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- PDB-6bom: Crystal structure of mutant 2-methylcitrate synthase mcsAG306A fr... -

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Basic information

Entry
Database: PDB / ID: 6bom
TitleCrystal structure of mutant 2-methylcitrate synthase mcsAG306A from Aspergillus fumigatus.
Components2-methylcitrate synthase, mitochondrial
KeywordsTRANSFERASE / mcsA / 2-methylcitrate synthase / citrate synthase
Function / homology
Function and homology information


2-methylcitrate synthase / 2-methylcitrate synthase activity / propionate catabolic process, 2-methylcitrate cycle / citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / tricarboxylic acid cycle / mitochondrial matrix
Similarity search - Function
Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily ...Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-methylcitrate synthase, mitochondrial
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSchlachter, C. / Chruszcz, M.
CitationJournal: Biol.Chem. / Year: 2019
Title: Comparative studies of Aspergillus fumigatus 2-methylcitrate synthase and human citrate synthase.
Authors: Schlachter, C.R. / Klapper, V. / Radford, T. / Chruszcz, M.
History
DepositionNov 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-methylcitrate synthase, mitochondrial
B: 2-methylcitrate synthase, mitochondrial
C: 2-methylcitrate synthase, mitochondrial
D: 2-methylcitrate synthase, mitochondrial
E: 2-methylcitrate synthase, mitochondrial
F: 2-methylcitrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,5517
Polymers291,4296
Non-polymers1221
Water19,0781059
1
A: 2-methylcitrate synthase, mitochondrial
B: 2-methylcitrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2653
Polymers97,1432
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: 2-methylcitrate synthase, mitochondrial
D: 2-methylcitrate synthase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)97,1432
Polymers97,1432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: 2-methylcitrate synthase, mitochondrial
F: 2-methylcitrate synthase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)97,1432
Polymers97,1432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.021, 128.860, 258.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEUAA30 - 4636 - 439
21THRTHRLEULEUBB30 - 4636 - 439
12THRTHRLEULEUAA30 - 4636 - 439
22THRTHRLEULEUCC30 - 4636 - 439
13THRTHRLYSLYSAA30 - 4646 - 440
23THRTHRLYSLYSDD30 - 4646 - 440
14ALAALALEULEUAA31 - 4637 - 439
24ALAALALEULEUEE31 - 4637 - 439
15ALAALALEULEUAA31 - 4637 - 439
25ALAALALEULEUFF31 - 4637 - 439
16THRTHRLYSLYSBB30 - 4646 - 440
26THRTHRLYSLYSCC30 - 4646 - 440
17THRTHRLEULEUBB30 - 4636 - 439
27THRTHRLEULEUDD30 - 4636 - 439
18ALAALALEULEUBB31 - 4637 - 439
28ALAALALEULEUEE31 - 4637 - 439
19ALAALALEULEUBB31 - 4637 - 439
29ALAALALEULEUFF31 - 4637 - 439
110THRTHRLEULEUCC30 - 4636 - 439
210THRTHRLEULEUDD30 - 4636 - 439
111ALAALALEULEUCC31 - 4637 - 439
211ALAALALEULEUEE31 - 4637 - 439
112ALAALALEULEUCC31 - 4637 - 439
212ALAALALEULEUFF31 - 4637 - 439
113ALAALALEULEUDD31 - 4637 - 439
213ALAALALEULEUEE31 - 4637 - 439
114ALAALALEULEUDD31 - 4637 - 439
214ALAALALEULEUFF31 - 4637 - 439
115ALAALALYSLYSEE31 - 4647 - 440
215ALAALALYSLYSFF31 - 4647 - 440

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
2-methylcitrate synthase, mitochondrial / / Methylcitrate synthase / (2S / 3S)-2-methylcitrate synthase / Citrate synthase 2


Mass: 48571.453 Da / Num. of mol.: 6 / Mutation: G306A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) (mold)
Strain: CEA10 / CBS 144.89 / FGSC A1163 / Gene: mcsA, AFUB_094700 / Production host: Escherichia coli (E. coli)
References: UniProt: B0YD89, 2-methylcitrate synthase, citrate synthase (unknown stereospecificity)
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1059 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Tris pH 7.5 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. obs: 171718 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.039 / Rrim(I) all: 0.091 / Rsym value: 0.065 / Net I/σ(I): 29.2
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8490 / Rpim(I) all: 0.323 / Rrim(I) all: 0.783 / Rsym value: 0.691 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UQO
Resolution: 2.05→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.16 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21159 8687 5.1 %RANDOM
Rwork0.18124 ---
obs0.18277 162833 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.877 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0 Å2-0 Å2
2---0.82 Å20 Å2
3---0.57 Å2
Refinement stepCycle: 1 / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20263 0 8 1059 21330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01920793
X-RAY DIFFRACTIONr_bond_other_d00.0219543
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.9728239
X-RAY DIFFRACTIONr_angle_other_deg3.632345365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.33352614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75324.178888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.688153477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.12615109
X-RAY DIFFRACTIONr_chiral_restr0.1160.23143
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02123123
X-RAY DIFFRACTIONr_gen_planes_other0.0140.024122
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_it1.9583.11510466
X-RAY DIFFRACTIONr_mcbond_other1.9583.11410464
X-RAY DIFFRACTIONr_mcangle_it2.9714.6613076
X-RAY DIFFRACTIONr_mcangle_other2.9714.6613077
X-RAY DIFFRACTIONr_scbond_it2.4873.40410327
X-RAY DIFFRACTIONr_scbond_other2.4873.40410327
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9084.9815164
X-RAY DIFFRACTIONr_long_range_B_refined6.32237.57924174
X-RAY DIFFRACTIONr_long_range_B_other6.32237.5824175
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A279600.08
12B279600.08
21A277140.08
22C277140.08
31A278400.08
32D278400.08
41A274940.09
42E274940.09
51A277140.08
52F277140.08
61B281020.08
62C281020.08
71B281140.07
72D281140.07
81B276540.09
82E276540.09
91B280000.07
92F280000.07
101C277600.08
102D277600.08
111C275200.09
112E275200.09
121C277360.08
122F277360.08
131D274540.09
132E274540.09
141D278400.07
142F278400.07
151E275440.09
152F275440.09
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 596 -
Rwork0.253 11731 -
obs--98.25 %
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)
10.8062-0.8001-0.20833.75170.32530.6721-0.1564-0.1593-0.06280.41270.04910.02270.06370.02910.10740.13880.03060.00260.11990.00420.072222.6768.833-47.545
20.529-0.1066-0.05430.54550.18740.4535-0.05070.0186-0.07720.02130.0503-0.04910.06070.01970.00030.1414-0.00660.04090.1358-0.01220.146925.8523.279-68.747
31.61050.9082-0.89741.138-0.99041.82340.06450.11110.11260.1637-0.00880.0385-0.1639-0.0372-0.05560.11850.00410.02810.13980.00830.140544.01223.567-72.711
40.339-0.0075-0.01180.65750.13050.1324-0.1158-0.0344-0.00570.06050.0397-0.04330.0323-0.00260.07610.1350.01050.01930.1639-0.01320.145618.97614.862-60.775
51.0862-0.81010.56271.4758-0.6811.112-0.1955-0.05110.19160.20120.0793-0.1436-0.1603-0.03330.11620.13780.0141-0.00370.1245-0.03340.111.24535.272-58.614
60.5319-0.1219-0.08450.5039-0.18680.4536-0.02070.0527-0.003-0.05040.04030.01660.0049-0.0984-0.01960.1203-0.01470.01060.1786-0.00360.117-0.73922.657-72.088
70.46750.0141-0.12822.0569-0.86311.2635-0.10820.0281-0.00860.09790.21930.14480.0273-0.1271-0.1110.09220.02240.01810.18880.03560.1263-15.40110.064-50.629
80.14680.0418-0.23090.1138-0.14980.5106-0.04050.06690.01850.04670.08-0.00880.0606-0.0761-0.03940.16470.0024-0.00790.1877-0.01070.15192.77417.388-58.985
90.8820.5121-0.86561.7337-0.67121.8123-0.06410.1514-0.1497-0.38960.02650.07420.33050.05540.03760.1818-0.0011-0.08160.2089-0.04220.0988-14.62125.546-119.776
100.6781-0.06430.00040.4877-0.03540.94740.04130.0272-0.0577-0.02770.02120.1040.0249-0.0697-0.06260.1149-0.0108-0.00870.15810.01150.124-22.01436.674-101.796
111.1692-0.25710.15422.7277-0.19561.9188-0.00570.15440.1361-0.31280.09470.166-0.1544-0.0383-0.08890.12830.0153-0.02170.14830.0710.1205-34.26756.32-117.102
120.8731-0.009-0.12350.4814-0.20840.9980.01310.1237-0.0552-0.1340.02220.0735-0.00930.0208-0.03540.157-0.0067-0.01590.198-0.01490.0842-10.86736.776-113.404
130.55180.14090.12360.61010.02530.83710.00260.11780.0597-0.07230.0267-0.0749-0.11730.1833-0.02940.1412-0.05270.02380.20460.00250.08447.22749.611-108.958
140.80540.7895-0.01874.2307-2.22466.2899-0.2502-0.0401-0.2668-0.39260.0051-0.21140.9581-0.00110.24520.36430.03820.06390.1161-0.03380.184419.69419.539-102.623
150.59-0.11470.3273.4378-0.48763.76440.01270.10860.0305-0.2959-0.1385-0.50130.59560.02360.12580.21880.06130.06510.2143-0.02860.146721.60928.009-108.348
160.4838-0.04270.48370.6140.58551.24580.05860.11740.0311-0.0817-0.0219-0.04850.06930.102-0.03660.1428-0.01770.01370.20250.020.0758-1.29541.61-113.348
172.0034-1.2815-1.57572.85521.53262.7028-0.2151-0.4614-0.31980.4890.15850.06310.38630.15580.05670.31030.1147-0.04820.33180.1150.135-9.94827.156-8.392
181.388-0.2551-0.11860.50940.36590.84340.0115-0.1926-0.02370.1290.1485-0.10570.03530.1655-0.16010.16070.0599-0.01020.1653-0.0350.1088-2.38335.407-27.709
190.43680.0794-0.62784.20990.50821.01850.2773-0.30370.21040.37530.0629-0.371-0.32040.4444-0.34020.3166-0.09840.04050.3369-0.2760.26329.63359.095-15.634
201.307-0.2556-0.44630.22170.15140.76570.0094-0.35180.09950.14440.2041-0.0706-0.10250.1097-0.21350.27930.05810.00950.256-0.03610.1418-6.69643.067-18.57
211.046-0.3293-0.03310.99110.06360.9232-0.0445-0.19690.01230.12810.11610.1937-0.0928-0.105-0.07170.14190.05290.05490.1280.0470.1297-31.2949.164-23.651
223.32312.00670.77594.1326-1.48883.2536-0.147-0.0475-0.59870.14960.06610.20910.13030.22440.08080.120.06490.16390.05750.1520.6102-42.33219.803-21.014
232.91510.88050.29314.1847-0.35741.2723-0.1539-0.1855-0.40540.1350.07690.94070.2486-0.09760.0770.1349-0.00360.1230.10190.13190.5465-47.15228.96-21.886
240.5898-0.12170.1551.6711-0.02411.1568-0.1078-0.2854-0.03360.25450.13230.1863-0.0128-0-0.02450.16980.0610.0560.20840.02410.0596-22.22342.72-16.907
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 74
2X-RAY DIFFRACTION2A75 - 304
3X-RAY DIFFRACTION3A305 - 422
4X-RAY DIFFRACTION4A423 - 464
5X-RAY DIFFRACTION5B30 - 75
6X-RAY DIFFRACTION6B76 - 304
7X-RAY DIFFRACTION7B305 - 395
8X-RAY DIFFRACTION8B396 - 464
9X-RAY DIFFRACTION9C30 - 77
10X-RAY DIFFRACTION10C78 - 304
11X-RAY DIFFRACTION11C305 - 424
12X-RAY DIFFRACTION12C425 - 464
13X-RAY DIFFRACTION13D30 - 304
14X-RAY DIFFRACTION14D305 - 340
15X-RAY DIFFRACTION15D341 - 420
16X-RAY DIFFRACTION16D421 - 464
17X-RAY DIFFRACTION17E31 - 75
18X-RAY DIFFRACTION18E76 - 310
19X-RAY DIFFRACTION19E311 - 399
20X-RAY DIFFRACTION20E400 - 464
21X-RAY DIFFRACTION21F31 - 304
22X-RAY DIFFRACTION22F305 - 357
23X-RAY DIFFRACTION23F358 - 422
24X-RAY DIFFRACTION24F423 - 464

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