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- PDB-8stc: S127A variant of LarB, a carboxylase/hydrolase involved in synthe... -

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Basic information

Entry
Database: PDB / ID: 8stc
TitleS127A variant of LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with Zinc and soaked with bicarbonate.
ComponentsPyridinium-3,5-biscarboxylic acid mononucleotide synthase
KeywordsLYASE / Carboxylase / Hydrolase / LYASE (CARBON-CARBON)
Function / homology
Function and homology information


pyridinium-3,5-biscarboxylic acid mononucleotide synthase / 'de novo' IMP biosynthetic process / transferase activity / hydrolase activity / plasma membrane
Similarity search - Function
Pyridinium-3,5-biscarboxylic acid mononucleotide synthase / PurE domain / AIR carboxylase / AIR carboxylase
Similarity search - Domain/homology
Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
Similarity search - Component
Biological speciesLactiplantibacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChatterjee, S. / Rankin, J.A. / Hu, J. / Hausinger, R.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1807073 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128959 United States
CitationJournal: To be published
Title: S127A variant of LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with Zinc and soaked with bicarbonate.
Authors: Chatterjee, S. / Rankin, J.A. / Hu, J. / Hausinger, R.P.
History
DepositionMay 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,14510
Polymers158,9656
Non-polymers1794
Water00
1
A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,31316
Polymers211,9548
Non-polymers3598
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area20770 Å2
ΔGint-362 kcal/mol
Surface area55090 Å2
MethodPISA
2
C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,31316
Polymers211,9548
Non-polymers3598
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area20880 Å2
ΔGint-357 kcal/mol
Surface area57220 Å2
MethodPISA
3
E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase


Theoretical massNumber of molelcules
Total (without water)211,9548
Polymers211,9548
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area14930 Å2
ΔGint-126 kcal/mol
Surface area64030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.380, 120.380, 213.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein
Pyridinium-3,5-biscarboxylic acid mononucleotide synthase / P2CMN synthase / Lactate racemase accessory protein LarB / Lactate racemase activation protein LarB ...P2CMN synthase / Lactate racemase accessory protein LarB / Lactate racemase activation protein LarB / Lactate racemase maturation protein LarB / Lactate racemization operon protein LarB / Nickel-pincer cofactor biosynthesis protein LarB / Nicotinic acid adenine dinucleotide carboxylase/hydrolase / NaAD carboxylase/hydrolase


Mass: 26494.227 Da / Num. of mol.: 6 / Mutation: S127A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum WCFS1 (bacteria)
Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: larB, lp_0105 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F9UST0, pyridinium-3,5-biscarboxylic acid mononucleotide synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM magnesium formate, 20% w/v PEG 3350, 2 mM nitrilotriacetic acid neutralized to a pH of ~7.5 with sodium hydroxide, and 0.7 mM zinc sulfate, soaked with 10 mM sodium bicarbonate at pH6 ...Details: 100 mM magnesium formate, 20% w/v PEG 3350, 2 mM nitrilotriacetic acid neutralized to a pH of ~7.5 with sodium hydroxide, and 0.7 mM zinc sulfate, soaked with 10 mM sodium bicarbonate at pH6 for 20 minutes during freezing

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.8→85.12 Å / Num. obs: 39278 / % possible obs: 99.7 % / Redundancy: 13.2 % / CC1/2: 0.995 / Net I/σ(I): 13.4
Reflection shellResolution: 2.8→2.91 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4351 / CC1/2: 0.665

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→42.91 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2734 2020 5.15 %
Rwork0.2367 --
obs0.2386 39221 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8009 0 4 0 8013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0198251
X-RAY DIFFRACTIONf_angle_d1.10111332
X-RAY DIFFRACTIONf_dihedral_angle_d12.7482666
X-RAY DIFFRACTIONf_chiral_restr0.0581447
X-RAY DIFFRACTIONf_plane_restr0.0081495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.37791430.33042611X-RAY DIFFRACTION100
2.87-2.950.32811400.31782599X-RAY DIFFRACTION100
2.95-3.030.3481420.29362555X-RAY DIFFRACTION98
3.03-3.130.32461420.27672587X-RAY DIFFRACTION99
3.13-3.240.26061270.27952663X-RAY DIFFRACTION100
3.24-3.370.34021360.28182628X-RAY DIFFRACTION100
3.37-3.530.28331330.23662657X-RAY DIFFRACTION100
3.53-3.710.25231470.2372632X-RAY DIFFRACTION100
3.71-3.950.24821300.2272667X-RAY DIFFRACTION100
3.95-4.250.28671540.22192650X-RAY DIFFRACTION100
4.25-4.680.23641580.18942670X-RAY DIFFRACTION100
4.68-5.350.23591590.20932694X-RAY DIFFRACTION100
5.35-6.740.28461300.27042708X-RAY DIFFRACTION98
6.74-42.910.2771790.22272880X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.03570.4197-3.13024.79744.52426.36580.1419-0.4422-0.62810.46630.3071-0.95341.031.31580.39840.81180.5451-0.01191.3222-0.51641.278244.771-24.4161.577
27.5365-1.9939-3.42097.96855.18785.30930.1822.2152-0.5676-1.1272-0.321-0.2162-0.1391-0.36930.18340.63930.1393-0.06151.1809-0.19010.572636.744-16.206-0.497
36.7159-1.9523-1.06192.90332.43467.17960.07570.25340.4846-0.4287-0.28430.6399-0.4599-0.53130.17510.33580.0166-0.09460.4046-0.03050.69430.955-3.72612.731
48.44891.7445-0.27087.13250.87539.2880.02870.53270.3710.2080.1296-0.638-0.51790.1671-0.15420.28680.0554-0.02140.2636-0.00090.480940.14-6.81518.591
53.2004-0.3348-2.67054.69412.47539.4603-0.2824-1.86471.08280.52490.03040.3949-0.9178-0.09560.29010.76210.0277-0.02281.081-0.27570.699632.683-7.21847.294
64.3922-0.72111.68786.38090.69813.3633-0.2972-1.0025-0.64370.379-0.00790.00730.38160.10480.3240.39630.03840.10820.42220.13870.590839.303-23.13335.773
74.5832-1.1804-2.83057.2037-0.64117.10350.1182-0.38720.1929-0.0294-0.2312-0.4153-0.08950.5160.13350.2482-0.03210.02240.3088-0.01230.433944.422-17.5326.004
88.24435.83956.15296.13144.568.78880.65560.02990.4543-0.3068-0.33031.22330.3598-2.11490.03670.7353-0.1278-0.20441.54290.18650.8525-4.493-32.24222.067
93.3309-0.5543-1.26333.17662.81827.06380.35061.1419-0.6961-1.1029-0.35530.61060.304-1.2495-0.00530.601-0.1816-0.12261.16670.21270.5761.528-32.86522.14
107.45640.80212.15136.2576-1.02157.5597-0.11090.8526-0.1835-0.98230.159-0.20780.29820.0379-0.04720.395-0.07130.10510.4277-0.00730.456415.575-36.70529.186
115.96751.24240.2715.3778-2.36396.7154-0.0855-0.2725-0.6779-0.06430.0930.24360.6741-0.2593-0.00090.279-0.00320.05510.35170.04660.461310.353-41.63439.731
124.0259-3.0889-1.17522.7774-0.49675.6610.3657-2.3764-1.41230.696-0.4014-0.54490.45851.01490.04710.9352-0.2866-0.23231.55830.50571.029419.823-36.75264.776
134.58381.85072.23364.5506-1.03395.66230.2052-2.71840.71880.7652-0.6890.4856-0.3075-0.53440.32880.5854-0.09170.12611.2935-0.21420.6562.68-30.68160.562
147.5386-3.67025.17919.0289-0.464.20430.0041-0.9412-0.18020.43740.04281.09030.4251-1.1957-0.05740.4462-0.09030.10080.6187-0.07920.5566-4.248-34.87147.724
155.68412.34471.18785.2672.21818.76510.1424-0.3354-0.95820.3767-0.1039-0.07070.596-0.3417-0.05280.2945-0.02840.07220.4381-0.00610.54333.036-38.42447.324
164.8729-0.66390.47593.61592.2851.613-2.1767-1.2102-0.61671.5007-0.38072.00861.7699-2.46712.46842.49980.07390.76412.4862-0.56141.609639.15-19.245118.168
175.45521.6511-5.62273.273-3.4958.71050.0463-1.67490.56631.156-0.58971.68720.62291.13760.57872.2728-0.51030.86381.8806-0.04731.597647.114-22.494123.053
180.8831-0.9152-0.02151.44210.60624.4899-0.588-0.2829-1.06820.01810.1270.17091.7964-0.58371.0073.3396-0.11711.43191.13190.02561.838954.639-33.712110.044
190.66161.4044-1.09363.1411-1.56774.4147-0.1421-1.0255-1.3580.4403-1.7219-0.78240.8650.3522-0.13992.8920.03061.53141.74720.26291.788261.563-30.055108.075
202.6853-2.66521.56798.36833.93926.2238-0.61660.6292-0.4061-0.4587-1.1408-0.49071.25380.00280.98912.1707-0.13510.92261.28940.20271.399563.374-18.7899.448
211.67810.6426-1.36942.30941.62795.79130.1812-0.49030.03040.1588-0.11360.00580.8091-0.09740.74673.05380.07631.32471.9039-0.24081.406452.218-25.095100.756
229.5419-3.678-5.07412.20091.60038.13530.2157-0.13750.049-0.7187-1.39290.12611.58221.17241.10931.8617-0.00490.57681.84570.05410.946862.893-29.1272.57
238.17974.53235.06948.53722.71964.2014-1.05680.7453-0.7747-0.2259-1.11141.49891.8972-0.50792.20281.44840.06510.40391.9346-0.40261.13755.463-24.32966.848
245.00111.37980.44470.6264-1.23547.75030.44510.55-1.30050.092-1.32171.06772.794-1.93231.03662.1264-0.59520.73672.0695-0.84891.60743.751-29.0281.68
251.15720.1933-0.21060.0439-0.14811.1224-0.7972-0.6477-0.77480.0441-0.22020.67610.8486-0.0503-0.04511.92750.00291.03232.937-1.46071.834845.153-24.57180.67
263.4491-3.60150.92233.98040.37848.3572-0.0892-1.91040.38950.4579-0.16080.5751-0.3639-1.4055-0.17281.3404-0.72090.67442.4524-0.88241.602331.079-19.08888.889
277.7023-7.3312-3.74488.31061.52017.1914-1.5224-1.26040.09641.34021.69470.25321.5153-1.2105-0.23451.7996-0.49840.67942.5177-0.76171.392141.239-19.65492.315
288.65967.09631.60039.5135-1.80542.9101-0.94680.67730.3774-0.015-0.29970.77741.1835-0.39610.57221.6164-0.35370.59041.6293-0.62471.213948.431-12.24691.078
290.132-0.0018-0.09421.16770.41110.230.27210.547-0.1132-0.53-0.7971-0.15590.44590.19180.02912.4406-0.29681.3252.3283-0.66961.341851.422-24.45290.966
305.918-2.37892.66326.43983.45115.0389-0.8921-0.3485-0.22990.5093-0.24070.28170.2308-0.2133-0.56790.35580.1375-0.18070.40390.2902-0.003314.345-17.85733.892
314.8753-1.55451.51811.79671.52924.026-0.1249-1.022-0.2719-0.0501-0.08810.1689-0.242-1.08830.23750.39410.7729-0.10781.8206-0.32730.145129.534-22.37226.758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 44:69 )A44 - 69
2X-RAY DIFFRACTION2( CHAIN A AND RESID 70:125 )A70 - 125
3X-RAY DIFFRACTION3( CHAIN A AND RESID 126:190 )A126 - 190
4X-RAY DIFFRACTION4( CHAIN A AND RESID 191:246 )A191 - 246
5X-RAY DIFFRACTION5( CHAIN B AND RESID 44:107 )B44 - 107
6X-RAY DIFFRACTION6( CHAIN B AND RESID 108:162 )B108 - 162
7X-RAY DIFFRACTION7( CHAIN B AND RESID 163:246 )B163 - 246
8X-RAY DIFFRACTION8( CHAIN C AND RESID 46:71 )C46 - 71
9X-RAY DIFFRACTION9( CHAIN C AND RESID 72:82 )C72 - 82
10X-RAY DIFFRACTION10( CHAIN C AND RESID 83:190 )C83 - 190
11X-RAY DIFFRACTION11( CHAIN C AND RESID 191:246 )C191 - 246
12X-RAY DIFFRACTION12( CHAIN D AND RESID 43:82 )D43 - 82
13X-RAY DIFFRACTION13( CHAIN D AND RESID 83:171 )D83 - 171
14X-RAY DIFFRACTION14( CHAIN D AND RESID 172:190 )D172 - 190
15X-RAY DIFFRACTION15( CHAIN D AND RESID 191:249 )D191 - 249
16X-RAY DIFFRACTION16( CHAIN E AND RESID 46:68 )E46 - 68
17X-RAY DIFFRACTION17( CHAIN E AND RESID 69:107 )E69 - 107
18X-RAY DIFFRACTION18( CHAIN E AND RESID 108:125 )E108 - 125
19X-RAY DIFFRACTION19( CHAIN E AND RESID 126:177 )E126 - 177
20X-RAY DIFFRACTION20( CHAIN E AND RESID 178:220 )E178 - 220
21X-RAY DIFFRACTION21( CHAIN E AND RESID 221:246 )E221 - 246
22X-RAY DIFFRACTION22( CHAIN F AND RESID 49:82 )F49 - 82
23X-RAY DIFFRACTION23( CHAIN F AND RESID 83:107 )F83 - 107
24X-RAY DIFFRACTION24( CHAIN F AND RESID 108:128 )F108 - 128
25X-RAY DIFFRACTION25( CHAIN F AND RESID 129:153 )F129 - 153
26X-RAY DIFFRACTION26( CHAIN F AND RESID 154:168 )F154 - 168
27X-RAY DIFFRACTION27( CHAIN F AND RESID 169:190 )F169 - 190
28X-RAY DIFFRACTION28( CHAIN F AND RESID 191:218 )F191 - 218
29X-RAY DIFFRACTION29( CHAIN F AND RESID 219:246 )F219 - 246
30X-RAY DIFFRACTION30( CHAIN A AND RESID 302:302 ) OR ( CHAIN D AND RESID 301:301 )A302
31X-RAY DIFFRACTION30( CHAIN A AND RESID 302:302 ) OR ( CHAIN D AND RESID 301:301 )D301
32X-RAY DIFFRACTION31( CHAIN A AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 )A301
33X-RAY DIFFRACTION31( CHAIN A AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 )C301

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  • 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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