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- PDB-8oqn: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -

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Basic information

Entry
Database: PDB / ID: 8oqn
TitleStructure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-M-53
Components
  • 3-hydroxyacyl-CoA dehydrogenase
  • Putative acyltransferase Rv0859
KeywordsOXIDOREDUCTASE / fatty acid beta oxidation complex / mycobacterium tuberculosis / TFE / fragment screening / substrate channeling
Function / homology
Function and homology information


long-chain-3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid beta-oxidation / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peptidoglycan-based cell wall / plasma membrane / cytosol
Similarity search - Function
3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. ...3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Thiolase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
1-benzyl-1H-pyrazole-4-carboxylic acid / Putative acyltransferase Rv0859 / Probable fatty oxidation protein FadB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDalwani, S. / Wierenga, R.K. / Venkatesan, R.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland293369 Finland
Academy of Finland289024 Finland
Academy of Finland319194 Finland
Citation
Journal: Biorxiv / Year: 2024
Title: Crystallographic fragment binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a ...Title: Crystallographic fragment binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate channeling path between them
Authors: Dalwani, S. / Metz, A. / Huschmann, F.U. / Weiss, M.S. / Wierenga, R.K. / Venkatesan, R.
#1: Journal: J Struct Biol / Year: 2021
Title: Substrate specificity and conformational flexibility properties of the Mycobacterium tuberculosis beta-oxidation trifunctional enzyme.
Authors: Dalwani, S.
#2: Journal: ACS Chem Biol / Year: 2013
Title: Structure of mycobacterial beta-oxidation trifunctional enzyme reveals its altered assembly and putative substrate channeling pathway.
Authors: Venkatesan, R. / Wierenga, R.K.
History
DepositionApr 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 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: 3-hydroxyacyl-CoA dehydrogenase
B: 3-hydroxyacyl-CoA dehydrogenase
C: Putative acyltransferase Rv0859
D: Putative acyltransferase Rv0859
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,75641
Polymers240,9324
Non-polymers4,82437
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15270 Å2
ΔGint-283 kcal/mol
Surface area83500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)247.309, 134.026, 116.408
Angle α, β, γ (deg.)90.000, 109.698, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein 3-hydroxyacyl-CoA dehydrogenase /


Mass: 78005.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: fadB, Rv0860 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53872, 3-hydroxyacyl-CoA dehydrogenase
#2: Protein Putative acyltransferase Rv0859


Mass: 42460.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: fadA, Rv0859 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53871, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 4 types, 227 molecules

#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-W3U / 1-benzyl-1H-pyrazole-4-carboxylic acid


Mass: 202.209 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C11H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.77 Å3/Da / Density % sol: 67.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2 M Ammonium Sulfate, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9198 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.2→116.42 Å / Num. obs: 179810 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 52.39 Å2 / CC1/2: 0.998 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 8441 / CC1/2: 0.345

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.98 Å / SU ML: 0.3282 / Cross valid method: FREE R-VALUE / σ(F): 0.74 / Phase error: 25.0742
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2216 9084 5.06 %
Rwork0.193 170526 -
obs0.1944 179610 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.07 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16704 0 306 190 17200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001917349
X-RAY DIFFRACTIONf_angle_d0.496923497
X-RAY DIFFRACTIONf_chiral_restr0.0412626
X-RAY DIFFRACTIONf_plane_restr0.00433279
X-RAY DIFFRACTIONf_dihedral_angle_d16.10716453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.37632920.3615107X-RAY DIFFRACTION90.09
2.23-2.250.36172910.32455644X-RAY DIFFRACTION99.9
2.25-2.280.32983070.31115721X-RAY DIFFRACTION99.9
2.28-2.310.34353510.29125630X-RAY DIFFRACTION99.97
2.31-2.340.3462940.28955669X-RAY DIFFRACTION100
2.34-2.370.31582650.29585722X-RAY DIFFRACTION99.98
2.37-2.410.3153280.28255663X-RAY DIFFRACTION100
2.41-2.440.29143170.26625710X-RAY DIFFRACTION99.95
2.44-2.480.27823120.26125685X-RAY DIFFRACTION100
2.48-2.520.28742930.25345693X-RAY DIFFRACTION99.98
2.52-2.560.28932690.23865750X-RAY DIFFRACTION100
2.56-2.610.26312980.2335681X-RAY DIFFRACTION99.98
2.61-2.660.27652970.22795702X-RAY DIFFRACTION99.95
2.66-2.710.27833030.23595681X-RAY DIFFRACTION99.97
2.71-2.770.27223060.24275710X-RAY DIFFRACTION99.98
2.77-2.840.3013320.24835671X-RAY DIFFRACTION99.97
2.84-2.910.29473320.25335669X-RAY DIFFRACTION99.97
2.91-2.990.26352880.24585723X-RAY DIFFRACTION100
2.99-3.080.26592830.23145712X-RAY DIFFRACTION99.98
3.08-3.180.25733010.23035689X-RAY DIFFRACTION99.97
3.18-3.290.25672950.21795724X-RAY DIFFRACTION99.9
3.29-3.420.25023000.21895736X-RAY DIFFRACTION99.9
3.42-3.580.23032850.19955687X-RAY DIFFRACTION99.87
3.58-3.760.20452950.18255730X-RAY DIFFRACTION99.82
3.76-40.18233230.16485691X-RAY DIFFRACTION99.8
4-4.310.17423200.14525689X-RAY DIFFRACTION99.72
4.31-4.740.16872840.1385718X-RAY DIFFRACTION99.77
4.74-5.430.18352960.15235776X-RAY DIFFRACTION99.87
5.43-6.840.19063180.17085728X-RAY DIFFRACTION99.57
6.84-48.980.16423090.14415815X-RAY DIFFRACTION99.24
Refinement TLS params.Method: refined / Origin x: -43.761 Å / Origin y: 34.098 Å / Origin z: -1.409 Å
111213212223313233
T0.369362059016 Å20.0222780620499 Å20.00617411633585 Å2-0.379383674184 Å2-0.0240507438227 Å2--0.43804760982 Å2
L0.264221424392 °20.126651591014 °2-0.0194848773376 °2-0.247527728792 °2-0.109360993572 °2--0.521543973414 °2
S-0.0160069756344 Å °-0.0154503529892 Å °-0.027266365326 Å °-0.0274640918732 Å °0.00183640590766 Å °-0.023356220899 Å °0.0115939395347 Å °-0.104676521952 Å °0.0238096071709 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )A-13 - 720
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )A801 - 803
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )A804
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )A805 - 810
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )A901 - 938
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )B-15 - 720
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )B801 - 807
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )B808
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )B809 - 814
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )B901 - 947
11X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )C2 - 403
12X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )C501 - 507
13X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )C601 - 657
14X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )D2 - 403
15X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )D501 - 506
16X-RAY DIFFRACTION1( CHAIN A AND ( RESID -13:720 OR RESID 801:803 OR RESID 804:804 OR RESID 805:810 OR RESID 901:938 ) ) OR ( CHAIN B AND ( RESID -15:720 OR RESID 801:807 OR RESID 808:808 OR RESID 809:814 OR RESID 901:947 ) ) OR ( CHAIN C AND ( RESID 2:403 OR RESID 501:507 OR RESID 601:657 ) ) OR ( CHAIN D AND ( RESID 2:403 OR RESID 501:506 OR RESID 601:648 ) )D601 - 648

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