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- PDB-3zt6: GlgE isoform 1 from Streptomyces coelicolor with alpha-cyclodextr... -

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Basic information

Entry
Database: PDB / ID: 3zt6
TitleGlgE isoform 1 from Streptomyces coelicolor with alpha-cyclodextrin and maltose bound
ComponentsPUTATIVE GLUCANOHYDROLASE PEP1A
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE FAMILY 13_3 / ALPHA-GLUCAN BIOSYNTHESIS
Function / homology
Function and homology information


starch synthase (maltosyl-transferring) / alpha-glucan biosynthetic process / hexosyltransferase activity / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Alpha-amylase domain / Glycosyl hydrolase, family 13, catalytic domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases ...Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Alpha-amylase domain / Glycosyl hydrolase, family 13, catalytic domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Immunoglobulin-like fold / Alpha-Beta Barrel / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / alpha-cyclodextrin / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsSyson, K. / Stevenson, C.E.M. / Rejzek, M. / Fairhurst, S.A. / Nair, A. / Bruton, C.J. / Field, R.A. / Chater, K.F. / Lawson, D.M. / Bornemann, S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure of a Streptomyces Maltosyltransferase Glge: A Homologue of a Genetically Validated Anti-Tuberculosis Target.
Authors: Syson, K. / Stevenson, C.E.M. / Rejzek, M. / Fairhurst, S.A. / Nair, A. / Bruton, C.J. / Field, R.A. / Chater, K.F. / Lawson, D.M. / Bornemann, S.
History
DepositionJul 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Nov 9, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE GLUCANOHYDROLASE PEP1A
B: PUTATIVE GLUCANOHYDROLASE PEP1A
C: PUTATIVE GLUCANOHYDROLASE PEP1A
D: PUTATIVE GLUCANOHYDROLASE PEP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,59212
Polymers310,2594
Non-polymers5,3338
Water8,269459
1
A: PUTATIVE GLUCANOHYDROLASE PEP1A
B: PUTATIVE GLUCANOHYDROLASE PEP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,7966
Polymers155,1302
Non-polymers2,6664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-17 kcal/mol
Surface area51860 Å2
MethodPISA
2
C: PUTATIVE GLUCANOHYDROLASE PEP1A
D: PUTATIVE GLUCANOHYDROLASE PEP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,7966
Polymers155,1302
Non-polymers2,6664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-17.1 kcal/mol
Surface area51960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.850, 114.160, 315.610
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
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A15 - 663
2010B15 - 663
1020A15 - 663
2020C15 - 663
1030A15 - 663
2030D15 - 663
1040B15 - 663
2040C15 - 663
1050B15 - 663
2050D15 - 663
1060C15 - 663
2060D15 - 663

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
PUTATIVE GLUCANOHYDROLASE PEP1A / GLGE ISOFORM 1 / PEP1A / SCO5443 / 1-4-ALPHA-D-


Mass: 77564.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (unknown) / Strain: M145 / Plasmid: PET15B-GLGE1-M145 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: Q9L1K2, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Polysaccharide
Cyclohexakis-(1-4)-(alpha-D-glucopyranose) / alpha-cyclodextrin / Α-Cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 990.860 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: alpha-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,6,6/[a2122h-1a_1-5]/1-1-1-1-1-1/a1-f4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsINCLUDES AN ADDITIONAL 20 RESIDUES AT THE N-TERMINUS FOR NICKEL AFFINITY PURIFICATION.

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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: 3.31 Å3/Da / Density % sol: 62.8 % / Description: NONE
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H,K,L10.514
11K,H,-L20.486
ReflectionResolution: 2.2→63.99 Å / Num. obs: 206349 / % possible obs: 98.9 % / Observed criterion σ(I): -9 / Redundancy: 5.4 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0101refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZST
Resolution: 2.19→56.39 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.903 / SU B: 7.449 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.23625 10447 5.1 %RANDOM
Rwork0.20804 ---
obs0.20949 195790 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1--11.68 Å20 Å20 Å2
2--15.08 Å20 Å2
3----3.41 Å2
Refinement stepCycle: LAST / Resolution: 2.19→56.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20395 0 356 459 21210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02121386
X-RAY DIFFRACTIONr_bond_other_d0.0060.0214435
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.96429318
X-RAY DIFFRACTIONr_angle_other_deg1.217334916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03252592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06722.481004
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.519153078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.21215210
X-RAY DIFFRACTIONr_chiral_restr0.0880.23289
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02123740
X-RAY DIFFRACTIONr_gen_planes_other0.0060.024490
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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 / Rms dev position: 0.03 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A24864
12B24864
21A24914
22C24914
31A24853
32D24853
41B24837
42C24837
51B24766
52D24766
61C24768
62D24768
LS refinement shellResolution: 2.193→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.505 609 -
Rwork0.469 11661 -
obs--79.91 %
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)
10.06240.04860.07850.3306-0.07410.46270.0270.05180.00820.01870.01670.0447-0.01990.0103-0.04370.0580.00420.00250.19590.01990.012-4.0764-11.646841.7157
20.8784-0.3563-0.99840.5481-0.00651.7046-0.00730.07410.0672-0.01750.0235-0.01820.0591-0.059-0.01630.0743-0.00770.01260.14780.03190.0384-19.3948-0.065563.1519
31.2332-0.3306-1.81270.7888-0.49214.0464-0.09490.1010.0188-0.05110.0232-0.070.2903-0.21720.07170.1013-0.01210.01120.16120.00090.01880.8296-9.198538.623
40.1592-0.05340.08380.2066-0.0360.048-0.00380.046-0.0029-0.01480.0031-0.0144-0.0024-0.00330.00070.0222-0.00210.00220.26470.00510.0093-2.8464-24.38546.0978
50.38840.1702-0.1220.49390.35320.73820.014-0.02590.0060.08180.02190.09830.0364-0.0968-0.03590.02590.01130.03010.26150.03390.0791-30.2827-27.57724.9272
60.1209-0.04630.04060.1614-0.10070.46810.00760.0491-0.00630.00990.00820.00240.04260.0363-0.01590.03920.0057-0.01040.2172-0.01350.026816.8077-32.368937.1857
70.2687-0.13160.08581.53911.00830.902-0.04040.0327-0.01250.13060.0091-0.02330.1163-0.08350.03130.0552-0.00340.02880.2229-0.0390.028528.3838-47.429816.0021
80.2526-0.01830.53720.80931.19383.10530.00130.0237-0.0295-0.09870.10450.0092-0.20440.1643-0.10580.04610.01840.03220.24910.00070.049119.1844-27.470540.2656
90.1119-0.07340.07270.2508-0.05330.15530.00890.03470.00850.04410.01070.01570.02040.033-0.01960.10140.0032-0.00680.143-0.00430.014.2051-31.352972.8065
100.20580.1027-0.12380.62870.12470.3879-0.0210.0851-0.1004-0.14720.0235-0.00040.09840.0044-0.00250.16040.0227-0.04770.1474-0.05960.0781.2918-58.749353.9829
110.1798-0.1616-0.26780.5439-0.0180.8305-0.01550.0216-0.017-0.00230.01020.0508-0.08580.04690.00520.07250.0041-0.00140.20130.00730.007350.8853-72.728643.3895
120.4352-0.2657-0.32090.59660.2151.1153-0.0935-0.0185-0.0368-0.0429-0.04110.0818-0.04060.02260.13460.09630.002-0.0090.1552-0.01150.02637.7738-62.604366.805
130.4214-0.0081-0.7740.42240.71022.79390.11190.0790.07470.08470.1907-0.06240.04850.0116-0.30260.1052-0.0051-0.02570.23870.02990.041355.6566-70.215640.1629
140.137-0.14780.04020.1841-0.02760.1909-0.01920.0247-0.009-0.00750.00840.0024-0.0451-0.03130.01070.0412-0.01010.00930.2528-0.00470.005749.6805-81.88256.5706
150.17860.28140.15110.52340.12620.7890.0328-0.00550.02020.0962-0.02240.0850.0332-0.102-0.01040.0408-0.00330.0420.26870.01170.046623.0486-86.193525.9628
160.2641-0.05550.26780.0317-0.1691.0457-0.01570.0715-0.03480.0126-0.00820.00230.00840.08570.0240.08590.02820.00770.201-0.00440.014970.4135-93.921435.6885
170.10390.12460.23441.69780.78450.7020.01680.0648-0.00110.0568-0.05730.11630.04030.05440.04050.05470.02920.01960.2861-0.03360.018580.6927-107.418612.5794
180.80040.29060.67730.7023-1.45875.44760.04880.02240.09820.0085-0.00390.08150.06660.0919-0.04480.08110.05730.00190.23950.00940.016273.1783-89.424439.0183
190.0106-0.02690.00680.3567-0.04050.2129-0.00720.0356-0.00470.0213-0.00610.03690.01420.02870.01330.0970.00230.00760.1509-0.00690.00660.5188-95.343772.2016
200.03290.04270.0090.76710.25450.3641-0.03450.0361-0.0293-0.14710.00350.11440.1084-0.01440.0310.1493-0.032-0.00720.1676-0.0390.064254.7126-120.987251.6874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 108
2X-RAY DIFFRACTION2A109 - 192
3X-RAY DIFFRACTION3A193 - 205
4X-RAY DIFFRACTION4A206 - 573
5X-RAY DIFFRACTION5A574 - 663
6X-RAY DIFFRACTION6B15 - 108
7X-RAY DIFFRACTION7B109 - 192
8X-RAY DIFFRACTION8B193 - 205
9X-RAY DIFFRACTION9B206 - 573
10X-RAY DIFFRACTION10B574 - 663
11X-RAY DIFFRACTION11C15 - 108
12X-RAY DIFFRACTION12C109 - 192
13X-RAY DIFFRACTION13C193 - 205
14X-RAY DIFFRACTION14C206 - 573
15X-RAY DIFFRACTION15C574 - 663
16X-RAY DIFFRACTION16D15 - 108
17X-RAY DIFFRACTION17D109 - 192
18X-RAY DIFFRACTION18D193 - 205
19X-RAY DIFFRACTION19D206 - 573
20X-RAY DIFFRACTION20D574 - 663

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