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- PDB-2fyf: Structure of a putative phosphoserine aminotransferase from Mycob... -

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Basic information

Entry
Database: PDB / ID: 2fyf
TitleStructure of a putative phosphoserine aminotransferase from Mycobacterium Tuberculosis
Componentsphosphoserine aminotransferasePhosphoserine transaminase
KeywordsTRANSFERASE / PLP-dependent enzyme / dimer / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB
Function / homology
Function and homology information


glycine biosynthetic process, by transamination of glyoxylate / serine-pyruvate transaminase activity / phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / alanine-glyoxylate transaminase activity / pyridoxine biosynthetic process / L-serine biosynthetic process / peroxisome / pyridoxal phosphate binding / extracellular region ...glycine biosynthetic process, by transamination of glyoxylate / serine-pyruvate transaminase activity / phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / alanine-glyoxylate transaminase activity / pyridoxine biosynthetic process / L-serine biosynthetic process / peroxisome / pyridoxal phosphate binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Phosphoserine aminotransferase, Mycobacterial-type / Phosphoserine aminotransferase / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Phosphoserine aminotransferase, Mycobacterial-type / Phosphoserine aminotransferase / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TETRACHLOROPLATINATE(II) / PYRIDOXAL-5'-PHOSPHATE / Phosphoserine aminotransferase / Phosphoserine aminotransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / MIRAS / Resolution: 1.5 Å
AuthorsCoulibaly, F. / Lassalle, E. / Baker, E.N. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of phosphoserine aminotransferase from Mycobacterium tuberculosis.
Authors: Coulibaly, F. / Lassalle, E. / Baker, H.M. / Baker, E.N.
History
DepositionFeb 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jun 13, 2012Group: Database references
Revision 1.4Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.5Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: phosphoserine aminotransferase
B: phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,29119
Polymers85,9382
Non-polymers3,35217
Water15,241846
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-174 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.478, 94.056, 101.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is the dimer present in the asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein phosphoserine aminotransferase / Phosphoserine transaminase / PSAT


Mass: 42969.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: serC / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pRP
References: UniProt: P63514, UniProt: P9WQ73*PLUS, phosphoserine transaminase

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Non-polymers , 5 types, 863 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PC4 / TETRACHLOROPLATINATE(II)


Mass: 336.890 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl4Pt
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 846 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris-HCl 100mM, NH4SO4 2.2M, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07198 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 25, 2005
RadiationMonochromator: high resolution Si(311) cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07198 Å / Relative weight: 1
Reflection
IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)D res low (Å)Num. obs% possible obs
18.45964360.0861.021.52511883599.7
29.73451960.0570.991.6209734999.7
37.81549870.1211.052.1154295598.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obsChi squared
3.23251235899.610.051.048
2.563.231202310010.0581.007
2.242.561193910010.071.013
2.042.241188110010.0861.024
1.892.041184610010.1151.042
1.781.891182510010.1671.023
1.691.781180510010.2331.001
1.621.691181610010.3240.999
1.551.621175310010.4441.025
1.51.551158998.110.5591.046
3.44201007998.920.0290.986
2.733.44988410020.0370.995
2.392.73979310020.050.979
2.172.39975110020.0620.986
2.022.17970110020.0790.993
1.92.02969210020.111.013
1.81.9966399.920.1520.978
1.721.8965899.720.1990.98
1.661.72960899.420.2611.007
1.61.66952098.920.3371.013
4.4915433494.130.0661.011
3.584.4942879730.0741.117
3.133.58428497.930.0931.043
2.853.13429798.630.1261.074
2.642.8542929930.1631.064
2.492.64429999.430.21.064
2.362.49430699.530.2331.056
2.262.36429599.730.2741.031
2.172.26431999.730.3171.024
2.12.17424299.330.3650.999
ReflectionResolution: 1.5→25 Å / Num. all: 118835 / Num. obs: 118835 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.086 / Χ2: 1.023 / Net I/σ(I): 17.38
Reflection shellResolution: 1.5→1.55 Å / % possible obs: 98.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.6 / Num. unique all: 11589 / Num. unique obs: 11589 / Χ2: 1.046 / % possible all: 98.1

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Phasing

PhasingMethod: MIRAS
Phasing set
ID
1
2
3
Phasing MIR der

Native set-ID: 1 / Resolution: 2.1→19.76 Å

IDDer set-IDPower acentricPower centricReflection acentricReflection centric
ISO_1100386483483
ISO_221.7441.505385461745
ISO_330.8020.701384061737
Phasing MIR der shell
Highest resolution (Å)Lowest resolution (Å)Der-IDPower acentricPower centricReflection acentricReflection centric
8.5219.76ISO_100370119
6.338.52ISO_100750160
5.266.33ISO_100993166
4.595.26ISO_1001172175
4.134.59ISO_1001323169
3.784.13ISO_1001501169
3.513.78ISO_1001625184
3.293.51ISO_1001760177
3.113.29ISO_1001896183
2.953.11ISO_1001992165
2.822.95ISO_1002126175
2.72.82ISO_1002233169
2.62.7ISO_1002296171
2.52.6ISO_1002423180
2.422.5ISO_1002488188
2.342.42ISO_1002605184
2.282.34ISO_1002689195
2.212.28ISO_1002747192
2.152.21ISO_1002824189
2.12.15ISO_1002835173
8.5219.76ISO_23.0343.05536661
6.338.52ISO_23.2672.80274576
5.266.33ISO_23.0521.8199087
4.595.26ISO_22.6331.974116692
4.134.59ISO_22.231.905132086
3.784.13ISO_22.0881.33149984
3.513.78ISO_21.9031.404162492
3.293.51ISO_21.8551.415175890
3.113.29ISO_21.7241.293189591
2.953.11ISO_21.6071.156199179
2.822.95ISO_21.511.036212390
2.72.82ISO_21.361.099223185
2.62.7ISO_21.2550.738229289
2.52.6ISO_21.1350.833241991
2.422.5ISO_21.0370.571248592
2.342.42ISO_20.9360.728260391
2.282.34ISO_20.8510.563268593
2.212.28ISO_20.7780.457273894
2.152.21ISO_20.7140.502282094
2.12.15ISO_20.6540.395279688
8.5219.76ISO_31.9842.09835258
6.338.52ISO_31.9141.49474472
5.266.33ISO_31.6531.29398786
4.595.26ISO_31.1751.049116391
4.134.59ISO_30.9270.659131984
3.784.13ISO_30.8540.534149183
3.513.78ISO_30.7680.48161591
3.293.51ISO_30.7820.538174890
3.113.29ISO_30.7470.535188493
2.953.11ISO_30.7280.481197879
2.822.95ISO_30.7110.419212190
2.72.82ISO_30.7040.478222485
2.62.7ISO_30.6820.384228990
2.52.6ISO_30.6570.519241491
2.422.5ISO_30.5970.42247493
2.342.42ISO_30.5670.499259591
2.282.34ISO_30.5620.382267493
2.212.28ISO_30.5210.426272295
2.152.21ISO_30.5270.373280294
2.12.15ISO_30.5050.419281088

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MIR / Resolution: 1.5→19.932 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.166 / WRfactor Rwork: 0.142 / SU B: 1.936 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Translation, Libration, Skew (TLS) Model
σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1664 5973 5.032 %Random
Rwork0.144 ---
all0.145 118697 --
obs0.145 118697 99.724 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 8.154 Å2
Baniso -1Baniso -2Baniso -3
1-0.034 Å20 Å20 Å2
2---0.027 Å20 Å2
3----0.007 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 99 846 6511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225953
X-RAY DIFFRACTIONr_bond_other_d0.0010.025426
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9718191
X-RAY DIFFRACTIONr_angle_other_deg0.862312623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8555808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04824.016244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37715891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5551538
X-RAY DIFFRACTIONr_chiral_restr0.0850.2937
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026752
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021184
X-RAY DIFFRACTIONr_nbd_refined0.2230.21231
X-RAY DIFFRACTIONr_nbd_other0.1840.25619
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23003
X-RAY DIFFRACTIONr_nbtor_other0.0840.23490
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2593
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.238
X-RAY DIFFRACTIONr_mcbond_it0.9211.54875
X-RAY DIFFRACTIONr_mcbond_other0.2191.51528
X-RAY DIFFRACTIONr_mcangle_it1.11826138
X-RAY DIFFRACTIONr_mcangle_other0.48625251
X-RAY DIFFRACTIONr_scbond_it2.03232521
X-RAY DIFFRACTIONr_scbond_other0.64834829
X-RAY DIFFRACTIONr_scangle_it2.9514.52017
X-RAY DIFFRACTIONr_scangle_other1.1784.57372
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allNum. reflection obs% reflection obs (%)
1.498-1.5360.2474470.20680190.2088703892097.277
1.536-1.5780.2274170.18880160.198436832099.964
1.578-1.6240.2043980.17678180.1788221794099.939
1.624-1.6730.1833970.16675760.1677976792099.962
1.673-1.7280.1793810.15573880.1577772760099.961
1.728-1.7880.1783900.14871130.1497507778099.947
1.788-1.8550.1613580.14469020.1457266714099.917
1.855-1.930.1553460.14266490.1437001690099.914
1.93-2.0150.1673530.13663550.1386710704099.97
2.015-2.1120.1493130.13161040.1326419624099.969
2.112-2.2250.1512980.12958540.136153594099.984
2.225-2.3580.1522780.1355330.1315817554099.897
2.358-2.5180.1632910.1351650.1315458580099.963
2.518-2.7160.1622770.13548530.1365131552099.981
2.716-2.970.1522300.13545130.1364744458099.979
2.97-3.3120.1652150.13640700.1384287428099.953
3.312-3.8060.1382040.13236410.1323846406099.974
3.806-4.620.1451610.12331400.1243305320099.879
4.62-6.3650.1731510.1624660.1612625300099.695
6.365-19.9320.207680.19615490.1961649134098.059
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)
10.3658-0.17590.11620.5449-0.04270.4984-0.00750.0108-0.01370.0070.01580.01930.00980.0398-0.00830.00140.00290.00090.0101-0.0030.015663.51543.8461.619
20.3739-0.24640.47531.3257-0.98362.3552-0.03630.0177-0.0579-0.02660.0621-0.0150.0407-0.086-0.02590.00990.00640.00280.0381-0.01640.021768.07636.219-6.301
30.5636-0.0361-0.08310.4261-0.06610.513-0.03330.02930.00730.03760.0252-0.0119-0.0045-0.01020.0081-0.0009-0.00210.00020.0035-0.0054-0.000862.86846.7792.559
41.1684-0.1657-0.46771.6174-0.24721.1217-0.0009-0.0128-0.0060.09870.0272-0.03640.00290.0334-0.02640.04420.0291-0.00520.03110.00130.032371.6727.23915.146
50.3708-0.1543-0.10970.6968-0.03940.3618-0.00470.02410.02030.00180.0019-0.02930.0263-0.04920.0029-0.01050.00830.00360.01390.00320.028751.37654.1940.115
60.3324-0.3323-0.65821.56761.08892.2187-0.03850.02560.07650.01080.09950.001-0.00820.1009-0.06110.00390.0077-0.00270.04940.00390.018846.72858.018-4.69
70.5626-0.09550.06170.48870.1340.6346-0.03550.0298-0.01430.03930.03470.02570.02070.01550.0009-0.0029-0.00160.00670.00590.00210.006451.21448.1232.527
81.1439-0.29590.32431.47010.14830.9051-0.0379-0.0007-0.01480.09680.03950.0454-0.016-0.0192-0.00160.03350.02710.0160.0279-0.00140.031941.77467.914.72
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA8 - 9830 - 120
22AA99 - 172121 - 194
33AA173 - 279195 - 301
44AA280 - 376302 - 398
55BB8 - 9830 - 120
66BB99 - 172121 - 194
77BB173 - 278195 - 300
88BB279 - 376301 - 398

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