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- PDB-2yav: ZN INHIBITED SULFUR OXYGENASE REDUCTASE -

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Basic information

Entry
Database: PDB / ID: 2yav
TitleZN INHIBITED SULFUR OXYGENASE REDUCTASE
ComponentsSULFUR OXYGENASE/REDUCTASE
KeywordsOXIDOREDUCTASE / MONONUCLEAR NON- HEME IRON / BIOGEOCHEMICAL SULFUR CYCLE / THERMOPHILIC / CYSTEINE PERSULPHIDE / ICOSATETRAMER
Function / homology
Function and homology information


sulfur oxygenase/reductase / sulfur oxygenase/reductase activity / metal ion binding / cytoplasm
Similarity search - Function
Sulphur oxygenase reductase / Sulphur oxygenase reductase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
ACETATE ION / : / Sulfur oxygenase/reductase
Similarity search - Component
Biological speciesACIDIANUS AMBIVALENS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 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)219,77330
Polymers218,4786
Non-polymers1,29524
Water24,4641358
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)879,090120
Polymers873,91224
Non-polymers5,17896
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 area149930 Å2
ΔGint-2403.7 kcal/mol
Surface area206800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.074, 162.074, 154.237
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 1:29 OR RESSEQ 31:307 )
211CHAIN B AND (RESSEQ 1:29 OR RESSEQ 31:307 )
311CHAIN C AND (RESSEQ 1:29 OR RESSEQ 31:307 )
411CHAIN D AND (RESSEQ 1:29 OR RESSEQ 31:307 )
511CHAIN E AND (RESSEQ 1:29 OR RESSEQ 31:307 )
611CHAIN F AND (RESSEQ 1:29 OR RESSEQ 31:307 )

NCS oper:
IDCodeMatrixVector
1given(-0.04024, -0.18335, 0.98222), (-0.18589, -0.96448, -0.18766), (0.98175, -0.19014, 0.00472)23.09034, 188.58577, 12.87873
2given(0.96561, -0.1804, 0.18725), (-0.18432, 0.03301, 0.98231), (-0.18339, -0.98304, -0.00138)2.70775, 17.51423, 172.02267
3given(0.0318, 0.18307, -0.98259), (0.1883, 0.96438, 0.18577), (0.9816, -0.19093, -0.0038)139.34917, -26.57843, 13.54691
4given(-0.18917, -0.96331, -0.19037), (0.03486, 0.18716, -0.98171), (0.98133, -0.19234, -0.00182)188.87772, 138.65227, 13.51067
5given(0.9285, -0.3713, 0.00445), (-0.37131, -0.92851, 0.00176), (0.00348, -0.00328, -0.99999)35.30276, 186.05386, 154.57269

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 36413.004 Da / Num. of mol.: 6 / 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

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Non-polymers , 5 types, 1382 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1358 / 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: 2.44 Å3/Da / Density % sol: 49.6 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: VAPOR DIFFUSION 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 DIFFUSION 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 ML 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 QUANTUM 4r / 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: 1.7→38.2 Å / Num. obs: 213677 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.8 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKLdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CB2
Resolution: 1.701→38.201 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 15.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1927 1149 0.6 %
Rwork0.1638 --
obs0.1623 191825 88.29 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.467 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-1.2695 Å20 Å20 Å2
2--1.2695 Å20 Å2
3----2.539 Å2
Refinement stepCycle: LAST / Resolution: 1.701→38.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14802 0 42 1358 16202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01715539
X-RAY DIFFRACTIONf_angle_d1.2220985
X-RAY DIFFRACTIONf_dihedral_angle_d14.5835803
X-RAY DIFFRACTIONf_chiral_restr0.0932219
X-RAY DIFFRACTIONf_plane_restr0.0052689
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2482X-RAY DIFFRACTIONPOSITIONAL
12B2482X-RAY DIFFRACTIONPOSITIONAL0.074
13C2472X-RAY DIFFRACTIONPOSITIONAL0.097
14D2462X-RAY DIFFRACTIONPOSITIONAL0.093
15E2468X-RAY DIFFRACTIONPOSITIONAL0.075
16F2472X-RAY DIFFRACTIONPOSITIONAL0.069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7012-1.77860.32321440.300920756X-RAY DIFFRACTION77
1.7786-1.87240.2661260.231121730X-RAY DIFFRACTION81
1.8724-1.98970.25811120.186823003X-RAY DIFFRACTION85
1.9897-2.14330.20391490.162224288X-RAY DIFFRACTION90
2.1433-2.35890.19881430.159224780X-RAY DIFFRACTION92
2.3589-2.70020.18111860.154825116X-RAY DIFFRACTION93
2.7002-3.40160.18971530.15225420X-RAY DIFFRACTION94
3.4016-38.21080.15611360.146925582X-RAY DIFFRACTION94
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)
10.09130.0139-0.16290.13720.01070.2446-0.00110.0464-0.0009-0.01160.0746-0.11860.01590.03610.00030.10310.0204-0.02970.1014-0.00290.110255.12778.12336.782
20.0196-0.01560.02930.0142-0.02130.01750.0598-0.08430.02990.0277-0.09420.20060.0374-0.0807-00.1358-0.0180.01350.1605-0.0090.1545.139768.708531.0777
30.2111-0.017-0.16010.01610.06390.2112-0.02160.0227-0.0206-0.02690.01650.00550.0065-0.0038-00.08940.007-0.01190.09040.00920.082652.32382.683826.2925
40.11810.06110.05280.0727-0.00540.0536-0.02160.02470.014-0.09560.0503-0.0554-0.0028-0.0079-00.12220.0127-0.0050.11650.01350.115655.824889.136324.8322
50.203-0.1025-0.16030.22930.06580.1182-0.0668-0.02480.00350.19030.07580.0354-0.0041-0.0165-0.00230.1210.0168-0.0340.10250.00410.081842.712196.12852.3088
60.02710.02630.02650.0252-0.00590.05670.06130.00330.0007-0.2256-0.02850.0334-0.0287-0.00190.00030.16750.02570.02730.13220.01840.128839.307108.188744.2337
70.1267-0.0652-0.16290.00930.01450.31330.01840.0110.01570.03130.00220.0169-0.0302-0.029800.05030.0083-0.01640.0580.0140.058131.63894.220448.6493
80.00050.0090.00840.05850.00590.0659-0.03480.01580.01440.04280.0340.06920.0039-0.004700.13050.005-0.00870.12520.00930.127628.712687.486350.6941
90.1430.14790.02870.16710.04230.0994-0.0156-0.0072-0.006-0.0335-0.0472-0.03680.04370.1674-00.1320.04080.02060.13260.01640.116964.2462125.630869.6995
100.0165-0.019-0.00860.02780.05670.0838-0.01780.08920.0507-0.07140.07260.0351-0.0981-0.17590.00090.098-0.019-0.00370.13470.02890.123757.3869132.580658.4313
110.27810.11180.01590.134-0.04370.0038-0.02350.01760.0391-0.03060.01760.003-0.02920.0138-00.10150.01410.00540.0870.00990.099262.6617136.501973.5557
120.123-0.01520.05720.0864-0.070.0663-0.0084-0.0184-0.00340.0035-0.0193-0.0049-0.10680.0547-00.11970.00610.01540.11580.0050.12264.9381137.666380.6912
130.2015-0.03990.17370.1019-0.00410.1355-0.08910.06720.0236-0.13810.1140.05210.02470.00430.00010.1274-0.01770.01070.1094-0.00740.107339.848281.1163102.124
140.0053-0.006-0.02170.10150.03210.02270.0709-0.0407-0.00480.1944-0.05990.06250.01830.0108-0.00040.1361-0.0251-0.02210.12820.03290.130532.085371.2781110.1782
150.2127-0.03560.17380.001-0.06540.37640.003-0.0109-0.017-0.00260.04020.04420.0045-0.05570.0110.0557-0.00260.00830.04990.00970.069130.393286.8638105.7186
160.02910.0372-0.02150.04660.00350.1295-0.06110.0001-0.0056-0.02970.07650.1131-0.0327-0.004600.1068-0.0022-0.0050.10820.01340.130630.092594.3609103.6993
170.17620.1222-0.00010.10430.04010.097-0.04970.012-0.04240.0044-0.00590.01180.1726-0.0375-0.00040.15160.03190.01230.10450.02080.10446.0235113.064284.8494
180.0071-0.0060.01520.01720.01050.02490.0715-0.0160.05610.02490.00960.0065-0.16880.0278-00.1291-0.01680.01480.1209-0.00710.12642.03121.985196.0733
190.19140.1734-0.05220.14730.0947-0.00650.0118-0.01120.0206-0.0149-0.01990.03380.0238-0.0395-00.11040.0186-0.00930.09650.01860.115836.4648118.566581.0103
200.05180.0201-0.01250.11220.10880.1105-0.02780.0253-0.0034-0.0247-0.00220.00520.0135-0.0883-00.11760.0107-0.01030.10930.02430.11334.4338116.926473.7316
210.08090.05310.12990.13530.01640.1884-0.00130.005-0.03860.04710.0949-0.14460.01420.05960.00030.1069-0.01280.02170.1142-0.0220.116958.015593.0833117.8315
220.04570.0914-0.04790.2001-0.07420.02090.06310.03820.09950.0154-0.05330.20420.01220.01520.00240.12540.0203-0.01660.1345-0.00760.136652.2829105.7876123.3009
230.2493-0.05730.16410.0541-0.07070.2795-0.0375-0.01330.01530.04740.0281-0.0014-0.0420.0064-00.0524-0.00030.00960.0345-0.0030.045353.760690.0558128.1696
240.049-0.04630.00750.0580.02520.06140.0034-0.0065-0.02070.07070.024-0.015-0.00220.0028-00.11320.00120.0010.10610.00420.104254.376482.6405129.8175
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:71)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 72:104)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 105:268)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 269:307)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1:71)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 72:104)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 105:268)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 269:307)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 1:71)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 72:104)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 105:268)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 269:307)
13X-RAY DIFFRACTION13(CHAIN D AND RESID 1:71)
14X-RAY DIFFRACTION14(CHAIN D AND RESID 72:104)
15X-RAY DIFFRACTION15(CHAIN D AND RESID 105:268)
16X-RAY DIFFRACTION16(CHAIN D AND RESID 269:307)
17X-RAY DIFFRACTION17(CHAIN E AND RESID 1:71)
18X-RAY DIFFRACTION18(CHAIN E AND RESID 72:104)
19X-RAY DIFFRACTION19(CHAIN E AND RESID 105:268)
20X-RAY DIFFRACTION20(CHAIN E AND RESID 269:307)
21X-RAY DIFFRACTION21(CHAIN F AND RESID 1:71)
22X-RAY DIFFRACTION22(CHAIN F AND RESID 72:104)
23X-RAY DIFFRACTION23(CHAIN F AND RESID 105:268)
24X-RAY DIFFRACTION24(CHAIN F AND RESID 269:307)

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  • 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

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