[English] 日本語
Yorodumi
- PDB-6s83: Crystal structure of methionine adenosyltransferase from Pyrococc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s83
TitleCrystal structure of methionine adenosyltransferase from Pyrococcus furiosus in complex with AMPPCP, SAM, and PCP
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / S-adenosyl methionine synthesis / cofactor biosynthesis / cytoplasmic
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding
Similarity search - Function
S-adenosylmethionine synthetase, archaea / S-adenosylmethionine synthase / S-adenosylmethionine synthetase, domain 3 / S-adenosylmethionine synthetase (AdoMet synthetase)
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / METHYLENEDIPHOSPHONIC ACID / PHOSPHATE ION / S-ADENOSYLMETHIONINE / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.336 Å
AuthorsDegano, M. / Minici, C. / Porcelli, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer Research Italy
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structures of catalytic cycle intermediates of the Pyrococcus furiosus methionine adenosyltransferase demonstrate negative cooperativity in the archaeal orthologues.
Authors: Minici, C. / Mosca, L. / Ilisso, C.P. / Cacciapuoti, G. / Porcelli, M. / Degano, M.
History
DepositionJul 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Jan 24, 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
C: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase
E: S-adenosylmethionine synthase
F: S-adenosylmethionine synthase
G: S-adenosylmethionine synthase
H: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,50147
Polymers354,7098
Non-polymers4,79239
Water8,179454
1
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,09313
Polymers88,6772
Non-polymers1,41511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-84 kcal/mol
Surface area28860 Å2
MethodPISA
2
C: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,67011
Polymers88,6772
Non-polymers9939
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-67 kcal/mol
Surface area29910 Å2
MethodPISA
3
E: S-adenosylmethionine synthase
F: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,06812
Polymers88,6772
Non-polymers1,39110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-72 kcal/mol
Surface area28960 Å2
MethodPISA
4
G: S-adenosylmethionine synthase
H: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,67011
Polymers88,6772
Non-polymers9939
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-71 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.196, 111.430, 400.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 7 or resid 9...
21(chain B and (resid 2 through 7 or resid 9...
31(chain C and (resid 2 through 7 or resid 9...
41(chain D and (resid 2 through 7 or resid 9...
51(chain E and (resid 2 through 7 or resid 9...
61(chain F and (resid 2 through 7 or resid 9...
71(chain G and (resid 2 through 7 or resid 9...
81(chain H and (resid 2 through 7 or resid 9...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 7 or resid 9...A2 - 7
121(chain A and (resid 2 through 7 or resid 9...A9 - 58
131(chain A and (resid 2 through 7 or resid 9...A60
141(chain A and (resid 2 through 7 or resid 9...A62
151(chain A and (resid 2 through 7 or resid 9...A207 - 401
161(chain A and (resid 2 through 7 or resid 9...A0
171(chain A and (resid 2 through 7 or resid 9...A301 - 313
181(chain A and (resid 2 through 7 or resid 9...A315 - 351
191(chain A and (resid 2 through 7 or resid 9...A353 - 401
211(chain B and (resid 2 through 7 or resid 9...B2 - 7
221(chain B and (resid 2 through 7 or resid 9...B9 - 58
231(chain B and (resid 2 through 7 or resid 9...B0
241(chain B and (resid 2 through 7 or resid 9...B207 - 248
251(chain B and (resid 2 through 7 or resid 9...B301 - 313
261(chain B and (resid 2 through 7 or resid 9...B2 - 505
271(chain B and (resid 2 through 7 or resid 9...B301 - 313
281(chain B and (resid 2 through 7 or resid 9...B315 - 351
291(chain B and (resid 2 through 7 or resid 9...B353 - 401
311(chain C and (resid 2 through 7 or resid 9...C2 - 7
321(chain C and (resid 2 through 7 or resid 9...C9 - 58
331(chain C and (resid 2 through 7 or resid 9...C60
341(chain C and (resid 2 through 7 or resid 9...C2 - 205
351(chain C and (resid 2 through 7 or resid 9...C207 - 248
361(chain C and (resid 2 through 7 or resid 9...C2 - 505
371(chain C and (resid 2 through 7 or resid 9...C2 - 505
381(chain C and (resid 2 through 7 or resid 9...C2 - 505
391(chain C and (resid 2 through 7 or resid 9...C315 - 351
3101(chain C and (resid 2 through 7 or resid 9...C353 - 401
411(chain D and (resid 2 through 7 or resid 9...D2 - 7
421(chain D and (resid 2 through 7 or resid 9...D9 - 58
431(chain D and (resid 2 through 7 or resid 9...D60
441(chain D and (resid 2 through 7 or resid 9...D62
451(chain D and (resid 2 through 7 or resid 9...D207 - 504
461(chain D and (resid 2 through 7 or resid 9...D0
471(chain D and (resid 2 through 7 or resid 9...D301 - 313
481(chain D and (resid 2 through 7 or resid 9...D315 - 351
491(chain D and (resid 2 through 7 or resid 9...D353 - 401
511(chain E and (resid 2 through 7 or resid 9...E2 - 7
521(chain E and (resid 2 through 7 or resid 9...E9 - 58
531(chain E and (resid 2 through 7 or resid 9...E60
541(chain E and (resid 2 through 7 or resid 9...E62
551(chain E and (resid 2 through 7 or resid 9...E162 - 205
561(chain E and (resid 2 through 7 or resid 9...E207 - 248
571(chain E and (resid 2 through 7 or resid 9...E250 - 299
581(chain E and (resid 2 through 7 or resid 9...E301 - 313
591(chain E and (resid 2 through 7 or resid 9...E315 - 351
5101(chain E and (resid 2 through 7 or resid 9...E353 - 401
611(chain F and (resid 2 through 7 or resid 9...F2 - 7
621(chain F and (resid 2 through 7 or resid 9...F9 - 58
631(chain F and (resid 2 through 7 or resid 9...F60
641(chain F and (resid 2 through 7 or resid 9...F62
651(chain F and (resid 2 through 7 or resid 9...F162 - 205
661(chain F and (resid 2 through 7 or resid 9...F207 - 248
671(chain F and (resid 2 through 7 or resid 9...F250 - 299
681(chain F and (resid 2 through 7 or resid 9...F301 - 313
691(chain F and (resid 2 through 7 or resid 9...F315 - 351
6101(chain F and (resid 2 through 7 or resid 9...F353 - 401
711(chain G and (resid 2 through 7 or resid 9...G2 - 7
721(chain G and (resid 2 through 7 or resid 9...G9 - 58
731(chain G and (resid 2 through 7 or resid 9...G60
741(chain G and (resid 2 through 7 or resid 9...G62
751(chain G and (resid 2 through 7 or resid 9...G162 - 205
761(chain G and (resid 2 through 7 or resid 9...G207 - 248
771(chain G and (resid 2 through 7 or resid 9...G250 - 299
781(chain G and (resid 2 through 7 or resid 9...G301 - 313
791(chain G and (resid 2 through 7 or resid 9...G315 - 351
7101(chain G and (resid 2 through 7 or resid 9...G353 - 401
811(chain H and (resid 2 through 7 or resid 9...H2 - 7
821(chain H and (resid 2 through 7 or resid 9...H9 - 58
831(chain H and (resid 2 through 7 or resid 9...H60
841(chain H and (resid 2 through 7 or resid 9...H62
851(chain H and (resid 2 through 7 or resid 9...H162 - 205
861(chain H and (resid 2 through 7 or resid 9...H207 - 248
871(chain H and (resid 2 through 7 or resid 9...H250 - 299
881(chain H and (resid 2 through 7 or resid 9...H301 - 313
891(chain H and (resid 2 through 7 or resid 9...H315 - 351
8101(chain H and (resid 2 through 7 or resid 9...H353 - 401

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
S-adenosylmethionine synthase / AdoMet synthase / Methionine adenosyltransferase


Mass: 44338.660 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: mat, PF1866 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8TZW1, methionine adenosyltransferase

-
Non-polymers , 6 types, 493 molecules

#2: Chemical
ChemComp-MDN / METHYLENEDIPHOSPHONIC ACID


Mass: 176.002 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH6O6P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis Tris pH 6.5, 5 mM MgCl2, 28% v/v PEG 600

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2014 / Details: Mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.336→200.2 Å / Num. obs: 149431 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 46.24 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.076 / Rrim(I) all: 0.281 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.34-2.4613.93.016300679215560.4510.8333.130.9
7.39-200.212.60.0926495351590.9960.0270.09622.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.2data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S81

6s81


Resolution: 2.336→74.466 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.05
RfactorNum. reflection% reflection
Rfree0.2398 7500 5.03 %
Rwork0.2071 --
obs0.2088 149249 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 193.23 Å2 / Biso mean: 69.6637 Å2 / Biso min: 25.24 Å2
Refinement stepCycle: final / Resolution: 2.336→74.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24872 0 383 454 25709
Biso mean--79.14 47.75 -
Num. residues----3200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00925717
X-RAY DIFFRACTIONf_angle_d0.5134746
X-RAY DIFFRACTIONf_chiral_restr0.0474022
X-RAY DIFFRACTIONf_plane_restr0.0024492
X-RAY DIFFRACTIONf_dihedral_angle_d8.67315687
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A18841X-RAY DIFFRACTION9.867TORSIONAL
12B18841X-RAY DIFFRACTION9.867TORSIONAL
13C18841X-RAY DIFFRACTION9.867TORSIONAL
14D18841X-RAY DIFFRACTION9.867TORSIONAL
15E18841X-RAY DIFFRACTION9.867TORSIONAL
16F18841X-RAY DIFFRACTION9.867TORSIONAL
17G18841X-RAY DIFFRACTION9.867TORSIONAL
18H18841X-RAY DIFFRACTION9.867TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3361-2.36260.4152330.36664712
2.3626-2.39040.38222280.35464621
2.3904-2.41960.36662500.35064690
2.4196-2.45020.38782560.33454638
2.4502-2.48250.37212740.32244634
2.4825-2.51650.33032540.29814687
2.5165-2.55240.32492460.2924641
2.5524-2.59050.31972410.27974709
2.5905-2.6310.33572480.2844658
2.631-2.67420.3072590.27974702
2.6742-2.72030.32542400.26364689
2.7203-2.76970.29962640.25834632
2.7697-2.8230.30282390.26484699
2.823-2.88060.31742350.25414715
2.8806-2.94330.30012450.24784694
2.9433-3.01170.30482500.244739
3.0117-3.08710.26672670.234651
3.0871-3.17050.25462660.22354672
3.1705-3.26380.27862500.22544735
3.2638-3.36920.22822430.21814705
3.3692-3.48960.24392270.2134763
3.4896-3.62930.23792460.19754698
3.6293-3.79450.23742500.18084742
3.7945-3.99450.19512620.16774778
3.9945-4.24480.19652460.16834730
4.2448-4.57250.17842550.15294795
4.5725-5.03250.16822500.14434801
5.0325-5.76050.21022610.17154798
5.7605-7.25660.21312580.18854896
7.2566-74.4660.18132570.17525125
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)
10.8995-0.27420.27270.9842-0.43472.3461-0.0062-0.0554-0.1144-0.02410.02280.09430.0959-0.113-0.0220.3167-0.0467-0.05980.36310.04830.4451-3.3091-22.629316.6484
21.2476-0.087-0.21490.75280.08742.6767-0.0128-0.16160.22220.0160.0445-0.0447-0.33890.1715-0.03620.30560.02050.01470.3381-0.00080.44986.1466-5.331468.9797
31.2143-0.1202-0.78070.96280.05172.99470.1418-0.21370.26360.1340.0531-0.1277-0.62330.4639-0.15880.4603-0.12870.01720.4108-0.05530.460342.0134-68.656484.5865
40.9827-0.18820.33030.9122-1.42673.3840.17180.05770.0695-0.2477-0.1092-0.01020.07190.2946-0.06290.4693-0.0362-0.00990.3450.04780.389848.8845-70.150833.3105
50.7172-0.2160.25430.59220.00812.7724-0.0029-0.0180.0628-0.0491-0.0474-0.0585-0.28460.21690.04880.3446-0.088-0.02930.35040.07670.412813.1813-5.270318.0004
61.006-0.2665-0.23161.0403-1.17352.98240.10680.1832-0.0492-0.49940.40940.36740.6932-0.7277-0.26240.7196-0.2545-0.24790.57430.16280.526727.7169-81.170531.8504
71.1144-0.262-1.2481.0850.70663.6223-0.03130.04840.0170.05650.08070.19480.0433-0.3948-0.03810.2425-0.0194-0.0080.40520.04940.405826.2737-85.952682.579
81.4271-0.4022-1.35530.71750.33593.2427-0.04710.15-0.07320.03620.0020.12020.2713-0.49950.02960.32790.00510.0250.49720.03330.4237-2.9108-27.099867.6431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'C' and resid 2 through 401)C2 - 401
2X-RAY DIFFRACTION2(chain 'A' and resid 2 through 401)A2 - 401
3X-RAY DIFFRACTION3(chain 'B' and resid 2 through 401)B2 - 401
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 401)D2 - 401
5X-RAY DIFFRACTION5(chain 'E' and resid 2 through 401)E2 - 401
6X-RAY DIFFRACTION6(chain 'F' and resid 2 through 401)F2 - 401
7X-RAY DIFFRACTION7(chain 'G' and resid 2 through 401)G2 - 401
8X-RAY DIFFRACTION8(chain 'H' and resid 2 through 401)H2 - 401

+
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