[English] 日本語
Yorodumi
- PDB-6fog: X-ray structure of homo sapiens Fumarylacetoacetate hydrolase dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fog
TitleX-ray structure of homo sapiens Fumarylacetoacetate hydrolase domain containing protein 1 (FAHD1) in complex with inhibitor oxalate at 1.94A resolution.
ComponentsAcylpyruvase FAHD1, mitochondrial
Keywordshydrolase/lyase / FAHD 1 / Fumarylacetoacetate hydrolase domain containing protein 1 / oxalate / inhibitor / hydrolase-lyase complex
Function / homology
Function and homology information


acylpyruvate hydrolase / fumarylpyruvate hydrolase activity / acylpyruvate hydrolase activity / oxaloacetate tautomerase / oxaloacetate tautomerase activity / acetylpyruvate hydrolase activity / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / oxaloacetate metabolic process / Pyruvate metabolism ...acylpyruvate hydrolase / fumarylpyruvate hydrolase activity / acylpyruvate hydrolase activity / oxaloacetate tautomerase / oxaloacetate tautomerase activity / acetylpyruvate hydrolase activity / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / oxaloacetate metabolic process / Pyruvate metabolism / pyruvate metabolic process / mitochondrial matrix / mitochondrion / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
OXALATE ION / Oxaloacetate tautomerase FAHD1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.94 Å
AuthorsNaschberger, A. / Weiss, A.K.H.
Funding support Austria, 3items
OrganizationGrant numberCountry
European integrated FP6-LIFESCIHEALTH project MiMAGE512020
Austria Wirtschaftsservice Gesellschaft (AWS) Austria
Austrian Science FundP28975 Austria
CitationJournal: Biochem. J. / Year: 2018
Title: Structural basis for the bi-functionality of human oxaloacetate decarboxylase FAHD1.
Authors: Weiss, A.K.H. / Naschberger, A. / Loeffler, J.R. / Gstach, H. / Bowler, M.W. / Holzknecht, M. / Cappuccio, E. / Pittl, A. / Etemad, S. / Dunzendorfer-Matt, T. / Scheffzek, K. / Liedl, K.R. / Jansen-Durr, P.
History
DepositionFeb 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.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.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_conn.ptnr2_label_seq_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acylpyruvase FAHD1, mitochondrial
G: Acylpyruvase FAHD1, mitochondrial
F: Acylpyruvase FAHD1, mitochondrial
D: Acylpyruvase FAHD1, mitochondrial
B: Acylpyruvase FAHD1, mitochondrial
C: Acylpyruvase FAHD1, mitochondrial
H: Acylpyruvase FAHD1, mitochondrial
E: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,13732
Polymers199,0008
Non-polymers1,13824
Water15,151841
1
A: Acylpyruvase FAHD1, mitochondrial
C: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0348
Polymers49,7502
Non-polymers2846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-44 kcal/mol
Surface area17250 Å2
MethodPISA
2
G: Acylpyruvase FAHD1, mitochondrial
E: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0348
Polymers49,7502
Non-polymers2846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-43 kcal/mol
Surface area17100 Å2
MethodPISA
3
F: Acylpyruvase FAHD1, mitochondrial
H: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0348
Polymers49,7502
Non-polymers2846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-44 kcal/mol
Surface area17170 Å2
MethodPISA
4
D: Acylpyruvase FAHD1, mitochondrial
B: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0348
Polymers49,7502
Non-polymers2846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-43 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.984, 116.679, 125.753
Angle α, β, γ (deg.)90.00, 89.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21G
12A
22F
13A
23D
14A
24B
15A
25C
16A
26H
17A
27E
18G
28F
19G
29D
110G
210B
111G
211C
112G
212H
113G
213E
114F
214D
115F
215B
116F
216C
117F
217H
118F
218E
119D
219B
120D
220C
121D
221H
122D
222E
123B
223C
124B
224H
125B
225E
126C
226H
127C
227E
128H
228E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALYSLYSAA6 - 2216 - 221
21ALAALALYSLYSGB6 - 2216 - 221
12PROPROPROPROAA9 - 2229 - 222
22PROPROPROPROFC9 - 2229 - 222
13PROPROPROPROAA9 - 2229 - 222
23PROPROPROPRODD9 - 2229 - 222
14ALAALALYSLYSAA6 - 2216 - 221
24ALAALALYSLYSBE6 - 2216 - 221
15PROPROPROPROAA9 - 2229 - 222
25PROPROPROPROCF9 - 2229 - 222
16ALAALALYSLYSAA6 - 2216 - 221
26ALAALALYSLYSHG6 - 2216 - 221
17ARGARGLYSLYSAA8 - 2218 - 221
27ARGARGLYSLYSEH8 - 2218 - 221
18PROPROLYSLYSGB9 - 2219 - 221
28PROPROLYSLYSFC9 - 2219 - 221
19PROPROLYSLYSGB9 - 2219 - 221
29PROPROLYSLYSDD9 - 2219 - 221
110ALAALAPROPROGB6 - 2226 - 222
210ALAALAPROPROBE6 - 2226 - 222
111PROPROLYSLYSGB9 - 2219 - 221
211PROPROLYSLYSCF9 - 2219 - 221
112ALAALAPROPROGB6 - 2226 - 222
212ALAALAPROPROHG6 - 2226 - 222
113ARGARGLYSLYSGB8 - 2218 - 221
213ARGARGLYSLYSEH8 - 2218 - 221
114PROPROGLUGLUFC9 - 2239 - 223
214PROPROGLUGLUDD9 - 2239 - 223
115PROPROLYSLYSFC9 - 2219 - 221
215PROPROLYSLYSBE9 - 2219 - 221
116PROPROPROPROFC9 - 2229 - 222
216PROPROPROPROCF9 - 2229 - 222
117PROPROLYSLYSFC9 - 2219 - 221
217PROPROLYSLYSHG9 - 2219 - 221
118PROPROLYSLYSFC9 - 2219 - 221
218PROPROLYSLYSEH9 - 2219 - 221
119PROPROLYSLYSDD9 - 2219 - 221
219PROPROLYSLYSBE9 - 2219 - 221
120PROPROPROPRODD9 - 2229 - 222
220PROPROPROPROCF9 - 2229 - 222
121PROPROLYSLYSDD9 - 2219 - 221
221PROPROLYSLYSHG9 - 2219 - 221
122PROPROLYSLYSDD9 - 2219 - 221
222PROPROLYSLYSEH9 - 2219 - 221
123PROPROLYSLYSBE9 - 2219 - 221
223PROPROLYSLYSCF9 - 2219 - 221
124ALAALAPROPROBE6 - 2226 - 222
224ALAALAPROPROHG6 - 2226 - 222
125ARGARGLYSLYSBE8 - 2218 - 221
225ARGARGLYSLYSEH8 - 2218 - 221
126PROPROLYSLYSCF9 - 2219 - 221
226PROPROLYSLYSHG9 - 2219 - 221
127PROPROLYSLYSCF9 - 2219 - 221
227PROPROLYSLYSEH9 - 2219 - 221
128ARGARGLYSLYSHG8 - 2218 - 221
228ARGARGLYSLYSEH8 - 2218 - 221

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

-
Components

#1: Protein
Acylpyruvase FAHD1, mitochondrial / Fumarylacetoacetate hydrolase domain-containing protein 1 / FAH domain-containing protein 1 / ...Fumarylacetoacetate hydrolase domain-containing protein 1 / FAH domain-containing protein 1 / Oxaloacetate decarboxylase / OAA decarboxylase / YisK-like protein


Mass: 24874.969 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAHD1, C16orf36, YISKL / Production host: Escherichia coli (E. coli)
References: UniProt: Q6P587, acylpyruvate hydrolase, oxaloacetate decarboxylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 841 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG4000, 50mM MgCl2, 100mM HEPES pH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.392
11-h,-k,l20.608
ReflectionResolution: 1.94→100 Å / Num. obs: 154275 / % possible obs: 94.3 % / Redundancy: 2.29 % / CC1/2: 0.991 / Rrim(I) all: 0.136 / Net I/σ(I): 6.43
Reflection shellResolution: 1.94→2.05 Å / CC1/2: 0.583 / Rrim(I) all: 1.005

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 1.94→85.53 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.201 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.028 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20826 7965 5.2 %RANDOM
Rwork0.18093 ---
obs0.1824 146296 94.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.808 Å2
Baniso -1Baniso -2Baniso -3
1--6.55 Å20 Å2-0.78 Å2
2--2.05 Å20 Å2
3---4.5 Å2
Refinement stepCycle: 1 / Resolution: 1.94→85.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13467 0 64 841 14372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01913857
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213277
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.9118776
X-RAY DIFFRACTIONr_angle_other_deg1.022330906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20951726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38323.633523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.551152449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1411578
X-RAY DIFFRACTIONr_chiral_restr0.0930.22085
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115085
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0192653
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_it3.4964.5116922
X-RAY DIFFRACTIONr_mcbond_other3.4944.516921
X-RAY DIFFRACTIONr_mcangle_it4.5788.4448642
X-RAY DIFFRACTIONr_mcangle_other4.5788.4448643
X-RAY DIFFRACTIONr_scbond_it4.3555.3856935
X-RAY DIFFRACTIONr_scbond_other4.3555.3856936
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2419.63210135
X-RAY DIFFRACTIONr_long_range_B_refined7.98830.26115036
X-RAY DIFFRACTIONr_long_range_B_other7.98830.26215037
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)
11A138440.06
12G138440.06
21A137000.07
22F137000.07
31A136440.07
32D136440.07
41A138740.06
42B138740.06
51A136760.06
52C136760.06
61A138980.06
62H138980.06
71A137560.06
72E137560.06
81G134880.07
82F134880.07
91G134660.07
92D134660.07
101G138200.06
102B138200.06
111G134200.07
112C134200.07
121G137140.07
122H137140.07
131G135460.07
132E135460.07
141F137420.07
142D137420.07
151F135500.07
152B135500.07
161F136340.07
162C136340.07
171F135540.07
172H135540.07
181F137020.06
182E137020.06
191D135760.06
192B135760.06
201D135900.06
202C135900.06
211D135100.06
212H135100.06
221D136800.06
222E136800.06
231B135900.07
232C135900.07
241B138860.06
242H138860.06
251B137360.06
252E137360.06
261C134640.07
262H134640.07
271C136040.06
272E136040.06
281H136440.06
282E136440.06
LS refinement shellResolution: 1.932→1.982 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 78 -
Rwork0.249 9762 -
obs--81.73 %
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)
10.07690.06740.05770.1510.13110.20160.02760.02430.00380.03970.0041-0.03320.0432-0.0114-0.03170.02850.00210.0220.0143-0.00160.11114.6445-0.13673.1551
20.1604-0.02630.06110.12870.01750.2589-0.0009-0.0108-0.0019-0.0030.019-0.0261-0.0463-0.0136-0.01810.0231-0.00040.0390.0044-0.00930.1057-32.61628.8132109.2281
30.2111-0.15950.03640.13220.01030.20060.0276-0.033-0.0137-0.02740.0183-0.00370.0255-0-0.04590.03120.00560.03040.01250.00330.10519.96354.331843.1789
40.08730.0463-0.02480.05940.00660.25520.03270.01180.0110.0158-0.0108-0.009-0.01720.0068-0.02180.02820.00410.04520.01110.00580.1131-27.454627.793668.5944
50.10010.0586-0.01930.07320.08130.26040.00960.00820.00710.01110.0032-0.02250.0423-0.0018-0.01280.03240.00630.03440.0035-0.00040.1107-32.71251.707364.9294
60.11430.1494-0.01020.21130.03640.21280.02010.0060.00270.02950.00080.0001-0.00690.0038-0.02080.0246-0.00010.03850.01140.00630.10619.906426.07285.0248
70.167-0.0467-0.01080.0840.05210.42530.0104-0.03920.0126-0.0380.0276-0.0362-0.0717-0.0069-0.03790.0346-0.01030.05170.0145-0.01660.11624.533430.611444.9251
80.09850.01020.04430.0432-0.0150.39550.0246-0.0166-0.006-0.0163-0.00150.00170.03380.0048-0.02310.0258-0.00280.0290.00330.0030.1097-27.56712.6521105.6671
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 223
2X-RAY DIFFRACTION2G6 - 222
3X-RAY DIFFRACTION3F9 - 223
4X-RAY DIFFRACTION4D9 - 223
5X-RAY DIFFRACTION5B6 - 222
6X-RAY DIFFRACTION6C9 - 224
7X-RAY DIFFRACTION7H6 - 222
8X-RAY DIFFRACTION8E8 - 222

+
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