[English] 日本語
Yorodumi
- PDB-3utc: Ec_IspH in complex with (E)-4-hydroxybut-3-enyl diphosphate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3utc
TitleEc_IspH in complex with (E)-4-hydroxybut-3-enyl diphosphate
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE / iron-sulfur protein / IspH / LytB / isoprenoid biosynthesis / non-mevalonate pathway
Function / homology
Function and homology information


hydroxymethylbutenyl pyrophosphate reductase activity / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity / dimethylallyl diphosphate biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
4-hydroxy-3-methylbut-2-enyl diphosphate reductase / LytB protein / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain / Rossmann fold - #11270 / Cobalt-precorrin-4 Transmethylase; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0JX / IRON/SULFUR CLUSTER / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSpan, I. / Wang, K. / Wang, W. / Zhang, Y. / Bacher, A. / Eisenreich, W. / Li, K. / Schulz, C. / Oldfield, E. / Groll, M.
CitationJournal: Nat Commun / Year: 2012
Title: Discovery of acetylene hydratase activity of the iron-sulphur protein IspH.
Authors: Span, I. / Wang, K. / Wang, W. / Zhang, Y. / Bacher, A. / Eisenreich, W. / Li, K. / Schulz, C. / Oldfield, E. / Groll, M.
History
DepositionNov 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7806
Polymers71,5812
Non-polymers1,1994
Water6,756375
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3903
Polymers35,7911
Non-polymers6002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3903
Polymers35,7911
Non-polymers6002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.120, 80.790, 112.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99973, 0.010319, 0.020805), (0.010185, 0.999927, -0.006537), (-0.020871, -0.006323, -0.999762)-65.6545, 0.31672, -0.47874

-
Components

#1: Protein 4-hydroxy-3-methylbut-2-enyl diphosphate reductase /


Mass: 35790.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ispH, lytB, yaaE, b0029, JW0027 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue
References: UniProt: P62623, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-0JX / (3E)-4-hydroxybut-3-en-1-yl trihydrogen diphosphate


Mass: 248.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O8P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS, 0.2 M ammonia sulfate, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2010
RadiationMonochromator: double-crystal fixed-exit monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→24.85 Å / Num. all: 51128 / Num. obs: 50463 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.8
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 3.9 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
RemDAqdata collection
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.5.0072phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KE8
Resolution: 1.9→24.85 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.299 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.593 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22726 2524 5 %RANDOM
Rwork0.14703 ---
obs0.15098 47938 98.89 %-
all-50462 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2---1.7 Å20 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 44 375 5192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194903
X-RAY DIFFRACTIONr_angle_refined_deg1.961.9776644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7645617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.04724.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95315853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7451544
X-RAY DIFFRACTIONr_chiral_restr0.1250.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213672
X-RAY DIFFRACTIONr_rigid_bond_restr6.61334899
X-RAY DIFFRACTIONr_sphericity_free24.5845119
X-RAY DIFFRACTIONr_sphericity_bonded16.74455073
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 161 -
Rwork0.157 3033 -
obs--90.84 %
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)
12.6805-0.16250.4130.65660.53140.5487-0.10940.11820.07080.19550.1009-0.03190.13850.10160.00850.06640.034-0.02240.05360.01820.086-8.9435-8.002-7.839
22.18470.16361.11730.9046-0.07220.5990.12640.0062-0.1413-0.0639-0.0502-0.00630.0760.0141-0.07620.03450.0055-0.00140.0487-0.0160.0409-29.8033-10.209-10.8631
32.4419-0.44431.36622.84020.10530.81060.31860.2653-0.1911-0.0667-0.2123-0.02610.16880.1251-0.10630.09460.0502-0.06960.0433-0.02990.0541-40.5092-13.4978-21.6956
42.6603-1.36090.1633.35570.42610.10830.10530.1991-0.2805-0.0528-0.10320.19680.00340.0136-0.0020.05020.0348-0.01470.0703-0.02330.0398-26.8124-10.3835-21.6884
54.7836-0.96692.19032.16080.58371.53980.20160.7285-0.1448-0.3376-0.1230.0093-0.05960.3444-0.07860.09090.0387-0.03010.1302-0.03410.0247-37.4981-9.8868-27.7891
60.29660.30520.15270.59430.85321.82130.08170.03650.10430.0653-0.04140.07990.0197-0.1563-0.04040.07340.0424-0.02150.0685-0.01290.0946-41.1989-4.7582-20.7148
72.78373.01421.08278.69722.88164.23190.04230.0240.2948-0.42620.0840.5029-0.0925-0.1283-0.12640.07050.0195-0.04980.0435-0.00310.1153-48.5908-0.2597-22.6921
80.59690.5083-0.42330.4343-0.36190.30160.04430.00680.06470.02990.00680.0622-0.0237-0.0036-0.0510.04040.0148-0.01790.0477-0.01320.0613-39.0542-0.5658-11.785
91.2605-2.72451.758910.6989-3.00315.11260.0441-0.02190.17790.86870.17050.49170.1442-0.2093-0.21460.19140.02950.1940.03620.05280.345-43.697815.3496-8.9473
100.8388-0.7438-0.98853.02040.81611.16780.0091-0.0030.0784-0.16150.09230.0543-0.0083-0.002-0.10140.04230.0204-0.01140.02830.01030.0395-31.070311.9194-17.4852
110.32870.56240.08531.3412-0.18540.8502-0.02490.06410.0794-0.13450.03750.2104-0.1206-0.0198-0.01260.09470.0508-0.02440.04810.00690.0851-34.496320.9-16.4452
120.5946-0.0754-0.04261.1001-0.5270.2633-0.0048-0.00190.02630.0945-0.0062-0.0235-0.04210.00320.01090.04990.0090.01010.0273-0.00370.0405-24.025914.3183-10.2983
132.13080.9979-0.25664.8725-2.85021.72330.1691-0.04910.24590.099-0.09090.1993-0.02760.0535-0.07820.07360.02390.01930.0227-0.01440.0371-29.174122.8539-5.5254
140.4586-0.3881-0.40640.37870.20650.81210.0205-0.00810.0578-0.0082-0.0153-0.0558-0.00270.0266-0.00520.0511-0.0131-0.00050.0434-0.01040.0552-19.21632.8642-5.9283
150.65010.2564-0.19050.21450.11890.41720.01490.0138-0.0599-0.04120.0037-0.0688-0.0567-0.0247-0.01860.06210.00450.03720.0291-0.00680.0852-11.44570.3004-16.0549
163.91651.2962.40351.91160.2353.8158-0.10460.1695-0.1801-0.30740.065-0.3460.10880.25190.03960.06180.01110.06230.0493-0.00910.0765-2.5555-8.6127-20.9527
170.11990.0562-0.09670.6917-0.00310.0899-0.003-0.00730.01890.02970.0091-0.06710.0251-0.0009-0.00610.0630.00940.0110.036-0.0130.0634-14.6848-11.7839-13.8208
181.2223-0.1484-0.41861.44920.65591.4014-0.0172-0.1262-0.07630.20720.0834-0.21860.31280.0796-0.06620.07970.0191-0.02520.03620.01590.0589-7.4273-11.9138-7.911
191.2788-0.39280.13850.1819-0.31011.1858-0.1959-0.00030.05580.05930.0095-0.0573-0.0212-0.02520.18640.0566-0.0138-0.0090.03790.00810.0416-31.5626-7.3373-2.0697
206.3676-9.6783-5.609722.22255.27946.3478-0.2329-0.1756-0.42510.6148-0.21120.52390.1070.35140.44410.0425-0.040.01530.1014-0.02540.0898-43.6979-14.3034-7.9933
210.183-0.31740.23580.5977-0.44710.3374-0.0044-0.0474-0.0108-0.0560.0590.07250.0539-0.0538-0.05460.0905-0.0067-0.03490.0509-0.03510.0892-56.5567-7.81578.6461
220.792-0.54980.47420.4856-0.1840.52080.03160.0004-0.03740.03650.01070.0060.0998-0.0144-0.04240.0649-0.0107-0.0260.03270.00140.034-33.3193-11.127318.0001
232.36281.6006-1.06722.5814-3.37875.310.238-0.026-0.50630.09990.0571-0.13470.0706-0.3334-0.29510.1153-0.0474-0.09840.18470.16360.2526-33.2438-17.931325.6424
240.5443-0.1740.59630.6113-0.37740.72590.03340.00260.00370.0539-0.0211-0.00420.02480.0271-0.01230.0505-0.0003-0.03880.0409-0.01930.0453-24.4599-5.876424.971
251.7443-1.29811.26623.628-1.57183.4867-0.07370.12990.08960.089-0.0665-0.2875-0.17110.14410.14020.0358-0.0234-0.04490.03550.00540.1027-17.92162.227820.7706
260.6426-0.59890.63210.5644-0.61460.9414-0.0599-0.00160.08190.05880.017-0.07490.018-0.01040.04290.05680.0089-0.02750.0477-0.00360.0437-22.8367-4.047315.801
272.2118-0.2776-1.17195.54922.47361.60290.21310.04960.2269-0.21330.0673-0.412-0.1864-0.001-0.28040.0369-0.01270.00790.0230.03020.1503-23.412612.2858.8702
280.90570.5208-0.79342.0998-0.78431.6243-0.0127-0.04790.13880.15570.096-0.19720.0004-0.0993-0.08330.0515-0.0061-0.03110.0337-0.02310.0645-32.702413.386116.8423
292.5722.7312-0.49135.47970.29850.5621-0.016-0.28370.12280.11210.0621-0.28310.12220.1541-0.04610.0817-0.008-0.03840.0941-0.05130.191-23.459215.133817.8963
300.98480.32-0.09591.4426-0.07570.52680.07110.0040.13470.1011-0.0365-0.0764-0.0408-0.0675-0.03460.0515-0.00110.01380.0110.00240.061-37.361119.919713.5575
312.8073-0.20080.13641.97331.37050.97960.1809-0.00840.19-0.1391-0.0926-0.1608-0.0769-0.0688-0.08830.0851-0.01130.01530.01490.02350.0651-35.98522.98665.4614
320.6290.9791-0.22061.8082-0.07250.343-0.00240.00240.0076-0.0683-0.02070.0255-0.0439-0.01990.02320.0590.0026-0.00270.02910.01340.0373-44.05763.31766.2718
337.0213-0.4435-4.09520.1377-0.04143.29420.23380.23820.174-0.0818-0.00350.07270.0709-0.1598-0.23020.0559-0.0064-0.0210.04890.00130.179-60.38080.35648.5992
341.0913-0.578-0.02240.3452-0.09280.3711-0.0943-0.0567-0.03490.10640.03410.0236-0.09520.03860.06020.11190.00610.03930.03650.01580.0605-48.99340.495517.8489
351.0176-1.2344-0.13133.9723-0.1770.10190.022-0.02540.01740.1719-0.0080.1695-0.0091-0.0307-0.0140.033-0.01960.03610.0447-0.00650.0498-56.3765-0.235518.7104
362.6384-2.23281.95582.0403-1.03484.1833-0.2859-0.1121-0.17880.3180.05940.25680.1114-0.25230.22650.0779-0.02530.07160.0645-0.00590.1165-63.6653-7.941821.8522
370.5544-0.0124-0.43130.3690.17220.66120.01210.0931-0.00240.0839-0.01510.07670.05520.05050.0030.04410.0021-0.00560.0879-0.00420.0634-50.7579-11.396114.3758
382.63310.6751-1.11623.0481-1.94121.85470.02510.233-0.1348-0.2260.06580.41240.1769-0.0807-0.09090.041-0.0148-0.01580.0452-0.0160.1077-57.9311-11.60528.7332
393.5934-0.27731.61490.04010.01951.8836-0.1350.17740.00630.0246-0.00190.01450.00210.16160.13690.06460.0041-0.00590.0341-0.00330.0286-32.898-7.65323.1293
4010.3133-6.759-6.969320.6785-6.295211.9717-0.07020.16120.002-0.7255-0.235-0.430.579-0.01340.30520.12770.0773-0.01370.0639-0.01890.0333-22.3276-15.65947.8487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 24
3X-RAY DIFFRACTION3A25 - 37
4X-RAY DIFFRACTION4A38 - 49
5X-RAY DIFFRACTION5A50 - 64
6X-RAY DIFFRACTION6A65 - 77
7X-RAY DIFFRACTION7A78 - 89
8X-RAY DIFFRACTION8A90 - 103
9X-RAY DIFFRACTION9A104 - 114
10X-RAY DIFFRACTION10A115 - 127
11X-RAY DIFFRACTION11A128 - 162
12X-RAY DIFFRACTION12A163 - 181
13X-RAY DIFFRACTION13A182 - 193
14X-RAY DIFFRACTION14A194 - 210
15X-RAY DIFFRACTION15A211 - 246
16X-RAY DIFFRACTION16A247 - 261
17X-RAY DIFFRACTION17A262 - 280
18X-RAY DIFFRACTION18A281 - 297
19X-RAY DIFFRACTION19A298 - 304
20X-RAY DIFFRACTION20A305 - 309
21X-RAY DIFFRACTION21B1 - 7
22X-RAY DIFFRACTION22B8 - 49
23X-RAY DIFFRACTION23B50 - 54
24X-RAY DIFFRACTION24B55 - 76
25X-RAY DIFFRACTION25B77 - 86
26X-RAY DIFFRACTION26B87 - 100
27X-RAY DIFFRACTION27B101 - 112
28X-RAY DIFFRACTION28B113 - 127
29X-RAY DIFFRACTION29B128 - 140
30X-RAY DIFFRACTION30B141 - 181
31X-RAY DIFFRACTION31B182 - 193
32X-RAY DIFFRACTION32B194 - 207
33X-RAY DIFFRACTION33B208 - 216
34X-RAY DIFFRACTION34B217 - 235
35X-RAY DIFFRACTION35B236 - 248
36X-RAY DIFFRACTION36B249 - 261
37X-RAY DIFFRACTION37B262 - 280
38X-RAY DIFFRACTION38B281 - 297
39X-RAY DIFFRACTION39B298 - 305
40X-RAY DIFFRACTION40B306 - 310

+
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