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- PDB-1vpx: Crystal structure of Transaldolase (EC 2.2.1.2) (TM0295) from The... -

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Basic information

Entry
Database: PDB / ID: 1vpx
TitleCrystal structure of Transaldolase (EC 2.2.1.2) (TM0295) from Thermotoga maritima at 2.40 A resolution
ComponentsPROTEIN (Transaldolase (EC 2.2.1.2))
KeywordsTRANSFERASE / TM0295 / TRANSALDOLASE (EC 2.2.1.2) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


transaldolase / transaldolase activity / aldehyde-lyase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Transaldolase type 3B, putative / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel ...Transaldolase type 3B, putative / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Transaldolase (EC 2.2.1.2) (TM0295) from Thermotoga maritima at 2.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (Transaldolase (EC 2.2.1.2))
B: PROTEIN (Transaldolase (EC 2.2.1.2))
C: PROTEIN (Transaldolase (EC 2.2.1.2))
D: PROTEIN (Transaldolase (EC 2.2.1.2))
E: PROTEIN (Transaldolase (EC 2.2.1.2))
F: PROTEIN (Transaldolase (EC 2.2.1.2))
G: PROTEIN (Transaldolase (EC 2.2.1.2))
H: PROTEIN (Transaldolase (EC 2.2.1.2))
I: PROTEIN (Transaldolase (EC 2.2.1.2))
J: PROTEIN (Transaldolase (EC 2.2.1.2))
K: PROTEIN (Transaldolase (EC 2.2.1.2))
L: PROTEIN (Transaldolase (EC 2.2.1.2))
M: PROTEIN (Transaldolase (EC 2.2.1.2))
N: PROTEIN (Transaldolase (EC 2.2.1.2))
O: PROTEIN (Transaldolase (EC 2.2.1.2))
P: PROTEIN (Transaldolase (EC 2.2.1.2))
Q: PROTEIN (Transaldolase (EC 2.2.1.2))
R: PROTEIN (Transaldolase (EC 2.2.1.2))
S: PROTEIN (Transaldolase (EC 2.2.1.2))
T: PROTEIN (Transaldolase (EC 2.2.1.2))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)516,08842
Polymers514,05820
Non-polymers2,03022
Water1,856103
1
A: PROTEIN (Transaldolase (EC 2.2.1.2))
B: PROTEIN (Transaldolase (EC 2.2.1.2))
C: PROTEIN (Transaldolase (EC 2.2.1.2))
D: PROTEIN (Transaldolase (EC 2.2.1.2))
E: PROTEIN (Transaldolase (EC 2.2.1.2))
F: PROTEIN (Transaldolase (EC 2.2.1.2))
G: PROTEIN (Transaldolase (EC 2.2.1.2))
H: PROTEIN (Transaldolase (EC 2.2.1.2))
I: PROTEIN (Transaldolase (EC 2.2.1.2))
J: PROTEIN (Transaldolase (EC 2.2.1.2))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,95020
Polymers257,02910
Non-polymers92110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42600 Å2
ΔGint-289 kcal/mol
Surface area71320 Å2
MethodPISA
2
K: PROTEIN (Transaldolase (EC 2.2.1.2))
L: PROTEIN (Transaldolase (EC 2.2.1.2))
M: PROTEIN (Transaldolase (EC 2.2.1.2))
N: PROTEIN (Transaldolase (EC 2.2.1.2))
O: PROTEIN (Transaldolase (EC 2.2.1.2))
P: PROTEIN (Transaldolase (EC 2.2.1.2))
Q: PROTEIN (Transaldolase (EC 2.2.1.2))
R: PROTEIN (Transaldolase (EC 2.2.1.2))
S: PROTEIN (Transaldolase (EC 2.2.1.2))
T: PROTEIN (Transaldolase (EC 2.2.1.2))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,13822
Polymers257,02910
Non-polymers1,10912
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40560 Å2
ΔGint-284 kcal/mol
Surface area69270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.298, 104.419, 171.124
Angle α, β, γ (deg.)90.00, 108.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / Refine code: 3

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LEULEUAA-1 - 21611 - 228
2GLUGLUBB-1 - 20711 - 219
3GLUGLUCC0 - 20712 - 219
4ASPASPDD-1 - 20811 - 220
5ASNASNEE0 - 21512 - 227
6LEULEUFF-1 - 21611 - 228
7GLUGLUGG-1 - 21411 - 226
8ASPASPHH0 - 20812 - 220
9GLUGLUII-1 - 21411 - 226
10LYSLYSJJ-1 - 21111 - 223
11ASNASNKK0 - 21512 - 227
12ASPASPLL-1 - 20811 - 220
13ARGARGMM0 - 20412 - 216
14METMETNN0 - 20612 - 218
15ASPASPOO-1 - 20811 - 220
16GLUGLUPP-1 - 20711 - 219
17GLUGLUQQ-1 - 21411 - 226
18ASNASNRR0 - 21512 - 227
19ARGARGSS0 - 20412 - 216
20ASNASNTT0 - 21512 - 227

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Components

#1: Protein
PROTEIN (Transaldolase (EC 2.2.1.2))


Mass: 25702.881 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0295 / Plasmid: pET BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYD1, transaldolase
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.75 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7
Details: 30.0% 1,2-propanediol, 0.2M (NH4)2SO4, 10.0% Glycerol, 0.1M HEPES, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Feb 17, 2004
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→104.19 Å / Num. obs: 162044 / % possible obs: 85.9 % / Redundancy: 2.5 % / Biso Wilson estimate: 59 Å2 / Rsym value: 0.07 / Net I/σ(I): 9.1
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 7812 / Rsym value: 0.581 / % possible all: 56.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALACCP4 4.2data scaling
MOLREPphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L6W
Resolution: 2.4→83.13 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 22.491 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.557 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24694 8140 5 %RANDOM
Rwork0.19632 ---
obs0.19884 153845 85.87 %-
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: 47.997 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-0.29 Å2
2--1.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→83.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31669 0 131 103 31903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02232347
X-RAY DIFFRACTIONr_bond_other_d0.0030.0230510
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9643783
X-RAY DIFFRACTIONr_angle_other_deg0.933370772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99454148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.79124.9561237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.614155634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.67615124
X-RAY DIFFRACTIONr_chiral_restr0.0980.25146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0235521
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025965
X-RAY DIFFRACTIONr_nbd_refined0.2050.27629
X-RAY DIFFRACTIONr_nbd_other0.1750.233321
X-RAY DIFFRACTIONr_nbtor_other0.090.220343
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2656
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1690.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.24
X-RAY DIFFRACTIONr_mcbond_it1.399321186
X-RAY DIFFRACTIONr_mcbond_other0.22838505
X-RAY DIFFRACTIONr_mcangle_it2.374533421
X-RAY DIFFRACTIONr_scbond_it5.626812437
X-RAY DIFFRACTIONr_scangle_it7.9251110362
X-RAY DIFFRACTIONr_nbtor_refined0.1790.216148
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1880.23
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1117tight positional0.050.05
2B1117tight positional0.050.05
3C1117tight positional0.060.05
4D1117tight positional0.050.05
5E1117tight positional0.060.05
6F1117tight positional0.050.05
7G1117tight positional0.060.05
8H1117tight positional0.050.05
9I1117tight positional0.050.05
10J1117tight positional0.060.05
11K1117tight positional0.040.05
12L1117tight positional0.040.05
13M1117tight positional0.040.05
14N1117tight positional0.050.05
15O1117tight positional0.050.05
16P1117tight positional0.050.05
17Q1117tight positional0.040.05
18R1117tight positional0.040.05
19S1117tight positional0.040.05
20T1117tight positional0.040.05
1A1476loose positional0.75
2B1476loose positional0.735
3C1476loose positional0.795
4D1476loose positional0.615
5E1476loose positional0.535
6F1476loose positional0.675
7G1476loose positional0.595
8H1476loose positional0.615
9I1476loose positional0.565
10J1476loose positional0.695
11K1476loose positional0.585
12L1476loose positional0.65
13M1476loose positional0.665
14N1476loose positional0.775
15O1476loose positional0.665
16P1476loose positional0.595
17Q1476loose positional0.615
18R1476loose positional0.775
19S1476loose positional0.645
20T1476loose positional0.75
1A1117tight thermal0.130.5
2B1117tight thermal0.130.5
3C1117tight thermal0.130.5
4D1117tight thermal0.160.5
5E1117tight thermal0.160.5
6F1117tight thermal0.130.5
7G1117tight thermal0.170.5
8H1117tight thermal0.150.5
9I1117tight thermal0.140.5
10J1117tight thermal0.140.5
11K1117tight thermal0.110.5
12L1117tight thermal0.090.5
13M1117tight thermal0.090.5
14N1117tight thermal0.090.5
15O1117tight thermal0.140.5
16P1117tight thermal0.120.5
17Q1117tight thermal0.10.5
18R1117tight thermal0.090.5
19S1117tight thermal0.10.5
20T1117tight thermal0.090.5
1A1476loose thermal2.5410
2B1476loose thermal2.7210
3C1476loose thermal2.8510
4D1476loose thermal2.8310
5E1476loose thermal2.8710
6F1476loose thermal2.8910
7G1476loose thermal2.9910
8H1476loose thermal2.9810
9I1476loose thermal310
10J1476loose thermal2.8610
11K1476loose thermal2.6310
12L1476loose thermal2.8910
13M1476loose thermal2.4510
14N1476loose thermal2.4310
15O1476loose thermal2.6710
16P1476loose thermal2.6110
17Q1476loose thermal2.7910
18R1476loose thermal2.4110
19S1476loose thermal2.4810
20T1476loose thermal2.5510
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 364 4.84 %
Rwork0.283 7161 -
obs--56.21 %
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)
11.71450.90960.61532.62011.71711.58520.1501-0.6399-0.19340.606-0.1305-0.1840.3685-0.0239-0.0196-0.0566-0.00420.02960.08580.0702-0.3-3.6392-11.857970.3083
22.48460.8418-0.49631.1492-0.47491.52220.0272-0.45560.55690.2489-0.0348-0.0484-0.22240.04150.0077-0.1073-0.003-0.0057-0.1356-0.2289-0.02090.936922.975361.8748
32.5884-0.686-1.12311.45051.47892.69680.10180.12970.7617-0.25910.1278-0.2751-0.44870.271-0.2296-0.0613-0.04160.0593-0.23170.1141-0.02418.360422.548927.8763
41.8565-0.78750.11552.1199-0.09360.72680.08570.4532-0.0056-0.2837-0.1066-0.2072-0.02120.10810.021-0.19370.01130.048-0.139-0.0179-0.31388.4054-10.663117.1477
51.539-0.15250.04050.7878-0.36652.51590.047-0.0972-0.53560.03590.0056-0.01670.32110.0756-0.0526-0.19450.01080.012-0.32190.0584-0.10880.9601-30.977642.6907
61.22120.14660.28931.85230.90471.06120.0651-0.5221-0.16290.3004-0.13130.29280.1301-0.21440.0662-0.1491-0.02980.1209-0.01290.0362-0.131-36.0385-16.153860.3744
72.07580.19790.08430.4772-0.23293.07610.02510.0869-0.4316-0.0666-0.09930.13830.3454-0.0570.0741-0.20230.00860.007-0.3236-0.0893-0.1062-29.7789-26.764327.6296
81.8919-0.62540.33872.1247-0.2780.76950.03350.55340.1681-0.4509-0.06450.1921-0.11230.02610.031-0.04970.021-0.0613-0.11790.0965-0.2311-23.41793.51629.0832
92.2941-0.5268-1.43681.05940.692.48890.15310.21910.7081-0.2492-0.10440.0989-0.3879-0.1205-0.0487-0.01540.0274-0.0345-0.35310.01610.1246-26.316329.196430.3508
103.28510.9419-0.80571.351-0.71141.59510.0766-0.64520.64880.2356-0.00530.4184-0.2069-0.1203-0.0713-0.11330.02580.0925-0.0449-0.255-0.0506-33.921416.959462.493
111.71360.14660.342.241-0.22761.1358-0.22580.55690.0227-0.59560.08560.184-0.14090.11240.1403-0.0131-0.0384-0.11150.0731-0.066-0.152748.3007-14.671810.6124
121.9307-0.8293-0.25662.56120.90631.029-0.13950.31930.5816-0.7004-0.08840.1183-0.5315-0.13050.22790.3380.018-0.3416-0.05670.1310.214250.736820.718418.5643
132.3280.0959-0.62260.93290.28741.5958-0.1508-0.38510.70260.0633-0.12760.3443-0.3732-0.13870.27830.06850.2118-0.24060.0478-0.33540.323241.396122.797452.114
141.96231.63440.58223.7310.82650.62980.0535-0.74620.28970.6366-0.37380.76360.0197-0.50.32030.02510.11430.14440.4319-0.18770.0334.1521-8.569363.049
152.07160.53870.98771.2320.58322.93660.0506-0.3253-0.45280.1969-0.02970.17010.2713-0.1595-0.021-0.21990.06720.0399-0.1351-0.033-0.022538.2091-30.973837.7811
161.9401-0.22840.37811.2341-0.33941.213-0.01370.3303-0.2879-0.18750.1195-0.21380.05680.1445-0.1058-0.18970.00860.0297-0.0318-0.1001-0.033877.6718-27.508825.2176
171.9954-0.03921.15221.46230.69173.45390.0287-0.4092-0.44680.43170.1402-0.19330.378-0.0359-0.1689-0.04620.0955-0.0555-0.02440.1183-0.031667.9183-31.619756.2306
181.96811.0940.55173.43060.15791.0636-0.0232-0.67090.07880.7837-0.157-0.20840.0669-0.07310.18020.16250.172-0.13950.2992-0.1277-0.152866.9545-1.74673.061
192.12620.2616-1.14351.3799-0.19181.453-0.0088-0.25650.6270.00590.1041-0.1858-0.29410.085-0.09520.00750.0197-0.1679-0.0265-0.16710.202977.520223.719249.3414
201.7314-0.8755-0.32452.90291.40321.5371-0.10250.37310.4422-0.57070.2153-0.6184-0.43360.2976-0.11280.0966-0.15530.03970.09920.04230.070482.90727.755921.7481
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-1 - 21611 - 228
22BB-1 - 20711 - 219
33CC0 - 20712 - 219
44DD-1 - 20811 - 220
55EE0 - 21512 - 227
66FF-1 - 21611 - 228
77GG-1 - 21411 - 226
88HH0 - 20812 - 220
99II-1 - 21411 - 226
1010JJ-1 - 21111 - 223
1111KK0 - 21512 - 227
1212LL-1 - 20811 - 220
1313MM0 - 20412 - 216
1414NN0 - 20612 - 218
1515OO-1 - 20811 - 220
1616PP-1 - 20711 - 219
1717QQ-1 - 21411 - 226
1818RR0 - 21512 - 227
1919SS0 - 20412 - 216
2020TT0 - 21512 - 227

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