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- PDB-2yax: IODOACETAMIDE INHIBITED SULFUR OXYGENASE REDUCTASE -

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Basic information

Entry
Database: PDB / ID: 2yax
TitleIODOACETAMIDE INHIBITED SULFUR OXYGENASE REDUCTASE
Components(SULFUR OXYGENASE/REDUCTASE) x 2
KeywordsOXIDOREDUCTASE / MONONUCLEAR NON-HEME IRON / BIOGEOCHEMICAL SULFUR CYCLE / THERMOPHILIC / CYSTEINE PERSULPHIDE / ICOSATETRAMER
Function / homologysulfur oxygenase/reductase / sulfur oxygenase/reductase activity / Sulphur oxygenase reductase / Sulphur oxygenase reductase / Dimeric alpha-beta barrel / metal ion binding / cytoplasm / : / Sulfur oxygenase/reductase
Function and homology information
Biological speciesACIDIANUS AMBIVALENS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVeith, A. / Urich, T. / Seyfarth, K. / Protze, J. / Frazao, C. / Kletzin, A.
Citation
Journal: Front.Microbiol. / Year: 2011
Title: Substrate Pathways and Mechanisms of Inhibition in the Sulfur Oxygenase Reductase of Acidianus Ambivalens.
Authors: Veith, A. / Urich, T. / Seyfarth, K. / Protze, J. / Frazao, C. / Kletzin, A.
#1: Journal: Science / Year: 2006
Title: X-Ray Structure of a Self-Compartmentalizing Sulfur Cycle Metalloenzyme.
Authors: Urich, T. / Gomes, C.M. / Kletzin, A. / Frazao, C.
History
DepositionFeb 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SULFUR OXYGENASE/REDUCTASE
B: SULFUR OXYGENASE/REDUCTASE
C: SULFUR OXYGENASE/REDUCTASE
D: SULFUR OXYGENASE/REDUCTASE
E: SULFUR OXYGENASE/REDUCTASE
F: SULFUR OXYGENASE/REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,98412
Polymers218,6496
Non-polymers3356
Water8,593477
1
A: SULFUR OXYGENASE/REDUCTASE
B: SULFUR OXYGENASE/REDUCTASE
C: SULFUR OXYGENASE/REDUCTASE
D: SULFUR OXYGENASE/REDUCTASE
E: SULFUR OXYGENASE/REDUCTASE
F: SULFUR OXYGENASE/REDUCTASE
hetero molecules

A: SULFUR OXYGENASE/REDUCTASE
B: SULFUR OXYGENASE/REDUCTASE
C: SULFUR OXYGENASE/REDUCTASE
D: SULFUR OXYGENASE/REDUCTASE
E: SULFUR OXYGENASE/REDUCTASE
F: SULFUR OXYGENASE/REDUCTASE
hetero molecules

A: SULFUR OXYGENASE/REDUCTASE
B: SULFUR OXYGENASE/REDUCTASE
C: SULFUR OXYGENASE/REDUCTASE
D: SULFUR OXYGENASE/REDUCTASE
E: SULFUR OXYGENASE/REDUCTASE
F: SULFUR OXYGENASE/REDUCTASE
hetero molecules

A: SULFUR OXYGENASE/REDUCTASE
B: SULFUR OXYGENASE/REDUCTASE
C: SULFUR OXYGENASE/REDUCTASE
D: SULFUR OXYGENASE/REDUCTASE
E: SULFUR OXYGENASE/REDUCTASE
F: SULFUR OXYGENASE/REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)875,93748
Polymers874,59724
Non-polymers1,34024
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area137200 Å2
ΔGint-1135 kcal/mol
Surface area210170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.897, 161.897, 154.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 2:30 OR RESSEQ 32:308)
211CHAIN B AND (RESSEQ 2:30 OR RESSEQ 32:308)
311CHAIN C AND (RESSEQ 2:30 OR RESSEQ 32:308)
411CHAIN D AND (RESSEQ 2:30 OR RESSEQ 32:308)
511CHAIN E AND (RESSEQ 2:30 OR RESSEQ 32:308)
611CHAIN F AND (RESSEQ 2:30 OR RESSEQ 32:308)

NCS oper:
IDCodeMatrixVector
1given(-0.03915, -0.181, 0.9827), (-0.18217, -0.96568, -0.18513), (0.98249, -0.18627, 0.00483)22.69089, 188.06915, 12.55392
2given(0.96637, -0.17994, 0.1837), (-0.1811, 0.03093, 0.98298), (-0.18256, -0.98319, -0.0027)2.95924, 17.35212, 171.91058
3given(0.03316, 0.18051, -0.98301), (0.1863, 0.9652, 0.18353), (0.98193, -0.18922, -0.00162)139.50494, -26.30194, 13.19506
4given(-0.18624, -0.96422, -0.18865), (0.03256, 0.18584, -0.98204), (0.98196, -0.18904, -0.00321)188.4415, 138.79659, 13.33485
5given(0.93026, -0.36685, 0.00616), (-0.36686, -0.93027, 0.00081), (0.00543, -0.00301, -0.99998)34.56972, 185.75613, 154.45821

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Components

#1: Protein SULFUR OXYGENASE/REDUCTASE / SULFUR OXYGENASE REDUCTASE / SOR


Mass: 36413.004 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACIDIANUS AMBIVALENS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P29082, sulfur oxygenase/reductase
#2: Protein SULFUR OXYGENASE/REDUCTASE / SULFUR OXYGENASE REDUCTASE / SOR


Mass: 36470.055 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACIDIANUS AMBIVALENS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P29082, sulfur oxygenase/reductase
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.2 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: VAPOR DIFUSION OF SITTING DROPS OF 1 MICRO LITER OF 13 MG/ML SOR IN 50 MM TRIS/HCL MIXED WITH 1 MICRO LITER OF WELL SOLUTION 0.1 M SODIUM ACETATE WITH 8% MPD AND 50 MM SODIUM CHLORIDE, ...Details: VAPOR DIFUSION OF SITTING DROPS OF 1 MICRO LITER OF 13 MG/ML SOR IN 50 MM TRIS/HCL MIXED WITH 1 MICRO LITER OF WELL SOLUTION 0.1 M SODIUM ACETATE WITH 8% MPD AND 50 MM SODIUM CHLORIDE, AGAINST 500 MICRO-L OF WELL SOLUTION, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→38.05 Å / Num. obs: 172862 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 30.72 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.7
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CB2
Resolution: 1.8→38.053 Å / SU ML: 0.19 / σ(F): 1.39 / Phase error: 15.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 8667 5 %
Rwork0.1689 --
obs0.1736 172845 94.39 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14814 0 6 477 15297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01315532
X-RAY DIFFRACTIONf_angle_d1.28421021
X-RAY DIFFRACTIONf_dihedral_angle_d15.2125833
X-RAY DIFFRACTIONf_chiral_restr0.0882214
X-RAY DIFFRACTIONf_plane_restr0.0062691
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2458X-RAY DIFFRACTIONPOSITIONAL
12B2458X-RAY DIFFRACTIONPOSITIONAL0.124
13C2468X-RAY DIFFRACTIONPOSITIONAL0.098
14D2460X-RAY DIFFRACTIONPOSITIONAL0.093
15E2470X-RAY DIFFRACTIONPOSITIONAL0.076
16F2474X-RAY DIFFRACTIONPOSITIONAL0.108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.31471840.29183819X-RAY DIFFRACTION65
1.8205-1.84190.30852060.28074069X-RAY DIFFRACTION70
1.8419-1.86440.282420.24564327X-RAY DIFFRACTION75
1.8644-1.8880.27292750.23024476X-RAY DIFFRACTION79
1.888-1.91280.22562520.22954741X-RAY DIFFRACTION82
1.9128-1.9390.26082780.21784910X-RAY DIFFRACTION85
1.939-1.96670.23462860.20685129X-RAY DIFFRACTION89
1.9667-1.99610.22942680.19955388X-RAY DIFFRACTION93
1.9961-2.02730.2273060.17735576X-RAY DIFFRACTION96
2.0273-2.06050.20463020.17585688X-RAY DIFFRACTION98
2.0605-2.0960.18552920.16885737X-RAY DIFFRACTION100
2.096-2.13410.18143240.16675786X-RAY DIFFRACTION100
2.1341-2.17520.19622920.17095780X-RAY DIFFRACTION100
2.1752-2.21960.19632950.17455799X-RAY DIFFRACTION100
2.2196-2.26780.21693120.17855808X-RAY DIFFRACTION100
2.2678-2.32060.20053030.16955770X-RAY DIFFRACTION100
2.3206-2.37860.19812950.17125850X-RAY DIFFRACTION100
2.3786-2.44290.19832920.17855738X-RAY DIFFRACTION100
2.4429-2.51480.20192900.18055837X-RAY DIFFRACTION100
2.5148-2.59590.22682800.18265828X-RAY DIFFRACTION100
2.5959-2.68870.21683180.18385771X-RAY DIFFRACTION100
2.6887-2.79630.20043340.18445789X-RAY DIFFRACTION100
2.7963-2.92350.19812860.17775782X-RAY DIFFRACTION100
2.9235-3.07760.1893310.18585800X-RAY DIFFRACTION100
3.0776-3.27030.18352930.1825814X-RAY DIFFRACTION100
3.2703-3.52260.18333060.17875843X-RAY DIFFRACTION100
3.5226-3.87680.17812850.16955814X-RAY DIFFRACTION100
3.8768-4.43710.15133190.14495788X-RAY DIFFRACTION100
4.4371-5.58740.13533050.13795875X-RAY DIFFRACTION100
5.5874-38.06110.1853160.18065844X-RAY DIFFRACTION99
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)
10.3384-0.079-0.4560.4529-0.03670.66150.00680.0189-0.060.05030.0947-0.14320.05720.01610.00010.18010.0264-0.0380.16330.00660.196455.080277.993536.776
20.16730.00840.1390.0706-0.0080.090.0072-0.0608-0.0203-0.0611-0.06360.2370.0813-0.067100.2593-0.01610.02020.2988-0.00570.291445.049368.457231.4774
30.4903-0.0309-0.16910.09820.13970.3631-0.01830.0379-0.021-0.04160.0161-0.0054-0.01030.0044-00.20610.0123-0.02060.19860.01620.18452.228682.541426.3157
40.36450.01320.00580.41090.35220.2951-0.0080.05870.0469-0.13560.0313-0.03450.0046-0.063800.24550.01660.00780.2380.02550.214755.734689.033524.8268
50.5735-0.1393-0.41060.26840.18420.3335-0.0823-0.0850.02830.22690.09950.0254-0.0151-0.0521-00.26260.0105-0.03410.22530.0050.230542.576195.902552.3325
60.0640.09790.05680.14890.01840.12020.02490.00570.0301-0.211-0.04270.0016-0.07970.0261-00.32990.02460.03450.2930.01860.295539.2439107.942944.2503
70.2228-0.0385-0.24530.0687-0.02510.53950.02110.00580.01620.02840.01110.0454-0.0293-0.055600.23130.0176-0.0090.24890.01660.254331.551393.983448.6282
80.3364-0.4337-0.05770.5360.01480.3045-0.0250.04410.02450.08560.01630.09480.0086-0.0197-00.22780.00120.01130.26660.01650.254228.609487.213950.6844
90.47120.4527-0.12710.62680.10230.3017-0.03320.0053-0.0231-0.1092-0.0269-0.03910.08090.1808-00.26780.04480.03650.26060.01040.244364.0657125.452769.7757
100.0511-0.0849-0.10140.11310.17120.21240.00760.17140.1026-0.15880.09090.0368-0.1789-0.2387-0.00010.2796-0.0261-0.0020.34320.04240.297757.0895131.972558.3795
110.53050.1390.09540.1716-0.11120.0753-0.0190.0170.0559-0.02870.0257-0.0121-0.06330.0081-00.24380.01780.02380.20170.00790.219262.4243136.340273.5729
120.5629-0.03570.11730.434-0.38360.34350.0214-0.06180.019-0.0368-0.00730.0228-0.18460.0715-00.2383-0.00290.03580.222-0.00370.256464.7274137.528480.7344
130.43030.04020.29530.39310.17410.4169-0.09520.1007-0.0196-0.12020.1530.05850.0084-0.0013-00.2726-0.01270.00180.23820.00320.257939.798480.9982102.0922
140.04220.0021-0.06880.14060.06020.10470.10030.0076-0.02920.1599-0.11160.0865-0.00980.0068-0.00010.2795-0.0258-0.01950.2850.04390.298532.393170.942110.1752
150.18270.01050.18310.0349-0.07190.41990.0082-0.0141-0.018-0.00150.0480.06350.0141-0.065200.2289-0.00110.01350.24250.01470.269830.343986.6778105.7067
160.3270.3009-0.01140.270.01010.3364-0.071-0.0044-0.0148-0.04180.09330.1747-0.02130.0082-00.21730.0072-0.0070.22090.01710.264930.00994.212103.6731
170.6420.3341-0.02610.2114-0.08840.2251-0.0827-0.0289-0.09450.03270.0044-0.00790.2073-0.0255-00.29370.03610.020.24320.03520.25245.9025112.863784.7354
180.0771-0.0430.05630.03680.00510.20240.091-0.02380.0951-0.00430.04210.0438-0.2770.0206-00.2835-0.01070.03350.2498-0.00780.278642.2615121.757896.1362
190.34810.268-0.05760.38760.14760.15480.01160.00430.025-0.0127-0.01710.0433-0.0065-0.0657-00.21740.0290.0030.22130.03380.225836.3281118.386880.9898
200.32390.1448-0.31250.30320.09460.4739-0.02060.04920.0269-0.05270.00340.01750.0366-0.1589-00.24430.0213-0.00360.26030.03670.246434.2509116.745273.68
210.29230.18330.32730.4387-0.14260.6739-0.01190.0242-0.01570.03250.1279-0.1761-0.00930.09470.00010.1624-0.01580.02280.171-0.00910.204957.917992.9272117.8586
220.1543-0.0468-0.09680.2177-0.01710.04870.019-0.00270.16310.0287-0.05250.2814-0.0825-0.03580.00010.26880.0233-0.03370.2641-0.01060.285252.1322105.6877122.8378
230.4949-0.11950.19570.1654-0.05570.2643-0.0311-0.02830.0050.06240.02870.0047-0.02460.0132-00.232-0.00430.01570.2018-0.00290.193953.6289.8979128.1605
240.2826-0.02550.12910.27090.20870.23050.0138-0.0118-0.08270.170.0005-0.0640.010.028400.24670.0011-0.0050.21780.00890.217654.253582.4516129.8422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:72)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 73:105)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 106:269)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 270:308)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 2:72)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 73:105)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 106:269)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 270:308)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 2:72)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 73:105)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 106:269)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 270:308)
13X-RAY DIFFRACTION13(CHAIN D AND RESID 2:72)
14X-RAY DIFFRACTION14(CHAIN D AND RESID 73:105)
15X-RAY DIFFRACTION15(CHAIN D AND RESID 106:269)
16X-RAY DIFFRACTION16(CHAIN D AND RESID 270:308)
17X-RAY DIFFRACTION17(CHAIN E AND RESID 2:72)
18X-RAY DIFFRACTION18(CHAIN E AND RESID 73:105)
19X-RAY DIFFRACTION19(CHAIN E AND RESID 106:269)
20X-RAY DIFFRACTION20(CHAIN E AND RESID 270:308)
21X-RAY DIFFRACTION21(CHAIN F AND RESID 2:72)
22X-RAY DIFFRACTION22(CHAIN F AND RESID 73:105)
23X-RAY DIFFRACTION23(CHAIN F AND RESID 106:269)
24X-RAY DIFFRACTION24(CHAIN F AND RESID 270:308)

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