[English] 日本語
Yorodumi
- PDB-4zdq: Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidyly... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zdq
TitleCrystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis complexed with CTP
Components2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
KeywordsTRANSFERASE / SSGCID / isoprenoid biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process
Similarity search - Function
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site / Cytidylyltransferase IspD/TarI / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature. / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CACODYLIC ACID / CYTIDINE-5'-TRIPHOSPHATE / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Crystal structure and biophysical characterization of IspD from Burkholderia thailandensis and Mycobacterium paratuberculosis.
Authors: Pierce, P.G. / Hartnett, B.E. / Laughlin, T.M. / Blain, J.M. / Mayclin, S.J. / Bolejack, M.J. / Myers, J.B. / Higgins, T.W. / Dranow, D.M. / Sullivan, A. / Lorimer, D.D. / Edwards, T.E. / ...Authors: Pierce, P.G. / Hartnett, B.E. / Laughlin, T.M. / Blain, J.M. / Mayclin, S.J. / Bolejack, M.J. / Myers, J.B. / Higgins, T.W. / Dranow, D.M. / Sullivan, A. / Lorimer, D.D. / Edwards, T.E. / Hagen, T.J. / Horn, J.R. / Myler, P.J.
History
DepositionApr 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Derived calculations
Revision 1.2Oct 11, 2017Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / reflns_shell
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
C: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
D: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,12120
Polymers103,2864
Non-polymers1,83516
Water3,369187
1
A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6248
Polymers25,8211
Non-polymers8037
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)25,8211
Polymers25,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1375
Polymers25,8211
Non-polymers3154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5396
Polymers25,8211
Non-polymers7185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4459
Polymers51,6432
Non-polymers8037
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-27 kcal/mol
Surface area18120 Å2
MethodPISA
6
C: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
D: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,67611
Polymers51,6432
Non-polymers1,0339
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-23 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.900, 138.950, 76.920
Angle α, β, γ (deg.)90.000, 101.940, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase / MEP cytidylyltransferase / MCT


Mass: 25821.379 Da / Num. of mol.: 4 / Fragment: ButhA.00168.a.A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: ispD, BTH_I2089 / Plasmid: ButhA.00168.a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2SWT6, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

-
Non-polymers , 6 types, 203 molecules

#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE


Mass: 137.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7AsO2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.05
Details: ButhA.00168.a.A1.PW33338 at 30.46 mg/ml mixed 1:1 with JCSG+(e11): 10.73% PEG-8000, 80mM Sodium Cacodylate/ HCl, pH=6.04, 160mM Calcium acetate, 20% glycerol. Apo crystals were soaked with ...Details: ButhA.00168.a.A1.PW33338 at 30.46 mg/ml mixed 1:1 with JCSG+(e11): 10.73% PEG-8000, 80mM Sodium Cacodylate/ HCl, pH=6.04, 160mM Calcium acetate, 20% glycerol. Apo crystals were soaked with 1mM MgCl2, CTP, and D-erythritol-4-phosphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 41718 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 31.72 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.094 / Χ2: 0.951 / Net I/σ(I): 13.44 / Num. measured all: 159992
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.360.8220.5392.8411811306930580.62699.6
2.36-2.420.8380.4893.0911664303330180.56799.5
2.42-2.490.9120.3873.8411163288828900.449100
2.49-2.570.930.3274.4211044287528590.3899.4
2.57-2.660.9370.2894.8810634274427480.335100
2.66-2.750.9530.2495.6510146264426300.28999.5
2.75-2.850.9670.26.799964257825820.233100
2.85-2.970.9790.1578.589532248224720.18399.6
2.97-3.10.9890.119119138238823770.13899.5
3.1-3.250.9910.09313.668737226622710.108100
3.25-3.430.9950.06917.678208214321360.0899.7
3.43-3.640.9960.05820.557755204920440.06899.8
3.64-3.890.9970.04824.067359193819360.05699.9
3.89-4.20.9970.04227.296848180618000.04899.7
4.2-4.60.9980.03531.116327165616560.04100
4.6-5.140.9980.03332.295680149114880.03999.8
5.14-5.940.9980.03828.244999131113100.04499.9
5.94-7.270.9980.03330.344231111311120.03999.9
7.27-10.290.9980.02737.5232038688660.03299.8
10.290.9980.03135.6515494924650.03794.5

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4YS8

4ys8


Resolution: 2.3→26.932 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 1948 4.67 %
Rwork0.205 39739 -
obs0.2074 41687 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.49 Å2 / Biso mean: 41.7333 Å2 / Biso min: 15.41 Å2
Refinement stepCycle: final / Resolution: 2.3→26.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6652 0 111 187 6950
Biso mean--63.4 37.2 -
Num. residues----898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026892
X-RAY DIFFRACTIONf_angle_d0.5639376
X-RAY DIFFRACTIONf_chiral_restr0.0281075
X-RAY DIFFRACTIONf_plane_restr0.0031240
X-RAY DIFFRACTIONf_dihedral_angle_d10.0672431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35750.3241420.27292794293699
2.3575-2.42120.28611390.258628572996100
2.4212-2.49240.31441100.243828162926100
2.4924-2.57280.29211450.240928633008100
2.5728-2.66470.27971410.241328092950100
2.6647-2.77120.30961440.2428352979100
2.7712-2.89720.30131490.236128132962100
2.8972-3.04980.29641430.23928593002100
3.0498-3.24060.30351290.22128572986100
3.2406-3.49030.26631280.208728422970100
3.4903-3.84060.22491470.189128512998100
3.8406-4.39430.21511370.172328062943100
4.3943-5.52850.20541370.162828753012100
5.5285-26.93350.24061570.1832862301999
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)
13.5476-0.7945-0.06134.21770.22782.3539-0.09980.0255-0.2748-0.1377-0.0022-0.310.15190.16560.12240.1477-0.01180.04870.2385-0.00990.265146.592589.729543.5234
20.67210.1795-0.18214.20850.0560.7020.1243-0.07680.08340.2773-0.08160.7878-0.03990.0564-0.02280.1934-0.0340.06180.2551-0.06580.297530.662482.594847.245
32.1093-0.7632-0.65015.56071.98443.47570.0546-0.0321-0.28890.21450.00940.16290.15350.1995-0.10180.1927-0.05520.0180.2771-0.01740.281435.694579.175646.118
41.83180.9959-0.17323.47220.45342.3593-0.1150.1056-0.0046-0.08020.07520.1307-0.1851-0.0670.03290.32130.0248-0.04920.2359-0.01260.196331.444748.098836.1317
50.8390.8679-0.45586.74710.37540.62680.0374-0.02870.0970.3021-0.07940.46610.1659-0.06670.00580.3223-0.0039-0.00470.2788-0.02720.264628.298560.794846.6621
65.00830.2466-0.75223.04621.82333.8215-0.0249-0.53930.180.34680.1588-0.4115-0.62260.3447-0.21680.46980.0401-0.05290.2423-0.00010.211228.1215116.75490.1197
72.14220.89070.39655.48361.07845.96910.10050.3419-0.3062-0.25890.12380.5220.59230.2228-0.28890.33130.0267-0.1420.3576-0.03520.291720.7855102.4349-11.815
85.19050.21381.38964.2171-1.82261.2736-0.11170.31240.2677-0.13880.1755-0.07020.1560.05740.00210.23590.035-0.0610.1866-0.00940.147724.5301112.448-10.9135
92.92961.21391.20933.3021-0.58054.1719-0.24710.2353-0.1468-0.39170.1523-0.17880.24130.07630.09920.26850.037-0.05020.28720.00720.200123.9021112.9246-14.1606
100.526-0.8898-1.40671.54832.41783.79580.27820.6716-0.5856-0.4626-0.2561-0.1801-0.71610.375-0.03680.3668-0.012-0.07060.36150.01890.57435.0914116.2704-8.3764
113.58690.09460.54363.1108-1.75913.27890.0595-0.44180.32570.7838-0.0474-0.4063-0.1166-0.00460.00640.3330.0451-0.06940.2765-0.01120.260928.5088108.3844.2667
125.57820.80881.55468.8141.54930.6349-0.40.08710.454-0.54060.0671-0.9089-0.9119-0.18580.12120.39910.0903-0.07390.29210.08930.459841.284481.3560.7951
134.6474-4.179-1.41993.75811.28280.4763-0.3999-0.5558-0.20430.47020.3187-0.1773-0.22950.24150.01110.43550.0107-0.17930.26970.01890.427338.735589.51136.6101
143.65060.05941.54818.1207-0.46486.3978-0.13170.33090.21180.14740.0788-1.0037-0.49120.50550.09360.283-0.027-0.13090.22760.04740.427740.4194113.822-0.3517
153.2570.81453.63849.2002-1.02576.08950.19160.43790.004-0.0975-0.0325-1.6710.22220.906-0.17280.36280.0769-0.16750.42260.02850.71444.3659106.97321.2236
166.21461.65323.25297.71232.42438.0717-0.1145-0.4513-0.3013-0.2818-0.05840.1153-0.5755-0.35020.14860.31060.0626-0.11150.19150.04240.328927.845896.87851.852
177.58121.4423-2.50179.3959-0.19713.76030.6910.5659-0.8931-0.76070.24751.02330.2104-0.6495-0.74230.71540.0272-0.2740.38120.10030.591219.210390.6738-7.599
184.7572-1.2587-0.93986.18140.0174.23020.2709-0.1440.4740.00620.0370.68960.0597-0.4337-0.19430.2177-0.06370.02890.3175-0.00580.343118.499869.18347.1175
195.8762-0.456-0.72164.3446-0.01742.6874-0.2248-0.56820.06690.69730.0980.64210.2116-0.22050.0260.34920.00010.02850.28530.01530.300221.605464.108712.32
201.48951.13550.42336.3723-0.31161.0563-0.25070.01630.0405-0.35620.2315-0.4589-0.06280.09080.02770.28030.0198-0.04720.28840.02790.235334.452579.31351.4788
215.118-1.33070.75644.878-0.40832.1611-0.0941-0.3184-0.05670.17880.0413-0.1521-0.04910.01030.02350.2487-0.0215-0.05070.27610.06920.371432.500874.87796.7112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 96 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 185 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 231 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 138 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 139 through 232 )B0
6X-RAY DIFFRACTION6chain 'C' and (resid 0 through 11 )C0
7X-RAY DIFFRACTION7chain 'C' and (resid 12 through 43 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 44 through 63 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 64 through 81 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 82 through 96 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 97 through 138 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 139 through 152 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 153 through 168 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 169 through 185 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 186 through 204 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 205 through 218 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 219 through 232 )C0
18X-RAY DIFFRACTION18chain 'D' and (resid 2 through 63 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 64 through 96 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 97 through 168 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 169 through 230 )D0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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

Read more