0.2479 Å2
L0.1249 °2-0.0721 °20.0236 °2-0.633 °2-0.2919 °2--0.1332 °2
S-0.0191 Å °-0.026 Å °-0.0079 Å °-0.0317 Å °0.0522 Å °0.0013 Å °0.0282 Å °-0.0211 Å °-0.0335 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allF7 - 402
2X-RAY DIFFRACTION1allC6 - 401
3X-RAY DIFFRACTION1allE6 - 178
4X-RAY DIFFRACTION1allE1201 - 1203
5X-RAY DIFFRACTION1allB4 - 178
6X-RAY DIFFRACTION1allB1201 - 1202
7X-RAY DIFFRACTION1allA62 - 582
8X-RAY DIFFRACTION1allA602 - 605
9X-RAY DIFFRACTION1allD60 - 578
10X-RAY DIFFRACTION1allD601 - 603
11X-RAY DIFFRACTION1allQ1 - 16
12X-RAY DIFFRACTION1allH1 - 4
13X-RAY DIFFRACTION1allJ2 - 3
14X-RAY DIFFRACTION1allS1 - 1135
15X-RAY DIFFRACTION1allI1 - 2
16X-RAY DIFFRACTION1allK1
17X-RAY DIFFRACTION1allM1 - 5

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