[English] 日本語
Yorodumi
- PDB-5ff7: Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ff7
TitleTagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes in complex with DHAP and G3P
ComponentsTagatose 1,6-diphosphate aldolase 2
KeywordsLYASE / Covalent intermediate / Substrate / Aldolase / Class I
Function / homology
Function and homology information


tagatose-bisphosphate aldolase / tagatose-bisphosphate aldolase activity / lactose catabolic process via tagatose-6-phosphate / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity
Similarity search - Function
Tagatose 1,6-diphosphate aldolase / : / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
GLYCERALDEHYDE-3-PHOSPHATE / SN-GLYCEROL-3-PHOSPHATE / Tagatose 1,6-diphosphate aldolase 2
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.092 Å
AuthorsLow-Kam, C. / Liotard, B.
CitationJournal: To Be Published
Title: NON-STEREOSPECIFIC SUBSTRATE CLEAVAGE BY TAGATOSE-BISPHOSPHATE CLASS I ALDOLASE
Authors: Low-Kam, C. / Liotard, B. / Sygusch, J.
History
DepositionDec 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tagatose 1,6-diphosphate aldolase 2
B: Tagatose 1,6-diphosphate aldolase 2
C: Tagatose 1,6-diphosphate aldolase 2
D: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,75116
Polymers146,4824
Non-polymers1,26912
Water19,5641086
1
A: Tagatose 1,6-diphosphate aldolase 2
B: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9159
Polymers73,2412
Non-polymers6757
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tagatose 1,6-diphosphate aldolase 2
D: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8357
Polymers73,2412
Non-polymers5945
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.081, 108.190, 238.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Tagatose 1,6-diphosphate aldolase 2 / D-tagatose-1 / 6-bisphosphate aldolase 2 / Tagatose-bisphosphate aldolase 2


Mass: 36620.457 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: lacD2, lacD.2, SPy_1919, M5005_Spy1635 / Production host: Escherichia coli (E. coli) / References: UniProt: P63705, tagatose-bisphosphate aldolase
#2: Chemical
ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C3H9O6P
#3: Chemical ChemComp-G3H / GLYCERALDEHYDE-3-PHOSPHATE


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1086 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris Acetate, Calcium Acetate, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.092→50 Å / % possible obs: 98.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.71
Reflection shellResolution: 2.26→2.37 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.89 / Num. unique all: 9639 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MHF
Resolution: 2.092→49.853 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 1990 2.05 %
Rwork0.1695 --
obs0.1703 96840 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.092→49.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10239 0 62 1086 11387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210536
X-RAY DIFFRACTIONf_angle_d0.46414234
X-RAY DIFFRACTIONf_dihedral_angle_d13.0366452
X-RAY DIFFRACTIONf_chiral_restr0.0391582
X-RAY DIFFRACTIONf_plane_restr0.0031837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0922-2.14450.31421180.30195878X-RAY DIFFRACTION86
2.1445-2.20250.35171390.25896564X-RAY DIFFRACTION97
2.2025-2.26730.27231400.23296700X-RAY DIFFRACTION99
2.2673-2.34050.2491410.19836746X-RAY DIFFRACTION99
2.3405-2.42410.24491430.1836764X-RAY DIFFRACTION99
2.4241-2.52120.2041430.1836784X-RAY DIFFRACTION99
2.5212-2.63590.21811430.17176795X-RAY DIFFRACTION99
2.6359-2.77490.23391440.16676860X-RAY DIFFRACTION99
2.7749-2.94870.22481430.16826826X-RAY DIFFRACTION100
2.9487-3.17630.22341450.15666866X-RAY DIFFRACTION100
3.1763-3.49590.18881460.14716916X-RAY DIFFRACTION100
3.4959-4.00160.16611450.13036917X-RAY DIFFRACTION100
4.0016-5.04080.14581460.12996969X-RAY DIFFRACTION99
5.0408-49.86740.21591540.20077265X-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)
13.9184-0.14721.68445.4207-1.46424.88430.0389-0.0322-0.16650.23530.0062-0.0860.23250.054-0.04730.11240.01530.05570.2846-0.03530.240662.594756.246135.5392
21.3796-1.052-0.25774.27391.46433.2294-0.85220.11320.8774-0.8584-0.1080.7845-1.3796-0.49070.12090.70210.0849-0.25640.4227-0.00790.834461.78285.841929.1593
34.55390.69170.19912.52-0.4243.3606-0.03230.43450.3408-0.0951-0.1019-0.1957-0.09210.28030.13440.268-0.01790.00620.27750.03990.32166.765969.391828.7901
43.8107-0.2765-1.17892.20371.072.3338-0.01280.06170.1065-0.03330.04270.125-0.0332-0.10090.00410.20120.0181-0.02170.21190.05120.193648.55462.722527.7928
54.77184.58521.39925.03760.07973.573-0.0321-0.1740.93280.0032-0.2981-0.0693-1.184-0.01630.77690.26950.0566-0.00560.27940.01760.417641.493178.413243.0048
63.8322-1.3641-1.98843.08283.86237.25120.15230.07960.20640.1689-0.14140.08880.0989-0.3223-0.00180.17950.0068-0.00460.13430.04620.17945.349961.425540.7528
72.2890.80540.71882.3921.39652.8795-0.194-0.25670.27360.315-0.0037-0.4595-0.34570.00840.18420.27010.00060.01790.2745-0.05710.27747.49474.127356.6028
85.00122.7952-1.33154.0224-0.37372.24030.012-0.16090.3170.0313-0.05060.198-0.0552-0.0013-0.01370.19780.0406-0.03040.19660.01420.224856.411165.846647.4028
95.3792-1.83661.44297.7025-4.37123.3076-0.41230.38671.10610.22390.0445-0.563-1.22880.6020.07790.4536-0.1005-0.06260.32410.02530.50374.325980.869537.6579
103.3401-0.47051.15666.98270.36427.58090.1735-0.3617-0.10180.3504-0.3009-0.3371-0.06580.33410.05030.11540.0683-0.01330.28030.01590.210765.323761.339148.8396
118.0487-1.32920.65696.68172.92646.10610.23450.2462-0.4159-0.15570.12630.01890.5451-0.0844-0.37280.323-0.09520.01280.2688-0.01480.140240.197940.40439.2059
123.0314-3.3193.46933.7022-4.32617.9075-0.1804-0.15150.7678-0.49040.04730.4254-1.2949-1.81030.32990.81010.2672-0.12751.0154-0.02430.579919.901660.23185.8163
133.73181.17460.38951.45361.47393.95630.0938-0.01840.2870.038-0.1320.3552-0.0346-0.6424-0.010.19070.0119-0.05180.40020.04090.210932.510351.928510.2134
142.75461.137-0.46593.4737-1.49756.2119-0.17690.2678-0.0515-0.37260.051-0.2349-0.05960.21390.0420.21310.002-0.0130.2356-0.01270.152146.801555.373211.086
152.37210.53643.01573.4142.95575.4377-0.38510.21010.8752-0.5407-0.04790.5513-1.1314-0.53010.12210.9642-0.2346-0.18220.62420.17640.503744.477366.139-9.8392
16-0.003-0.03090.06331.0429-1.5542.4763-0.21020.7187-0.2345-0.62930.34880.08840.17920.4404-0.02260.5045-0.1318-0.04420.5792-0.01680.21851.032553.0322-1.2652
172.87951.37650.50512.57840.59111.14520.00920.70240.3902-0.54090.2290.1862-0.41450.76970.08080.8878-0.187-0.11170.87620.01320.24444.290752.4183-20.0891
184.27230.11613.21662.0627-0.05775.3679-0.2070.2143-0.0291-0.50240.2915-0.042-0.10260.2243-0.06490.5079-0.1181-0.06290.4814-0.03090.176742.603545.2748-6.9329
190.8026-0.11090.12820.0385-0.05530.2294-0.08840.3040.0798-0.0475-0.27270.2686-0.0446-1.2113-2.72040.39530.0122-0.22781.4415-0.03140.345217.252347.414-0.554
204.46570.25313.44395.32361.68514.6460.01910.3489-0.6744-0.18950.10720.38350.8328-0.1048-0.46660.4608-0.137-0.04580.392-0.04480.316337.995635.9534-4.1302
214.5760.3871-0.94217.23090.99286.24480.16310.13670.4569-0.055-0.1068-0.3486-0.47350.11820.06440.1315-0.0333-0.01660.2883-0.00550.261630.938455.242747.6635
220.91910.2795-0.49813.05850.020.351-0.62230.0391-1.02470.31980.01320.19541.0190.1814-0.03510.48630.01910.25620.20130.02190.517631.842226.741157.0874
232.1083-0.46240.26135.7267-3.25652.9134-0.0923-0.0993-0.20730.0537-0.0062-0.27530.2650.30740.09950.21240.0167-0.01790.22510.02040.260437.967741.033253.6923
244.3973.5248-2.03835.9412-2.40633.97350.2699-0.7691-1.03740.0508-0.5447-0.5881-0.00690.22960.07670.22570.0465-0.01690.18890.00050.284727.076243.088855.5817
255.29542.52732.97092.4891.68942.9395-0.0054-0.0502-0.0778-0.010.02850.06890.1057-0.12980.07870.19440.00370.01120.14480.02540.232417.267944.123557.3074
266.12123.63490.97644.56961.36954.07950.08-0.21830.1879-0.0244-0.1325-0.1263-0.1330.01980.05590.19090.00470.00780.12670.03980.213115.39452.731757.7863
272.84640.74660.19434.00061.66972.8119-0.08180.1668-0.2649-0.21470.00050.067-0.0208-0.1137-0.00470.1779-0.00680.01390.21240.01160.228212.942143.116543.7832
283.38270.83810.01424.13051.22173.4546-0.06060.3377-0.3436-0.1917-0.12380.22860.1958-0.18170.12370.2282-0.01470.03350.282-0.04530.23420.416341.619532.3684
293.1767-3.12832.14746.1366-3.88833.8541-0.4372-0.1999-0.26340.02870.1177-0.19190.78720.30180.16660.45280.09450.10480.23660.00340.387839.959629.009947.0618
305.007-1.48352.09766.7654-3.56245.87360.21240.3781-0.1075-0.4297-0.3188-0.11820.29340.02970.08240.1065-0.07960.01380.26180.00580.172733.387747.486836.0403
317.66481.3134-1.27084.06761.38714.72030.14490.03580.44390.32970.2315-0.1983-0.76270.0754-0.02420.3980.02580.01710.2371-0.060.27798.824869.888874.7263
326.88485.0439-3.32017.6459-4.8523.4621-0.37360.0275-1.04190.1983-0.09090.08170.8916-1.38860.36160.7249-0.26840.2080.7961-0.10320.6037-11.191547.755777.8587
335.7616-3.2801-0.18533.35021.56264.36640.25010.0651-0.1084-0.2352-0.28730.3024-0.248-0.8047-0.06430.23340.00820.05470.3714-0.00670.1822-3.055360.293173.6329
343.3044-2.2023.51464.6794-4.23067.1082-0.0491-0.1093-0.19170.3279-0.0737-0.08640.09650.15960.08660.21780.00160.05770.2462-0.00050.226311.184849.928472.9211
354.6944-3.24360.69942.8282-2.39566.31430.08620.01990.1372-0.3095-0.1156-0.2118-0.01330.2690.08670.164-0.05870.00580.1974-0.01630.233417.470154.801970.0492
362.55010.5971-0.95473.6827-2.35682.8112-0.0773-0.5391-0.34510.55180.0652-0.07420.37290.17270.02720.52010.03050.02130.40170.02780.207415.841349.178689.0041
372.24140.3187-1.27380.33940.0430.93930.1175-0.64910.04620.67640.04550.0911-0.28840.54820.0280.61840.05820.08010.44070.00260.245812.20756.092593.064
382.6990.1671-0.04351.72080.16354.16450.1067-0.5182-0.09840.55090.03410.12330.2527-0.0444-0.12390.5330.01570.0730.3955-0.02580.1539.307162.35292.181
394.90592.53320.32192.83260.22892.32440.0647-0.28840.60950.3382-0.16010.9026-0.1794-1.4964-0.29730.45420.06150.19490.8021-0.07490.3588-10.262464.424986.6008
404.7354-2.75173.52184.41991.52617.13550.3457-0.01330.4307-0.33680.0565-0.2309-1.05471.3649-0.37770.7304-0.16180.04110.4382-0.05110.357915.967673.538181.3842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:30)
2X-RAY DIFFRACTION2(chain A and resid 31:44)
3X-RAY DIFFRACTION3(chain A and resid 45:97)
4X-RAY DIFFRACTION4(chain A and resid 98:169)
5X-RAY DIFFRACTION5(chain A and resid 170:180)
6X-RAY DIFFRACTION6(chain A and resid 181:210)
7X-RAY DIFFRACTION7(chain A and resid 211:233)
8X-RAY DIFFRACTION8(chain A and resid 234:284)
9X-RAY DIFFRACTION9(chain A and resid 285:306)
10X-RAY DIFFRACTION10(chain A and resid 307:324)
11X-RAY DIFFRACTION11(chain B and resid 3:29)
12X-RAY DIFFRACTION12(chain B and resid 30:52)
13X-RAY DIFFRACTION13(chain B and resid 53:110)
14X-RAY DIFFRACTION14(chain B and resid 111:168)
15X-RAY DIFFRACTION15(chain B and resid 169:179)
16X-RAY DIFFRACTION16(chain B and resid 180:211)
17X-RAY DIFFRACTION17(chain B and resid 212:233)
18X-RAY DIFFRACTION18(chain B and resid 234:280)
19X-RAY DIFFRACTION19(chain B and resid 281:307)
20X-RAY DIFFRACTION20(chain B and resid 308:324)
21X-RAY DIFFRACTION21(chain C and resid 2:27)
22X-RAY DIFFRACTION22(chain C and resid 28:51)
23X-RAY DIFFRACTION23(chain C and resid 52:82)
24X-RAY DIFFRACTION24(chain C and resid 83:97)
25X-RAY DIFFRACTION25(chain C and resid 98:138)
26X-RAY DIFFRACTION26(chain C and resid 139:159)
27X-RAY DIFFRACTION27(chain C and resid 160:210)
28X-RAY DIFFRACTION28(chain C and resid 211:276)
29X-RAY DIFFRACTION29(chain C and resid 277:303)
30X-RAY DIFFRACTION30(chain C and resid 304:326)
31X-RAY DIFFRACTION31(chain D and resid 2:27)
32X-RAY DIFFRACTION32(chain D and resid 28:51)
33X-RAY DIFFRACTION33(chain D and resid 52:97)
34X-RAY DIFFRACTION34(chain D and resid 98:137)
35X-RAY DIFFRACTION35(chain D and resid 138:161)
36X-RAY DIFFRACTION36(chain D and resid 162:196)
37X-RAY DIFFRACTION37(chain D and resid 197:225)
38X-RAY DIFFRACTION38(chain D and resid 226:284)
39X-RAY DIFFRACTION39(chain D and resid 285:320)
40X-RAY DIFFRACTION40(chain D and resid 321:326)

+
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