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- PDB-3ooj: C1A mutant of E. coli GlmS in complex with glucose-6P and glutamate -

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Basic information

Entry
Database: PDB / ID: 3ooj
TitleC1A mutant of E. coli GlmS in complex with glucose-6P and glutamate
ComponentsGlucosamine/fructose-6-phosphate aminotransferase, isomerizing
KeywordsTRANSFERASE / ammonia channel / glutamine amidotransferase
Function / homology
Function and homology information


glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / protein N-linked glycosylation / glutamine metabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function
Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / Glutamine amidotransferase type 2 domain profile. / SIS domain / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain profile. ...Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / Glutamine amidotransferase type 2 domain profile. / SIS domain / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / GLUCOSE-6-PHOSPHATE / GLUTAMIC ACID / : / Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMouilleron, S. / Golinelli-Pimpaneau, B.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for morpheein-type allosteric regulation of Escherichia coli glucosamine-6-phosphate synthase: equilibrium between inactive hexamer and active dimer.
Authors: Mouilleron, S. / Badet-Denisot, M.A. / Pecqueur, L. / Madiona, K. / Assrir, N. / Badet, B. / Golinelli-Pimpaneau, B.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
B: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
C: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
D: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
E: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
F: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
G: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
H: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)540,58840
Polymers534,5128
Non-polymers6,07632
Water26,1761453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32710 Å2
ΔGint-76 kcal/mol
Surface area119490 Å2
MethodPISA
2
B: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
D: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
E: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
F: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
H: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
hetero molecules

B: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
D: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
E: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
F: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
H: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
hetero molecules

B: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
D: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
E: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
F: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
H: Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,013,60275
Polymers1,002,20915
Non-polymers11,39260
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area32510 Å2
ΔGint-75 kcal/mol
Surface area119560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)247.599, 247.599, 630.862
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11H-676-

HOH

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Components

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Protein / Sugars , 2 types, 16 molecules ABCDEFGH

#1: Protein
Glucosamine/fructose-6-phosphate aminotransferase, isomerizing


Mass: 66813.945 Da / Num. of mol.: 8 / Fragment: glucosamine-6P synthase / Mutation: C1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PMA1 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: C9QXA7, UniProt: P17169*PLUS
#3: Sugar
ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 1477 molecules

#2: Chemical
ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-G6Q / GLUCOSE-6-PHOSPHATE / Glucose 6-phosphate


Mass: 260.136 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1453 / 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: 3.48 Å3/Da / Density % sol: 64.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% PEG3350, 0.2 ammonium acetate, 0.1M HEPES pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC / Detector: CCD / Date: Mar 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 250723 / % possible obs: 98.6 % / Redundancy: 7.9 % / Rsym value: 0.113 / Net I/σ(I): 5.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 1.1 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.993 Å / SU ML: 0.82 / σ(F): 1.34 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 12632 5.04 %
Rwork0.1784 --
obs0.1805 250721 98.51 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.223 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0299 Å2-0 Å20 Å2
2---0.0299 Å20 Å2
3---0.0598 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37120 0 384 1453 38957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00838279
X-RAY DIFFRACTIONf_angle_d1.17851885
X-RAY DIFFRACTIONf_dihedral_angle_d17.57414271
X-RAY DIFFRACTIONf_chiral_restr0.0785959
X-RAY DIFFRACTIONf_plane_restr0.0056724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52840.33353910.27926941X-RAY DIFFRACTION87
2.5284-2.5580.28424030.24587123X-RAY DIFFRACTION89
2.558-2.58920.29643960.25687363X-RAY DIFFRACTION92
2.5892-2.62190.31684110.24767511X-RAY DIFFRACTION94
2.6219-2.65630.28394090.22827695X-RAY DIFFRACTION96
2.6563-2.69260.26384350.21837889X-RAY DIFFRACTION98
2.6926-2.7310.28344530.21917956X-RAY DIFFRACTION100
2.731-2.77160.29844140.2218023X-RAY DIFFRACTION100
2.7716-2.81480.26064320.20818028X-RAY DIFFRACTION100
2.8148-2.86090.28553950.21538020X-RAY DIFFRACTION100
2.8609-2.910.24274380.20738019X-RAY DIFFRACTION100
2.91-2.96280.26694340.21018033X-RAY DIFFRACTION100
2.9628-3.01960.24484050.20218019X-RAY DIFFRACTION100
3.0196-3.0810.27884220.20577984X-RAY DIFFRACTION100
3.081-3.14780.23614320.19118039X-RAY DIFFRACTION100
3.1478-3.22070.24674130.19548040X-RAY DIFFRACTION100
3.2207-3.30090.234320.19028022X-RAY DIFFRACTION100
3.3009-3.38970.24874770.19578013X-RAY DIFFRACTION100
3.3897-3.48890.24454300.1958020X-RAY DIFFRACTION100
3.4889-3.60090.22024220.18138019X-RAY DIFFRACTION100
3.6009-3.72880.22934300.18328035X-RAY DIFFRACTION100
3.7288-3.87710.21353880.17028083X-RAY DIFFRACTION100
3.8771-4.05220.19624180.16328061X-RAY DIFFRACTION100
4.0522-4.26390.17264300.14218047X-RAY DIFFRACTION100
4.2639-4.52810.16363950.13388110X-RAY DIFFRACTION100
4.5281-4.8730.17364020.13168157X-RAY DIFFRACTION100
4.873-5.35490.18954360.14588095X-RAY DIFFRACTION100
5.3549-6.11030.19254290.17258167X-RAY DIFFRACTION100
6.1103-7.62660.21914130.17528227X-RAY DIFFRACTION100
7.6266-19.9940.16724470.15578350X-RAY DIFFRACTION100
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)
10.09480.0417-0.02730.074-0.00370.05140.149-0.2431-0.16110.0773-0.05580.00450.1873-0.03130.01030.3126-0.1075-0.09410.21130.08180.2977-41.8049-72.2583-45.453
20.19140.1009-0.06880.08160.0020.2041-0.016-0.0124-0.0450.0068-0.00610.03850.0423-0.0017-0.02830.1901-0.031-0.05310.1366-0.01010.1834-29.5226-53.3377-71.4381
30.0513-0.02730.01640.03580.00130.04390.02770.2149-0.2722-0.1899-0.02680.1996-0.05930.0335-00.3817-0.08860.01940.5097-0.19370.5624-12.3329-82.5125-115.7691
40.17220.0183-0.03550.0612-0.02670.1016-0.03310.05550.019-0.04110.0424-0.0001-0.02340.02760.02370.2491-0.0628-0.04180.167-0.01850.1418-12.6214-43.3184-92.4306
50.0825-0.07950.04410.0885-0.03260.03770.0416-0.0284-0.23530.01140.05960.06340.23820.04170.07010.61560.5882-0.050.18050.08250.294629.1032-69.0807-17.9412
60.1775-0.0608-0.00890.1232-0.0070.16270.0025-0.0259-0.03230.0118-0.0049-0.00180.05480.0162-0.0220.1070.0056-0.00920.0723-0.01810.07167.1234-42.8558-24.3872
70.02080.0104-0.00980.0270.00240.02110.1146-0.11120.05910.3472-0.21820.25680.1286-0.2397-0.00190.5321-0.2680.13640.702-0.14040.3646-50.663-51.1412-12.0792
80.15840.00660.09040.14530.01320.1384-0.0072-0.02140.0035-0.0279-0.01290.0158-0.0225-0.0307-0.03490.1140.00920.00040.1215-0.00570.1062-14.7863-27.4665-33.233
90.04180.0491-0.02320.1601-0.01450.04550.02410.38740.0776-0.00820.1129-0.0568-0.0684-0.3040.06670.30580.08760.14020.50570.0740.269642.85394.0694-161.614
100.06790.055-0.05930.2095-0.06060.11210.03830.1105-0.0824-0.0646-0.048-0.1523-0.04510.0269-0.00980.11810.03550.0130.2355-0.00340.205831.4446-15.1644-135.2227
110.0340.00850.01160.02250.0220.0435-0.01340.0186-0.04780.0504-0.0305-0.03790.12180.0494-0.0010.29150.10590.07430.6975-0.27460.615512.8518-63.7158-152.0205
120.17040.0969-0.03280.1279-0.12940.13420.051-0.0081-0.1070.0686-0.0359-0.0670.0165-0.0175-00.23690.0113-0.0310.1839-0.02790.225915.3175-31.6694-118.8418
130.0274-0.0237-0.00320.01750.00560.0237-0.1323-0.1162-0.11460.0105-0.0616-0.0110.00280.1418-00.47660.22510.02640.71560.19660.66266.6789-62.5745-30.7264
140.13770.1071-0.03410.13680.04320.0985-0.0085-0.03140.0203-0.02580.0166-0.06260.00310.03620.00610.12680.03020.02250.1608-0.03050.171538.9486-37.3885-60.4357
150.0984-0.0016-0.00670.07330.04940.0556-0.11140.0691-0.19450.15160.03270.00640.2511-0.0369-0.03510.4394-0.04390.14120.2396-0.07530.510317.4249-87.9666-89.7574
160.18740.04910.10360.19440.07460.10910.0135-0.1203-0.4184-0.13040.23560.05910.1688-0.140.35360.1470.10650.2399-0.0516-0.28080.025730.6313-58.3957-77.8995
17-0.00390.02360.0026-0.0019-0.0081-0.0022-0.0243-0.0024-0.00740.01140.0039-0.00880.00770.0275-00.5482-0.0389-0.03670.5794-0.00370.57064.7472-34.6579-76.7594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:239) OR (CHAIN I AND RESID 701:701)A1 - 239
2X-RAY DIFFRACTION1(CHAIN A AND RESID 1:239) OR (CHAIN I AND RESID 701:701)I701
3X-RAY DIFFRACTION2(CHAIN A AND RESID 240:608) OR (CHAIN T AND RESID 611:611)A240 - 608
4X-RAY DIFFRACTION2(CHAIN A AND RESID 240:608) OR (CHAIN T AND RESID 611:611)T611
5X-RAY DIFFRACTION3(CHAIN B AND RESID 1:239)B1 - 239
6X-RAY DIFFRACTION4(CHAIN B AND RESID 240:608) OR (CHAIN T AND RESID 612:612)B240 - 608
7X-RAY DIFFRACTION4(CHAIN B AND RESID 240:608) OR (CHAIN T AND RESID 612:612)T612
8X-RAY DIFFRACTION5(CHAIN C AND RESID 1:236)C1 - 236
9X-RAY DIFFRACTION6(CHAIN C AND RESID 244:608) OR (CHAIN T AND RESID 610:610)C244 - 608
10X-RAY DIFFRACTION6(CHAIN C AND RESID 244:608) OR (CHAIN T AND RESID 610:610)T610
11X-RAY DIFFRACTION7(CHAIN D AND RESID 1:235)D1 - 235
12X-RAY DIFFRACTION8(CHAIN U AND RESID 1:1) OR (CHAIN D AND RESID 242:608) OR (CHAIN T AND RESID 609:609)U1
13X-RAY DIFFRACTION8(CHAIN U AND RESID 1:1) OR (CHAIN D AND RESID 242:608) OR (CHAIN T AND RESID 609:609)D242 - 608
14X-RAY DIFFRACTION8(CHAIN U AND RESID 1:1) OR (CHAIN D AND RESID 242:608) OR (CHAIN T AND RESID 609:609)T609
15X-RAY DIFFRACTION9(CHAIN E AND RESID 1:236)E1 - 236
16X-RAY DIFFRACTION10(CHAIN E AND RESID 243:608) OR (CHAIN T AND RESID 616:616)E243 - 608
17X-RAY DIFFRACTION10(CHAIN E AND RESID 243:608) OR (CHAIN T AND RESID 616:616)T616
18X-RAY DIFFRACTION11(CHAIN F AND RESID 1:230)F1 - 230
19X-RAY DIFFRACTION12(CHAIN T AND RESID 615:615) OR (CHAIN F AND RESID 245:608)T615
20X-RAY DIFFRACTION12(CHAIN T AND RESID 615:615) OR (CHAIN F AND RESID 245:608)F245 - 608
21X-RAY DIFFRACTION13(CHAIN G AND RESID 1:238)G1 - 238
22X-RAY DIFFRACTION14(CHAIN T AND RESID 613:613) OR (CHAIN G AND RESID 242:608)T613
23X-RAY DIFFRACTION14(CHAIN T AND RESID 613:613) OR (CHAIN G AND RESID 242:608)G242 - 608
24X-RAY DIFFRACTION15(CHAIN H AND RESID 1:240)H1 - 240
25X-RAY DIFFRACTION16(CHAIN H AND RESID 241:608) OR (CHAIN T AND RESID 614:614)H241 - 608
26X-RAY DIFFRACTION16(CHAIN H AND RESID 241:608) OR (CHAIN T AND RESID 614:614)T614
27X-RAY DIFFRACTION17(CHAIN V AND RESID 1:8)V1 - 8

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