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- PDB-2q59: Crystal Structure of PPARgamma LBD bound to full agonist MRL20 -

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Basic information

Entry
Database: PDB / ID: 2q59
TitleCrystal Structure of PPARgamma LBD bound to full agonist MRL20
Components(Peroxisome Proliferator-Activated Receptor gamma) x 2
KeywordsLigand binding protein / Protein-ligand complex
Function / homology
Function and homology information


prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / : ...prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / : / arachidonate binding / positive regulation of adiponectin secretion / negative regulation of triglyceride storage / DNA binding domain binding / lipoprotein transport / positive regulation of vascular associated smooth muscle cell apoptotic process / STAT family protein binding / WW domain binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / lipid homeostasis / E-box binding / alpha-actinin binding / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / cell fate commitment / negative regulation of osteoblast differentiation / positive regulation of fat cell differentiation / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / negative regulation of MAPK cascade / retinoic acid receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cell maturation / negative regulation of signaling receptor activity / positive regulation of adipose tissue development / hormone-mediated signaling pathway / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / response to nutrient / regulation of cellular response to insulin stimulus / negative regulation of miRNA transcription / peptide binding / negative regulation of angiogenesis / transcription coregulator binding / Regulation of PTEN gene transcription / fatty acid metabolic process / placenta development / positive regulation of apoptotic signaling pathway / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / mRNA transcription by RNA polymerase II / PPARA activates gene expression / regulation of circadian rhythm / lipid metabolic process / regulation of blood pressure / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / rhythmic process / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / cellular response to hypoxia / sequence-specific DNA binding / nucleic acid binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / receptor complex / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / positive regulation of gene expression / chromatin binding
Similarity search - Function
Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-240 / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBruning, J.B. / Nettles, K.W.
CitationJournal: Structure / Year: 2007
Title: Partial Agonists Activate PPARgamma Using a Helix 12 Independent Mechanism
Authors: Bruning, J.B. / Chalmers, M.J. / Prasad, S. / Busby, S.A. / Kamenecka, T.M. / He, Y. / Nettles, K.W. / Griffin, P.R.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxisome Proliferator-Activated Receptor gamma
B: Peroxisome Proliferator-Activated Receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7224
Polymers62,6672
Non-polymers1,0552
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.161, 63.939, 119.187
Angle α, β, γ (deg.)90.000, 103.430, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-7087-

HOH

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Components

#1: Protein Peroxisome Proliferator-Activated Receptor gamma / PPAR-gamma


Mass: 31371.428 Da / Num. of mol.: 1 / Fragment: Ligand binding domain
Source method: isolated from a genetically manipulated source
Details: CYS A 285 IS 2-HYDROXYETHYLATED / Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: P37231
#2: Protein Peroxisome Proliferator-Activated Receptor gamma / PPAR-gamma


Mass: 31295.314 Da / Num. of mol.: 1 / Fragment: Ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: P37231
#3: Chemical ChemComp-240 / (2S)-2-(2-{[1-(4-METHOXYBENZOYL)-2-METHYL-5-(TRIFLUOROMETHOXY)-1H-INDOL-3-YL]METHYL}PHENOXY)PROPANOIC ACID / MRL20


Mass: 527.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H24F3NO6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4 M sodium citrate, 0.125 M Tris 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Details: Mirrors
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 32936 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 57.4 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Χ2: 1.008 / Net I/σ(I): 23.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3140 / Rsym value: 0.42 / Χ2: 1.02 / % possible all: 95.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KNU

1knu


Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.961 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.233 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1667 5.1 %RANDOM
Rwork0.183 ---
obs0.185 32930 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.892 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0.33 Å2
2--1.25 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4025 0 76 244 4345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224236
X-RAY DIFFRACTIONr_angle_refined_deg1.3022.0115738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23925.165182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00515783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4021517
X-RAY DIFFRACTIONr_chiral_restr0.0720.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023108
X-RAY DIFFRACTIONr_nbd_refined0.2010.22047
X-RAY DIFFRACTIONr_nbtor_refined0.30.22998
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.210
X-RAY DIFFRACTIONr_mcbond_it0.3841.52655
X-RAY DIFFRACTIONr_mcangle_it0.64424147
X-RAY DIFFRACTIONr_scbond_it1.0431841
X-RAY DIFFRACTIONr_scangle_it1.6084.51581
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 107 -
Rwork0.236 2142 -
obs-2249 94.77 %
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)
112.9267-10.7688-1.528836.94563.52571.98470.10270.6165-0.3785-0.1651-0.3520.19780.00680.2480.2492-0.03280.06210.00720.11060.00840.10074.907-1.52-22.752
26.2849-1.82390.88378.5328-0.91930.9160.0343-0.36210.18230.54970.0044-0.1089-0.10530.0731-0.03870.0584-0.0127-0.03180.0910.00810.09330.42411.853-15.616
36.017-3.1358-2.71082.88573.09753.4893-0.0652-0.3844-0.11630.07330.2279-0.10320.01130.0927-0.16260.05790.0162-0.0010.09940.01950.0616-9.16914.3160.484
435.39787.3166-2.90727.459913.870710.59010.003-0.89841.9466-1.2872-0.0834-0.4455-1.4358-0.28560.08040.20550.17770.02960.0264-0.09540.2075-21.16329.1992.172
520.06543.85036.29628.3564-13.259229.45240.2278-0.7011.17541.0191-0.32810.5935-2.7003-0.67080.10040.22940.0649-0.00920.0691-0.06660.0601-22.8130.701-9.575
616.9323-12.5885-7.577910.87266.22616.2995-0.1721-0.09230.41340.15120.2116-0.2336-0.29720.0577-0.03950.11370.0138-0.0613-0.00130.00270.0857-8.6321.209-19.268
72.4512-0.2814-0.39362.1147-0.15023.060.08660.22070.128-0.1844-0.05690.155-0.24320.0736-0.02970.06460.0323-0.05050.0561-0.01340.0708-7.72613.855-30.934
81.7893-1.6524-1.24495.68933.51697.5467-0.07060.0322-0.01710.02880.0821-0.0656-0.1735-0.0849-0.01150.010.0283-0.01960.08980.01470.0662-14.64715.46-6.706
93.5313-4.19852.65958.46111.37977.94830.14950.235-0.1492-0.2693-0.34410.4641-0.3098-1.00050.1946-0.06090.0596-0.01260.25030.0020.1131-27.19319.279-9.31
108.4501-4.5488-4.74157.20590.63213.6535-0.0724-0.1536-0.64450.1363-0.13220.53940.284-0.3030.20460.0181-0.035-0.02260.0656-0.02550.0783-15.6934.506-10.804
112.7509-0.44212.271.4622-1.57525.7412-0.00350.1969-0.2178-0.1755-0.03820.05160.1016-0.05970.04170.05830.0225-0.03320.063-0.0540.1019-8.2965.812-30.048
121.9678-0.84612.56864.917-3.060513.7236-0.01980.0624-0.5318-0.16230.1406-0.33580.13240.0509-0.12080.00190.0271-0.02190.0424-0.03410.1867-3.254-4.301-22.381
135.98680.14422.37057.8106-2.44977.4465-0.1463-0.1482-0.390.2922-0.28970.05510.4036-0.44140.436-0.0105-0.02060.01080.0835-0.09430.1318-12.039-5.423-16.618
1410.5873-13.92610.464837.64741.87321.18120.37740.2332-0.4276-0.1427-0.3670.4690.1161-0.0995-0.0103-0.03160.0251-0.05450.0672-0.0250.0802-25.80618.582-22.572
159.1615-4.7048-1.273317.28281.140.95030.11890.57110.2594-0.15180.10750.4947-0.1704-0.2886-0.22640.11820.09730.02940.03340.07690.0858-17.66925.984-26.176
1628.3423-1.208810.240745.347-23.298133.66950.2476-1.1957-0.25492.1673-0.9691-1.3680.79051.07280.72150.10060.0907-0.1530.0026-0.10420.3646-9.766-25.778-21.539
171.7244-1.07390.32433.1758-2.7375.55690.12960.3421-0.4606-0.31280.12620.12410.5081-0.0669-0.25590.0832-0.0158-0.00610.0365-0.07330.1056-23.1-22.79-35.317
1823.8448-6.3567.38517.3759-4.450717.65930.60231.4572-1.2002-0.6304-0.45140.470.7958-0.1593-0.15090.0754-0.00820.02230.2034-0.0543-0.2538-32.318-11.779-55.117
1912.67661.09620.07040.6109-3.123118.9734-0.17391.1096-0.3046-0.77140.260.33150.6762-1.6339-0.08610.12890.07480.00370.5251-0.0299-0.0952-43.926-10.384-48.538
203.78150.831.324513.6694-11.111621.17180.16940.06230.0303-0.24140.15310.2278-0.3077-1.0246-0.32250.00140.080.02680.2034-0.0133-0.0025-40.65-9.071-38.904
212.0185-0.49820.28491.92730.04065.05770.04910.0832-0.21270.0884-0.13430.01490.2987-0.28120.08520.0344-0.03110.00740.05990.01750.1033-31.232-18.945-20.71
221.88460.6942-6.47571.6307-0.122625.97390.2410.25140.1696-0.09630.090.0711-0.5614-0.7757-0.33090.01130.02570.00350.07950.01810.1025-29.076-9.549-29.481
236.12942.30284.74736.44641.344311.8170.14410.0096-0.3045-0.1655-0.175-0.12230.0348-0.09710.03090.0830.04270.06040.0516-0.0228-0.0152-28.819-11.303-47.695
2413.1455-4.14110.03524.95963.95384.30110.14770.54221.3118-0.0826-0.46570.0504-1.0332-0.640.31810.4380.11890.06540.11990.11480.1025-33.4961.461-46.004
259.1015-5.73526.95228.9415-3.85857.8882-0.61180.22180.25940.0290.4416-0.5414-0.85340.31360.17020.1925-0.08560.09490.0443-0.0246-0.0206-19.213-6.358-39.118
261.2661-0.8736-2.08251.60641.45075.25150.1417-0.0721-0.0794-0.0351-0.0049-0.1254-0.12760.0189-0.13680.0304-0.0317-0.00290.0785-0.00940.0991-22.804-13.105-19.904
274.9627-0.7263-1.58523.74792.87975.4874-0.05270.0903-0.1706-0.09110.1636-0.503-0.13420.5374-0.1109-0.0077-0.0212-0.00180.0626-0.06620.1272-10.077-14.201-27.637
2845.6832-19.3252-1.3689.01143.29378.85471.2987-0.26491.5504-0.644-0.4899-0.8003-0.43690.2714-0.80880.1521-0.02860.0081-0.0511-0.00150.1283-24.417-1.023-29.329
29136.22035.987246.685923.152316.073268.56440.0147-2.14444.5196-1.8644-1.34990.3095-3.3144-5.38791.33520.27740.2995-0.03430.3761-0.10340.1059-37.4594.477-32.236
3042.9373-5.82515.679714.66784.783739.12420.15210.85482.89990.0355-0.2192-0.2026-1.80781.30190.06720.07960.00240.0509-0.03940.12710.0913-48.833-6.852-30.913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA207 - 2174 - 14
2X-RAY DIFFRACTION2AA218 - 22815 - 25
3X-RAY DIFFRACTION3AA229 - 25026 - 47
4X-RAY DIFFRACTION4AA251 - 25948 - 56
5X-RAY DIFFRACTION5AA260 - 28257 - 79
6X-RAY DIFFRACTION6AA283 - 30280 - 99
7X-RAY DIFFRACTION7AA303 - 326100 - 123
8X-RAY DIFFRACTION8AA327 - 348124 - 145
9X-RAY DIFFRACTION9AA349 - 367146 - 164
10X-RAY DIFFRACTION10AA368 - 381165 - 178
11X-RAY DIFFRACTION11AA382 - 410179 - 207
12X-RAY DIFFRACTION12AA411 - 423208 - 220
13X-RAY DIFFRACTION13AA424 - 438221 - 235
14X-RAY DIFFRACTION14AA439 - 462236 - 259
15X-RAY DIFFRACTION15AA463 - 475260 - 272
16X-RAY DIFFRACTION16BB207 - 2124 - 9
17X-RAY DIFFRACTION17BB213 - 23610 - 33
18X-RAY DIFFRACTION18BB237 - 25634 - 53
19X-RAY DIFFRACTION19BB257 - 27954 - 76
20X-RAY DIFFRACTION20BB280 - 29177 - 88
21X-RAY DIFFRACTION21BB292 - 31589 - 112
22X-RAY DIFFRACTION22BB316 - 333113 - 130
23X-RAY DIFFRACTION23BB334 - 347131 - 144
24X-RAY DIFFRACTION24BB348 - 365145 - 162
25X-RAY DIFFRACTION25BB366 - 380163 - 177
26X-RAY DIFFRACTION26BB381 - 409178 - 206
27X-RAY DIFFRACTION27BB410 - 437207 - 234
28X-RAY DIFFRACTION28BB438 - 449235 - 246
29X-RAY DIFFRACTION29BB450 - 456247 - 253
30X-RAY DIFFRACTION30BB466 - 475263 - 272

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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