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- PDB-3q0j: Crystal Structure of the Mycobacterium tuberculosis Crotonase in ... -

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Basic information

Entry
Database: PDB / ID: 3q0j
TitleCrystal Structure of the Mycobacterium tuberculosis Crotonase in complex with the Inhibitor AcetoacetylCoA
Componentsenoyl-CoA hydratase echA8
KeywordsLYASE/LYASE INHIBITOR / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Crotonase / Enoyl CoA Hydratase / LYASE / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


enoyl-CoA hydratase / enoyl-CoA hydratase activity / fatty acid beta-oxidation / peptidoglycan-based cell wall / fatty acid metabolic process / plasma membrane
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETOACETYL-COENZYME A / Probable enoyl-CoA hydratase echA8 / Probable enoyl-CoA hydratase EchA8
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsBruning, J.B. / Delgado, E. / Ghosh, S. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal Structure and Mechanism of the Prokaryotic Crotonase
Authors: Bruning, J.B. / Delgado, E. / Ghosh, S. / Sacchettini, J.C.
History
DepositionDec 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: enoyl-CoA hydratase echA8
B: enoyl-CoA hydratase echA8
C: enoyl-CoA hydratase echA8
D: enoyl-CoA hydratase echA8
E: enoyl-CoA hydratase echA8
F: enoyl-CoA hydratase echA8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0268
Polymers164,3236
Non-polymers1,7032
Water17,583976
1
A: enoyl-CoA hydratase echA8
B: enoyl-CoA hydratase echA8
C: enoyl-CoA hydratase echA8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0134
Polymers82,1613
Non-polymers8521
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14050 Å2
ΔGint-94 kcal/mol
Surface area27260 Å2
MethodPISA
2
D: enoyl-CoA hydratase echA8
E: enoyl-CoA hydratase echA8
F: enoyl-CoA hydratase echA8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0134
Polymers82,1613
Non-polymers8521
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13980 Å2
ΔGint-87 kcal/mol
Surface area26530 Å2
MethodPISA
3
A: enoyl-CoA hydratase echA8
B: enoyl-CoA hydratase echA8
C: enoyl-CoA hydratase echA8
hetero molecules

A: enoyl-CoA hydratase echA8
B: enoyl-CoA hydratase echA8
C: enoyl-CoA hydratase echA8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0268
Polymers164,3236
Non-polymers1,7032
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area34310 Å2
ΔGint-210 kcal/mol
Surface area48310 Å2
MethodPISA
4
D: enoyl-CoA hydratase echA8
E: enoyl-CoA hydratase echA8
F: enoyl-CoA hydratase echA8
hetero molecules

D: enoyl-CoA hydratase echA8
E: enoyl-CoA hydratase echA8
F: enoyl-CoA hydratase echA8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0268
Polymers164,3236
Non-polymers1,7032
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area34100 Å2
ΔGint-191 kcal/mol
Surface area46900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.962, 134.701, 134.334
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-502-

HOH

21C-833-

HOH

31E-504-

HOH

41F-892-

HOH

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Components

#1: Protein
enoyl-CoA hydratase echA8


Mass: 27387.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: h37rv / Gene: echA8, MT1100, MTV017.23c, Rv1070c / Plasmid: pVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P64016, UniProt: P9WNN9*PLUS, enoyl-CoA hydratase
#2: Chemical ChemComp-CAA / ACETOACETYL-COENZYME A / Acetoacetyl-CoA


Mass: 851.607 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 976 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350, 0.2 M LiCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 13, 2009 / Details: mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 70073 / Num. obs: 70073 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.4-2.443.40.4783.890.478199.9
2.44-2.493.40.4324.290.432199.9
2.49-2.533.50.3814.90.381199.9
2.53-2.593.50.3665.140.366199.8
2.59-2.643.50.3175.820.317199.7
2.64-2.73.50.3116.020.311199.7
2.7-2.773.50.2726.890.272199.6
2.77-2.853.50.2357.870.235199.7
2.85-2.933.50.1989.570.198199.5
2.93-3.023.50.17210.880.172199.5
3.02-3.133.50.14613.270.146199.2
3.13-3.263.50.11116.960.111199.4
3.26-3.413.60.09420.050.094199.1
3.41-3.583.60.0823.770.08198.8
3.58-3.813.60.06826.470.068198.9
3.81-4.13.60.06628.270.066198.6
4.1-4.523.70.0632.030.06198.4
4.52-5.173.70.05732.420.057198
5.17-6.513.70.0629.350.06197.4
6.51-503.50.0345.670.03192

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MJ3
Resolution: 2.4→26.42 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.08 / SU B: 16.23 / SU ML: 0.164 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.414 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22809 3522 5.1 %RANDOM
Rwork0.19796 ---
obs0.19951 66199 98.41 %-
all-69721 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.673 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→26.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11203 0 108 976 12287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02211478
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0421.97715553
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.79951531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41623.925456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.683151875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7961590
X-RAY DIFFRACTIONr_chiral_restr0.0690.21823
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218564
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5141.57572
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.335211982
X-RAY DIFFRACTIONr_scbond_it3.39733906
X-RAY DIFFRACTIONr_scangle_it5.0574.53566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.399→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 252 -
Rwork0.269 4805 -
obs--98.4 %
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)
12.7068-0.42260.27613.20181.6243.74750.0805-0.4267-0.14730.2264-0.01160.10530.6111-0.317-0.06890.4253-0.14370.09820.48460.07540.431826.0075-20.18735.1105
22.08390.63941.22071.23440.77932.20350.0605-0.4147-0.28110.129-0.01870.08840.3906-0.163-0.04180.3901-0.10890.09090.46440.03430.380332.2477-14.654235.4226
30.2098-0.10910.16850.4309-0.24860.5228-0.0043-0.21-0.13060.115-0.08860.03560.1809-0.26550.09290.3853-0.0540.03830.5193-0.05270.450729.743-7.346231.6151
40.21490.19530.03970.20370.01470.6665-0.0309-0.05970.0783-0.1335-0.01680.03220.0532-0.18910.04770.4002-0.01330.00290.4671-0.05560.461230.2041-6.589518.9491
59.67572.90054.83790.71521.24218.7626-0.343-0.40950.1509-0.1774-0.2229-0.01610.8064-0.89560.56590.5971-0.28840.09110.4591-0.27260.486726.3447-24.1765-0.4028
60.93531.8214-1.13663.5435-2.84765.87030.0092-0.26450.35390-0.17760.4332-0.5025-0.15720.16840.55630.0969-0.07340.3368-0.25770.592236.84532.207632.6187
71.0514-0.17810.31531.4939-0.93823.509-0.0634-0.24910.15960.0985-0.16330.0218-0.5790.19680.22670.51150.0437-0.0450.3481-0.16640.503442.03526.720832.2316
80.4064-0.4780.4540.66570.03433.1787-0.16470.06830.2368-0.1246-0.15250.03-0.83060.20370.31730.58390.039-0.15520.1712-0.01210.669545.592630.870213.8012
90.26930.160.15440.2516-0.04940.7835-0.0472-0.12630.0967-0.0358-0.15150.0781-0.0731-0.10230.19860.41070.075-0.05330.4046-0.09420.502135.56715.124823.99
109.9123-3.1173-3.80511.39960.17873.08120.3611-0.2710.07530.20070.0406-0.0092-0.48320.1028-0.40170.4405-0.06380.0490.7069-0.06750.380834.72684.069851.691
111.1310.66890.51021.78080.56521.6817-0.0620.29840.0836-0.30020.0513-0.05040.0849-0.05180.01080.4788-0.0265-0.13040.4480.01350.356732.18621.7371-13.3223
120.60090.3456-0.5242.7251-0.9260.9138-0.18730.3330.0013-0.42450.0382-0.08280.1112-0.20270.14910.4602-0.047-0.10230.412-0.02580.344934.9969-3.0134-7.7421
130.36940.15240.20430.84330.07390.3459-0.1110.01220.0819-0.1337-0.03580.0320.0997-0.14720.14680.4227-0.0208-0.05990.4432-0.04340.442732.1234-2.29581.9685
140.24680.19860.0940.36610.3880.6374-0.1051-0.12990.0746-0.0597-0.05810.1002-0.167-0.11110.16320.4270.0572-0.0980.3725-0.02330.503632.31498.8086.0803
152.7722-2.74892.46615.7145-1.33432.7835-0.16540.0314-0.0476-0.43740.1850.1831-0.4280.322-0.01960.6504-0.0102-0.17410.25850.06960.512144.198530.08272.8052
161.3860.22860.74261.2357-0.78981.9872-0.04090.2876-0.195-0.06660.083-0.10470.36340.1913-0.0420.39440.13620.05780.5516-0.10770.374619.0293-16.725862.622
170.2223-0.05110.01640.6131-0.22671.1510.06820.1775-0.0818-0.0438-0.0310.00450.02760.2119-0.03720.32050.07010.03990.5921-0.01150.375620.9339-5.219767.1085
181.7436-1.3831-0.23441.31130.36960.3614-0.119-0.06280.15630.1510.1773-0.1664-0.18590.2438-0.05830.3135-0.06960.00870.60380.02750.447725.4382.316371.427
190.5803-0.1642-0.12130.3480.25750.66970.02180.0990.03660.1101-0.03770.02810.20190.11510.01590.47520.0823-0.01960.4537-0.00850.390515.3678-14.121786.1706
2029.434-2.672823.513610.863714.899150.0402-0.00321.560.88443.2885-1.24080.14876.23981.24291.2441.69250.66240.27210.77270.38780.169924.4267-23.873997.977
212.9316-1.61790.99572.0679-1.04081.43770.10920.68190.92810.1827-0.0616-0.3046-0.7744-0.0568-0.04770.82560.02660.23710.36720.30320.530411.323932.438467.1453
221.0247-0.3445-0.35270.91020.90511.43930.01890.23340.3574-0.1944-0.1202-0.0502-0.762-0.11780.10120.7057-0.01340.00380.32030.14460.41015.7927.895373.0283
230.4751-0.176-0.32380.48060.27591.45060.06290.0640.0488-0.006-0.0486-0.1274-0.31130.1103-0.01430.4675-0.11150.02240.40390.04960.448612.617119.877279.9606
243.52170.5829-0.97071.46630.93720.5998-0.14030.03140.0071-0.2270.2182-0.1127-0.07820.1484-0.07790.3536-0.22020.04020.60680.05120.446126.110517.815775.0341
250.99060.0936-0.46030.60730.54030.8050.11850.2488-0.0056-0.01650.0149-0.0312-0.1943-0.1426-0.13350.40840.02830.04830.56020.02770.35511.65636.022157.9948
260.7832-0.75640.29252.75760.72941.8205-0.0458-0.22690.01650.40840.14370.07490.01460.0294-0.09790.496-0.0046-0.110.4656-0.01210.35216.54612.1589111.1795
270.3751-0.1166-0.61130.9865-0.39931.2437-0.0948-0.21320.01830.27040.02510.06530.08080.28140.06980.48690.0105-0.12450.4122-0.04760.411315.0798-3.6677105.275
280.1656-0.18690.12280.67810.14730.75610.0110.05410.06250.1688-0.005-0.0440.10860.1825-0.00590.41020.0047-0.05290.4773-0.01310.419617.7037-2.412995.0355
290.3667-0.06-0.03610.9588-0.59091.29180.04320.13430.06920.1103-0.1485-0.1564-0.29760.34860.10530.3726-0.1292-0.06980.4506-0.00060.432921.94869.938895.3678
300.424-0.23040.07912.44571.27430.78590.04480.16370.14750.05870.0201-0.3103-0.0245-0.0525-0.0650.5430.00160.00520.35180.04110.48124.064721.990890.4634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 39
2X-RAY DIFFRACTION2A40 - 81
3X-RAY DIFFRACTION3A82 - 139
4X-RAY DIFFRACTION4A140 - 234
5X-RAY DIFFRACTION5A235 - 255
6X-RAY DIFFRACTION6B1 - 26
7X-RAY DIFFRACTION7B27 - 57
8X-RAY DIFFRACTION8B58 - 81
9X-RAY DIFFRACTION9B82 - 233
10X-RAY DIFFRACTION10B234 - 254
11X-RAY DIFFRACTION11C1 - 39
12X-RAY DIFFRACTION12C40 - 79
13X-RAY DIFFRACTION13C80 - 153
14X-RAY DIFFRACTION14C154 - 227
15X-RAY DIFFRACTION15C228 - 255
16X-RAY DIFFRACTION16D2 - 91
17X-RAY DIFFRACTION17D92 - 146
18X-RAY DIFFRACTION18D147 - 185
19X-RAY DIFFRACTION19D186 - 237
20X-RAY DIFFRACTION20D238 - 256
21X-RAY DIFFRACTION21E2 - 31
22X-RAY DIFFRACTION22E32 - 80
23X-RAY DIFFRACTION23E81 - 164
24X-RAY DIFFRACTION24E165 - 185
25X-RAY DIFFRACTION25E186 - 254
26X-RAY DIFFRACTION26F1 - 42
27X-RAY DIFFRACTION27F43 - 79
28X-RAY DIFFRACTION28F80 - 158
29X-RAY DIFFRACTION29F159 - 209
30X-RAY DIFFRACTION30F210 - 254

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  • 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

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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

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