[English] 日本語
Yorodumi
- PDB-3zt7: GlgE isoform 1 from Streptomyces coelicolor with beta-cyclodextri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zt7
TitleGlgE isoform 1 from Streptomyces coelicolor with beta-cyclodextrin and maltose bound
ComponentsPUTATIVE GLUCANOHYDROLASE PEP1A
KeywordsHYDROLASE / ALPHA-GLUCAN BIOSYNTHESIS / GLYCOSIDE HYDROLASE FAMILY 13_3
Function / homology
Function and homology information


starch synthase (maltosyl-transferring) / alpha-glucan biosynthetic process / oligosaccharide catabolic process / hexosyltransferase activity / alpha-amylase activity
Similarity search - Function
: / GLGE, C-terminal / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...: / GLGE, C-terminal / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / beta-cyclodextrin / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)316,24112
Polymers310,2594
Non-polymers5,9818
Water6,648369
1
A: PUTATIVE GLUCANOHYDROLASE PEP1A
B: PUTATIVE GLUCANOHYDROLASE PEP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,1206
Polymers155,1302
Non-polymers2,9914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-25.5 kcal/mol
Surface area51660 Å2
MethodPISA
2
C: PUTATIVE GLUCANOHYDROLASE PEP1A
D: PUTATIVE GLUCANOHYDROLASE PEP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,1206
Polymers155,1302
Non-polymers2,9914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-25.1 kcal/mol
Surface area51610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.270, 113.380, 315.000
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:

Component-ID: 0 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 15 - 663 / Label seq-ID: 35 - 683

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

-
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 (bacteria) / Strain: M145 / Plasmid: PET15B-GLGE1-M145 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: Q9L1K2, Transferases; Glycosyltransferases; Hexosyltransferases, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Polysaccharide
Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin / Cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 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.: 369 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsINCLUDES AN ADDITIONAL 20 RESIDUES AT THE N-TERMINUS FOR NICKEL AFFINITY PURIFICATION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.8 % / Description: NONE
Crystal growpH: 7 / Details: pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H,K,L10.553
11K,H,-L20.447
ReflectionResolution: 2.5→71.42 Å / Num. obs: 140547 / % possible obs: 99.8 % / Observed criterion σ(I): -9 / Redundancy: 4.9 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.6.0101refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZST

3zst


Resolution: 2.5→55.8 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.738 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.047 / 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
Rfree0.22117 6958 5 %RANDOM
Rwork0.19159 ---
obs0.19305 133513 99.35 %-
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: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1--19.93 Å20 Å20 Å2
2--30.01 Å20 Å2
3----10.09 Å2
Refinement stepCycle: LAST / Resolution: 2.5→55.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20354 0 400 369 21123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02121393
X-RAY DIFFRACTIONr_bond_other_d0.0060.0214400
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.96729340
X-RAY DIFFRACTIONr_angle_other_deg1.231334866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85352592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11322.525994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.394153062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.16115204
X-RAY DIFFRACTIONr_chiral_restr0.0930.23310
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02123694
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024466
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 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A247920.04
12B247920.04
21A249340.03
22C249340.03
31A247320.03
32D247320.03
41B247570.04
42C247570.04
51B246440.03
52D246440.03
61C247180.03
62D247180.03
LS refinement shellResolution: 2.496→2.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 485 -
Rwork0.402 9209 -
obs--93.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5868-0.17860.4051.077-0.13943.78190.02850.14610.1012-0.0519-0.0349-0.049-0.13170.00950.00640.09040.02040.0120.05550.03760.0643-4.0731-11.44641.6206
23.1419-0.8855-1.80411.9451.48313.03690.00370.23050.0198-0.1602-0.02320.07080.0382-0.17220.01950.15330.0046-0.01120.03230.00710.1373-19.26010.113163.062
32.04530.2332-0.38140.03950.28513.2313-0.23210.09930.1118-0.053-0.01740.0216-0.47250.35010.24950.13630.03270.01140.0860.00960.0830.8195-9.07738.5207
40.9614-0.0268-0.04850.4197-0.04710.5939-0.01590.1301-0.0263-0.06540.01320.00380.01440.03550.00270.09290.00130.00560.24280.02130.07-2.963-24.10886.0742
51.74140.62950.65791.33550.38571.941-0.0351-0.14410.08510.263-0.01420.43880.0137-0.29670.04930.19860.01090.04120.31430.03470.1837-30.3158-27.128224.9457
60.9787-0.19480.38510.6105-0.32873.7582-0.04140.1782-0.0006-0.06060.03990.01070.03240.1470.00140.07160.0167-0.01070.1111-0.01760.100116.4766-32.164136.9472
70.3942-0.3619-0.48083.93740.63413.3065-0.03680.0315-0.01920.15970.018-0.04730.2787-0.10980.01880.2249-0.010.02330.2925-0.04740.224828.114-47.20416.0326
81.6001-0.3559-4.37761.3157-1.221616.91270.22740.17790.09810.0887-0.083-0.1754-0.86590.0126-0.14430.04940.0072-0.0130.1954-0.02280.091219.0817-27.315340.1912
90.3060.02880.08111.1418-0.04880.55040.02850.00560.010.1285-0.00630.02330.01250.038-0.02210.10640.0055-0.00820.003-0.00330.02224.1918-31.039772.7611
101.61591.18350.43472.249-0.00152.3166-0.02920.2161-0.2658-0.40610.06550.01860.44350.0227-0.03620.33450.0421-0.0420.0429-0.04450.15361.1707-58.328753.9442
110.7985-0.20970.26240.87230.33613.5811-0.02150.1605-0.0208-0.0250.0086-0.019-0.14140.04010.0130.07670.0322-0.01470.13320.03460.079650.4754-72.21543.3158
121.85110.1002-0.51921.90331.53382.68-0.09270.0991-0.0399-0.0206-0.13790.14560.0347-0.13930.23060.13010.0176-0.00620.0601-0.01410.098437.5227-62.028866.696
131.17850.1630.54241.14053.261316.01620.27880.11210.1312-0.09590.2842-0.0843-0.14610.7374-0.5630.0985-0.02070.02490.15120.04310.076655.186-69.745140.1106
140.9446-0.07250.04990.31730.0220.974-0.02780.1357-0.0354-0.07940.01430.0015-0.0306-0.02510.01350.0989-0.01630.00320.29130.01150.071149.1385-81.34296.5918
151.25891.0880.78631.63820.04441.6638-0.0213-0.0410.00520.1910.01610.22040.0497-0.14780.00520.2472-0.00290.0620.38150.02690.233422.5895-85.549225.9652
161.1889-0.15740.34330.4942-0.1943.73810.04360.13930.0614-0.0237-0.06620.04750.07610.14210.02260.11020.04350.00580.1706-0.02770.07369.9182-93.235235.6216
170.39150.6182-0.33243.18420.82421.588-0.00930.1022-0.12160.082-0.04840.09060.2057-0.00410.05760.30830.06860.01950.4039-0.04610.237779.7036-106.506212.4985
180.7728-0.19711.69751.6096-5.358119.2858-0.06970.11330.0344-0.01330.04340.007-0.04390.02520.02630.14660.08440.01350.16760.02760.00772.6679-88.739738.9625
190.4187-0.07670.04641.0775-0.16860.65890.00380.0666-0.02630.0822-0.02580.05560.05150.00760.0220.08490.00210.00560.0491-0.01050.021860.1845-94.532272.0776
200.3650.0850.10811.48260.32950.9286-0.04160.1495-0.2503-0.26920.03210.16340.3411-0.10110.00960.3513-0.0356-0.02440.1959-0.0670.258754.3759-120.178151.7525
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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

-
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

Read more