[English] 日本語
Yorodumi
- PDB-6s81: Crystal structure of methionine adenosyltransferase from Pyrococc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s81
TitleCrystal structure of methionine adenosyltransferase from Pyrococcus furiosus
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, C-terminal domain / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, archaea / S-adenosylmethionine synthase / S-adenosylmethionine synthetase, domain 3 / S-adenosylmethionine synthetase (AdoMet synthetase) / GMP Synthetase; Chain A, domain 3 - #10 / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.784 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,10714
Polymers177,3554
Non-polymers75210
Water15,997888
1
A: S-adenosylmethionine synthase
C: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0898
Polymers88,6772
Non-polymers4116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-56 kcal/mol
Surface area30190 Å2
MethodPISA
2
B: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0186
Polymers88,6772
Non-polymers3414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-29 kcal/mol
Surface area30230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.108, 133.900, 213.100
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 16 or resid 18...
21(chain B and (resid 2 through 16 or resid 18...
31(chain C and (resid 2 through 16 or resid 18...
41(chain D and (resid 2 through 16 or resid 18...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 16 or resid 18...A2 - 16
121(chain A and (resid 2 through 16 or resid 18...A18 - 109
131(chain A and (resid 2 through 16 or resid 18...A111 - 119
141(chain A and (resid 2 through 16 or resid 18...A121 - 133
151(chain A and (resid 2 through 16 or resid 18...A135 - 136
161(chain A and (resid 2 through 16 or resid 18...A138 - 157
171(chain A and (resid 2 through 16 or resid 18...A159 - 186
181(chain A and (resid 2 through 16 or resid 18...A188 - 2232
191(chain A and (resid 2 through 16 or resid 18...A234232
1101(chain A and (resid 2 through 16 or resid 18...A234 - 248
1111(chain A and (resid 2 through 16 or resid 18...A250 - 274
1121(chain A and (resid 2 through 16 or resid 18...A276 - 289
1131(chain A and (resid 2 through 16 or resid 18...A291 - 319
1141(chain A and (resid 2 through 16 or resid 18...A321 - 327
1151(chain A and (resid 2 through 16 or resid 18...A329 - 3369
1161(chain A and (resid 2 through 16 or resid 18...A371369
1171(chain A and (resid 2 through 16 or resid 18...A371 - 380
1181(chain A and (resid 2 through 16 or resid 18...A382 - 401
211(chain B and (resid 2 through 16 or resid 18...B2 - 16
221(chain B and (resid 2 through 16 or resid 18...B18 - 109
231(chain B and (resid 2 through 16 or resid 18...B111 - 19
241(chain B and (resid 2 through 16 or resid 18...B2 - 401
251(chain B and (resid 2 through 16 or resid 18...B135 - 136
261(chain B and (resid 2 through 16 or resid 18...B138 - 157
271(chain B and (resid 2 through 16 or resid 18...B159 - 186
281(chain B and (resid 2 through 16 or resid 18...B188 - 2232
291(chain B and (resid 2 through 16 or resid 18...B234232
2101(chain B and (resid 2 through 16 or resid 18...B234 - 248
2111(chain B and (resid 2 through 16 or resid 18...B250 - 274
2121(chain B and (resid 2 through 16 or resid 18...B276 - 289
2131(chain B and (resid 2 through 16 or resid 18...B291 - 319
2141(chain B and (resid 2 through 16 or resid 18...B321 - 327
2151(chain B and (resid 2 through 16 or resid 18...B329 - 3369
2161(chain B and (resid 2 through 16 or resid 18...B371369
2171(chain B and (resid 2 through 16 or resid 18...B371 - 380
2181(chain B and (resid 2 through 16 or resid 18...B382 - 401
311(chain C and (resid 2 through 16 or resid 18...C2 - 16
321(chain C and (resid 2 through 16 or resid 18...C18 - 109
331(chain C and (resid 2 through 16 or resid 18...C111 - 119
341(chain C and (resid 2 through 16 or resid 18...C121 - 133
351(chain C and (resid 2 through 16 or resid 18...C135 - 136
361(chain C and (resid 2 through 16 or resid 18...C138 - 142
371(chain C and (resid 2 through 16 or resid 18...C154 - 157
381(chain C and (resid 2 through 16 or resid 18...C159 - 1212
391(chain C and (resid 2 through 16 or resid 18...C214212
3101(chain C and (resid 2 through 16 or resid 18...C214 - 232
3111(chain C and (resid 2 through 16 or resid 18...C234 - 248
3121(chain C and (resid 2 through 16 or resid 18...C250 - 274
3131(chain C and (resid 2 through 16 or resid 18...C276 - 289
3141(chain C and (resid 2 through 16 or resid 18...C291 - 319
3151(chain C and (resid 2 through 16 or resid 18...C321 - 3335
3161(chain C and (resid 2 through 16 or resid 18...C337335
3171(chain C and (resid 2 through 16 or resid 18...C337 - 369
3181(chain C and (resid 2 through 16 or resid 18...C371 - 380
3191(chain C and (resid 2 through 16 or resid 18...C382 - 401
411(chain D and (resid 2 through 16 or resid 18...D2 - 16
421(chain D and (resid 2 through 16 or resid 18...D18 - 109
431(chain D and (resid 2 through 16 or resid 18...D111 - 119
441(chain D and (resid 2 through 16 or resid 18...D121 - 133
451(chain D and (resid 2 through 16 or resid 18...D135 - 136
461(chain D and (resid 2 through 16 or resid 18...D138 - 142
471(chain D and (resid 2 through 16 or resid 18...D154 - 157
481(chain D and (resid 2 through 16 or resid 18...D159 - 1212
491(chain D and (resid 2 through 16 or resid 18...D214212
4101(chain D and (resid 2 through 16 or resid 18...D214 - 232
4111(chain D and (resid 2 through 16 or resid 18...D234 - 248
4121(chain D and (resid 2 through 16 or resid 18...D250 - 274
4131(chain D and (resid 2 through 16 or resid 18...D276 - 289
4141(chain D and (resid 2 through 16 or resid 18...D291 - 319
4151(chain D and (resid 2 through 16 or resid 18...D321 - 3335
4161(chain D and (resid 2 through 16 or resid 18...D337335
4171(chain D and (resid 2 through 16 or resid 18...D337 - 369
4181(chain D and (resid 2 through 16 or resid 18...D371 - 380
4191(chain D and (resid 2 through 16 or resid 18...D382 - 401

-
Components

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


Mass: 44338.660 Da / Num. of mol.: 4
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) / References: UniProt: Q8TZW1, methionine adenosyltransferase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 888 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M MES pH 5.5, 0.05 M Mn(HCOO)2, 30% v/v PEG MME 550

-
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: Jan 30, 2010 / 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: 1.78→133.9 Å / Num. obs: 166737 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 25.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.073 / Rrim(I) all: 0.267 / Net I/σ(I): 8.2 / Num. measured all: 2208219 / Scaling rejects: 28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.78-1.8812.35.085294645239460.4741.4885.3050.699.4
5.64-133.912.60.0557203257110.9990.0160.05730.499.9

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.1data scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1p7l, 1rg9, 3iml, 1qm4
Resolution: 1.784→106.55 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.16
RfactorNum. reflection% reflection
Rfree0.2311 8245 4.98 %
Rwork0.2095 --
obs0.2106 165455 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.47 Å2 / Biso mean: 35.1319 Å2 / Biso min: 16.92 Å2
Refinement stepCycle: final / Resolution: 1.784→106.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12260 0 32 888 13180
Biso mean--38.01 37.28 -
Num. residues----1578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512639
X-RAY DIFFRACTIONf_angle_d0.71717158
X-RAY DIFFRACTIONf_chiral_restr0.0531998
X-RAY DIFFRACTIONf_plane_restr0.0052233
X-RAY DIFFRACTIONf_dihedral_angle_d11.8427854
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8817X-RAY DIFFRACTION8.871TORSIONAL
12B8817X-RAY DIFFRACTION8.871TORSIONAL
13C8817X-RAY DIFFRACTION8.871TORSIONAL
14D8817X-RAY DIFFRACTION8.871TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.784-1.80430.43382460.4284479091
1.8043-1.82550.4522470.4243488694
1.8255-1.84780.37532580.3949522199
1.8478-1.87120.38882780.3737516199
1.8712-1.89580.33262420.3344523799
1.8958-1.92180.31572670.3167523699
1.9218-1.94920.36252590.30995207100
1.9492-1.97830.33332780.2936521499
1.9783-2.00920.32162900.2732518799
2.0092-2.04220.27222970.2663520699
2.0422-2.07740.25232800.2631515199
2.0774-2.11520.27123030.25635239100
2.1152-2.15580.28012540.22825199100
2.1558-2.19990.23352680.21415270100
2.1999-2.24770.20492950.19765196100
2.2477-2.30.24122790.19685241100
2.3-2.35750.23372800.18785255100
2.3575-2.42130.23312590.19145235100
2.4213-2.49250.23982860.18675256100
2.4925-2.5730.21242610.17895286100
2.573-2.66490.21312940.18245257100
2.6649-2.77160.22592740.19645267100
2.7716-2.89780.2352880.19215278100
2.8978-3.05060.21843050.19725282100
3.0506-3.24170.20852620.20065322100
3.2417-3.4920.22872770.19295306100
3.492-3.84350.19422630.17895379100
3.8435-4.39960.17352770.1645386100
4.3996-5.54310.18152820.16365441100
5.5431-106.550.21952960.2208561999
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)
10.0773-0.0408-0.34540.6006-0.03511.2375-0.0023-0.07180.0615-0.00610.0706-0.0734-0.05520.0932-0.08210.18130.00280.00350.2811-0.02170.2587-29.886113.6292-9.6368
21.17580.0168-0.02930.4131-0.39762.2997-0.0713-0.0564-0.1072-0.14160.14730.19840.20320.1539-0.09850.22330.0040.03570.2815-0.03640.2122-24.67674.9258-28.8623
32.5132-1.267-0.28556.5423-2.20743.16780.10330.01560.3417-0.30670.0361-0.2558-0.38020.1384-0.06970.3364-0.03710.06190.2645-0.03030.2867-21.385520.3666-31.0189
40.5118-0.0685-0.01910.5116-0.09071.7713-0.06350.16490.0801-0.1444-0.0031-0.132-0.24660.05690.06370.2535-0.0371-0.01360.27540.02090.261-27.545915.5099-21.9444
53.0659-0.9146-1.46941.41620.4442.51060.01230.05030.2118-0.0498-0.0256-0.28060.02120.4046-0.00250.21350.0493-0.00030.3670.00290.3123-18.01850.6365-5.7478
60.52510.3123-0.48820.3451-0.13132.372-0.0803-0.088-0.0868-0.03810.0157-0.11360.35880.28080.0690.25770.05930.01480.2823-0.00940.2621-24.34-4.5969-10.7756
71.4463-0.34660.4691.7527-0.45482.3657-0.1012-0.12940.1850.10170.1198-0.1286-0.37870.03430.02110.2670.0032-0.03230.2841-0.04340.2956-31.733622.50280.2501
80.2239-0.1524-0.19610.73040.16440.8078-0.01990.05480.07350.04490.07090.0419-0.0741-0.0282-0.07230.18620.00790.00190.23820.02370.2489-31.005713.16-71.6206
90.91750.08080.0920.12840.37491.9975-0.0451-0.0164-0.1170.1250.065-0.1280.1519-0.0537-0.02740.24030.03250.04540.23330.0180.2215-36.34024.7553-52.2891
102.32251.96980.31977.27962.71333.57990.1625-0.24020.14070.3926-0.13270.1009-0.2376-0.21320.02650.30090.06780.04260.25680.04430.2502-39.279520.2863-50.3698
110.50560.0746-0.14680.4972-0.00061.8183-0.05690.0614-0.00440.03370.03610.09310.1392-0.2050.02870.1933-0.00350.00680.22320.01690.2539-36.71440.3713-68.4392
121.68480.24650.26561.54440.40732.1057-0.07450.1540.2297-0.11280.05410.0685-0.3124-0.03340.01590.2515-0.0084-0.02520.24660.05240.3103-29.120221.8191-81.6492
130.2451-0.1584-0.36020.4809-0.22081.4648-0.0169-0.0386-0.0113-0.03150.02410.05490.1321-0.2674-0.02140.2368-0.0120.00530.33570.00930.2426-48.02722.3454-15.9993
141.4013-0.1852-0.26080.38580.22211.40230.01890.12480.087-0.1169-0.061-0.2531-0.0893-0.04130.00970.2682-0.00470.01850.28740.00410.2242-41.915810.9812-34.3326
152.1117-2.1901-0.59366.51490.27872.84220.0630.0823-0.154-0.7006-0.0201-0.09590.4460.05020.00670.3776-0.02770.01570.32080.03320.24-43.3358-4.7171-37.8702
161.06520.07040.21442.1578-0.24331.7174-0.12720.0285-0.2045-0.11590.18770.09250.1447-0.1766-0.04430.3033-0.05250.02430.292-0.00960.2201-42.35122.6354-37.679
171.3286-0.1917-0.31971.47440.2021.6004-0.07480.2224-0.3018-0.25650.1025-0.17260.56150.024-0.0130.452-0.01460.04890.3695-0.05880.3056-43.146-12.3925-16.1529
182.16480.24593.08081.89020.54977.41540.0430.2937-0.1047-0.00060.0920.27270.1778-0.702-0.14630.17830.03020.02450.49270.02260.3119-60.688614.9559-19.3477
190.6004-0.14990.0150.9178-0.8663.66710.0215-0.01250.19210.11230.11610.1675-0.6251-0.6589-0.12870.37190.1370.03560.39040.02570.332-57.289626.3552-19.3728
200.10950.2093-0.04010.7292-0.77691.5353-0.03210.01710.0182-0.08150.0514-0.01110.0932-0.1687-0.01780.23050.00470.01270.3008-0.00920.2488-46.45292.5694-13.9812
211.3101-0.0524-0.93071.202-0.33320.7797-0.05780.0773-0.0676-0.12150.04920.04280.1316-0.36310.03020.2193-0.04090.00580.3226-0.00740.2417-53.4234-6.9506-5.5111
220.23860.1513-0.32750.54540.03051.5378-0.01990.0244-0.03090.0708-0.0019-0.09010.12170.30520.0310.21470.04190.00160.3001-0.00180.2396-12.96241.8165-65.0952
231.48790.2012-0.480.3939-0.05521.5492-0.0641-0.0860.11530.0482-0.01050.2003-0.09940.16930.06080.25590.0264-0.00940.24930.00770.1912-19.005910.7155-46.8554
242.32492.5149-0.49127.2388-0.45332.68230.1231-0.2358-0.14520.798-0.17930.07860.32790.0250.0830.37680.06550.03160.3149-0.00290.2551-17.7145-4.9408-43.1024
250.4827-0.3313-0.14840.2281-0.06871.6325-0.1182-0.0832-0.12530.12080.04840.0490.29670.13470.07590.3090.0360.05050.29560.03980.262-18.3017-5.347-54.24
260.7501-0.0691-0.39340.96190.79443.4063-0.0803-0.06270.08150.04560.0642-0.1842-0.28920.67580.02520.2522-0.0793-0.03510.41240.02520.324-1.762721.4059-61.3007
270.5756-0.0239-0.07230.59840.03941.9394-0.0646-0.01220.11890.07980.0232-0.0476-0.18420.17420.03250.2382-0.0258-0.02210.24940.01690.2708-11.561520.9562-61.417
281.3048-0.019-0.35621.01690.21652.1051-0.0917-0.1243-0.10290.07490.0529-0.01860.2550.24360.03440.20460.05320.01650.2580.02260.2029-11.3559-6.3507-73.2223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 54 )A2 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 91 )A55 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 119 )A92 - 119
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 170 )A120 - 170
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 191 )A171 - 191
6X-RAY DIFFRACTION6chain 'A' and (resid 192 through 313 )A192 - 313
7X-RAY DIFFRACTION7chain 'A' and (resid 314 through 401 )A314 - 401
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 54 )B2 - 54
9X-RAY DIFFRACTION9chain 'B' and (resid 55 through 91 )B55 - 91
10X-RAY DIFFRACTION10chain 'B' and (resid 92 through 119 )B92 - 119
11X-RAY DIFFRACTION11chain 'B' and (resid 120 through 313 )B120 - 313
12X-RAY DIFFRACTION12chain 'B' and (resid 314 through 401 )B314 - 401
13X-RAY DIFFRACTION13chain 'C' and (resid 2 through 54 )C2 - 54
14X-RAY DIFFRACTION14chain 'C' and (resid 55 through 91 )C55 - 91
15X-RAY DIFFRACTION15chain 'C' and (resid 92 through 119 )C92 - 119
16X-RAY DIFFRACTION16chain 'C' and (resid 120 through 143 )C120 - 143
17X-RAY DIFFRACTION17chain 'C' and (resid 144 through 170 )C144 - 170
18X-RAY DIFFRACTION18chain 'C' and (resid 171 through 191 )C171 - 191
19X-RAY DIFFRACTION19chain 'C' and (resid 192 through 266 )C192 - 266
20X-RAY DIFFRACTION20chain 'C' and (resid 267 through 354 )C267 - 354
21X-RAY DIFFRACTION21chain 'C' and (resid 355 through 401 )C355 - 401
22X-RAY DIFFRACTION22chain 'D' and (resid 2 through 54 )D2 - 54
23X-RAY DIFFRACTION23chain 'D' and (resid 55 through 91 )D55 - 91
24X-RAY DIFFRACTION24chain 'D' and (resid 92 through 119 )D92 - 119
25X-RAY DIFFRACTION25chain 'D' and (resid 120 through 170 )D120 - 170
26X-RAY DIFFRACTION26chain 'D' and (resid 171 through 247 )D171 - 247
27X-RAY DIFFRACTION27chain 'D' and (resid 248 through 298 )D248 - 298
28X-RAY DIFFRACTION28chain 'D' and (resid 299 through 401 )D299 - 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://pdbjlvh1.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