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- PDB-3rxy: Crystal structure of NIF3 superfamily protein from Sphaerobacter ... -

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Basic information

Entry
Database: PDB / ID: 3rxy
TitleCrystal structure of NIF3 superfamily protein from Sphaerobacter thermophilus
ComponentsNIF3 protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / NIF3 superfamily
Function / homologyDUF34/NIF3 superfamily / ACETATE ION / FORMIC ACID / Uncharacterized protein
Function and homology information
Biological speciesSphaerobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMichalska, K. / Tesar, C. / Clancy, S. / Otwinowski, Z. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of NIF3 superfamily protein from Sphaerobacter thermophilus
Authors: Michalska, K. / Tesar, C. / Clancy, S. / Otwinowski, Z. / Joachimiak, A.
History
DepositionMay 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: NIF3 protein
B: NIF3 protein
C: NIF3 protein
D: NIF3 protein
E: NIF3 protein
F: NIF3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,38528
Polymers181,4346
Non-polymers95222
Water12,448691
1
A: NIF3 protein
E: NIF3 protein
F: NIF3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,20414
Polymers90,7173
Non-polymers48811
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-80 kcal/mol
Surface area31300 Å2
MethodPISA
2
B: NIF3 protein
C: NIF3 protein
D: NIF3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,18114
Polymers90,7173
Non-polymers46411
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-87 kcal/mol
Surface area31200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.770, 96.483, 128.470
Angle α, β, γ (deg.)90.00, 115.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
NIF3 protein


Mass: 30238.973 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus (bacteria) / Strain: DSM 20745 / Gene: Sthe_0840 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: D1C210
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate, 3.5 M sodium formate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 13, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 139620 / Num. obs: 138727 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 27.02 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 13.13
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.16 / Num. unique all: 6951 / % possible all: 99.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
BUSTER2.8.0refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: different crystal form of the same protein solved by SAD

Resolution: 2→38.37 Å / Cor.coef. Fo:Fc: 0.9219 / Cor.coef. Fo:Fc free: 0.9099 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 1373 0.99 %thin resolution shells
Rwork0.2091 ---
all0.2093 138722 --
obs0.2093 138722 --
Displacement parametersBiso mean: 28.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.2197 Å20 Å22.6551 Å2
2--3.3683 Å20 Å2
3----3.1486 Å2
Refine analyzeLuzzati coordinate error obs: 0.257 Å
Refinement stepCycle: LAST / Resolution: 2→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12382 0 53 691 13126
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01412650HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1517166HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5901SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes295HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1897HARMONIC5
X-RAY DIFFRACTIONt_it12650HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion2.7
X-RAY DIFFRACTIONt_chiral_improper_torsion1680SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact15517SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2552 68 0.68 %
Rwork0.2054 9908 -
all0.2057 9976 -
obs-9976 -
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)
10.54910.00320.67071.2153-0.19231.1020.05810.2056-0.11730.0249-0.0346-0.2373-0.01180.1884-0.0235-0.08370.0139-0.031-0.0522-0.01690.066828.1627-53.760454.1627
21.34930.09990.01240.88090.42580.64990.0996-0.1196-0.18660.1355-0.0229-0.0190.1017-0.0191-0.0767-0.0338-0.0055-0.0471-0.08150.0470.075215.1084-58.211464.2234
33.1090.5208-0.34191.1951-1.1961-0.9843-0.0754-0.1926-0.05410.1362-0.0171-0.20820.03390.10830.0924-0.0121-0.0024-0.0965-0.09390.04240.012726.379-44.862374.7223
41.87780.6450.22171.3650.1140.99330.0357-0.30770.1930.3254-0.0728-0.0451-0.0567-0.09210.03720.01280.0011-0.036-0.0325-0.03220.015218.1467-36.571277.3026
50.6040.43790.22663.1004-0.48512.1891-0.0044-0.18530.00330.2686-0.12620.35150.0258-0.38540.1306-0.0765-0.03460.02920.0083-0.0068-0.01097.4395-44.233477.2114
61.1763-0.62352.16011.55280.4062.0810.05580.1377-0.00280.232-0.0758-0.2989-0.0430.21420.0199-0.046-0.0304-0.0527-0.08050.02130.084730.2361-43.57458.6889
71.18390.53591.06821.3480.15910.8233-0.06560.26530.0013-0.27830.01630.0139-0.11670.28020.04920.0836-0.0182-0.0659-0.03040.0055-0.1041-43.9161-39.4155-10.8892
81.13750.6045-0.36641.6732-0.3991.7758-0.04540.03080.1191-0.1796-0.04740.1095-0.2707-0.10860.09280.06810.0552-0.1138-0.0825-0.0402-0.0357-56.3172-35.45823.6256
90.93020.49810.63321.18340.18540.8104-0.09330.01090.1105-0.02180.00650.1051-0.0931-0.04980.08680.08750.0275-0.0917-0.1070.0122-0.0733-49.3547-34.48375.4826
100.09220.3946-0.02521.69920.01762.72780.06920.0224-0.0845-0.1437-0.06090.1801-0.0752-0.4064-0.00830.01220.0454-0.1222-0.0306-0.00760.0212-67.7568-50.2827-3.4569
110.65170.11640.53382.11280.35021.34220.0506-0.17050.00610.0383-0.04560.30040.0432-0.2124-0.00490.001-0.0197-0.053-0.0652-0.0044-0.0423-64.3746-53.03877.026
121.6970.6576-1.97332.47180.52790.7933-0.0119-0.12850.01890.14490.01970.0153-0.0242-0.0775-0.00780.03080.0296-0.01890.03270.0025-0.0737-61.7656-51.780716.9768
132.3731.19651.26531.646-0.39670.803-0.0020.251-0.0587-0.3511-0.02860.2815-0.02950.1170.03050.0910.0222-0.071-0.0735-0.0447-0.0425-48.9942-49.0473-10.6273
140.9851-0.16080.61741.3366-0.40211.00890.14760.1922-0.207-0.3431-0.0271-0.23440.24040.2895-0.12050.07540.0636-0.0699-0.078-0.0589-0.0142-28.061-65.54535.6427
150.48320.0988-0.44091.0712-0.05182.40510.0563-0.1004-0.074-0.224-0.01270.09390.28520.0898-0.04360.01210.0212-0.0933-0.12190.0067-0.0025-38.4766-64.390715.2421
160.7004-0.19950.54210.6663-0.38831.53260.0569-0.0151-0.1225-0.09190.0040.03450.1691-0.028-0.06090.01220.0137-0.0711-0.1195-0.01530.0141-38.0758-63.49719.1314
171.4334-0.45730.46771.784-0.7922.99890.0968-0.19370.05620.1250.0731-0.0868-0.10450.0365-0.1699-0.0009-0.0004-0.0848-0.0514-0.00080.0012-26.6929-57.245535.7962
180.90711.1452-0.74622.10561.8384-0.90710.0163-0.0388-0.07620.01270.060.02220.0492-0.025-0.07630.01810.0266-0.03-0.01330.0170.0248-37.0371-63.744931.4782
191.87770.3517-0.29192.315-0.15020.94290.0906-0.03640.1212-0.0044-0.05980.0999-0.0369-0.2805-0.0308-0.02820.0037-0.0549-0.00850.0264-0.0085-42.3432-60.193834.034
203.08340.8353-0.92562.12690.5591.21550.00690.03560.1420.0622-0.05780.1077-0.2111-0.05970.05090.01340.0384-0.058-0.04920.0383-0.0403-41.5969-52.178234.7128
21-0.57811.21651.07280.8805-0.87981.97940.1898-0.0141-0.1592-0.0309-0.0446-0.19770.06830.0943-0.14520.02330.0574-0.0732-0.0275-0.01760.0353-21.6831-63.069214.2828
220.9004-0.71970.26761.19380.11741.0966-0.14620.27870.0013-0.09850.0128-0.2513-0.21150.35370.13350.0071-0.0668-0.0457-0.01050.0488-0.0287-18.5391-32.585311.0363
233.0115-1.31871.24370.9706-0.17071.1499-0.1646-0.35170.11080.18990.1516-0.3064-0.1403-0.26770.0130.05610.0357-0.0708-0.0690.027-0.0777-30.4315-31.774828.701
240.2349-0.72770.68360.97380.02531.8588-0.05980.0247-0.09770.00150.04520.0028-0.2105-0.05760.01460.0037-0.01-0.0382-0.07840.0086-0.0161-28.6135-40.859922.8535
250.24430.7449-0.66910.00250.70762.3597-0.0690.07480.07930.00710.0658-0.1396-0.12220.11720.00330.1342-0.0201-0.1312-0.07270.0016-0.0436-31.7665-16.433222.725
261.9638-0.2428-0.80282.4969-0.07612.6916-0.09680.00530.14040.18650.12520.0922-0.3875-0.2755-0.02840.11040.0765-0.1194-0.08730.0344-0.0867-45.149-14.758218.6028
270.4907-0.4509-0.16950.73110.25352.7687-0.0889-0.214-0.04760.17890.08250.1393-0.2079-0.35150.00640.08020.085-0.0432-0.02960.0312-0.1009-45.3146-25.682827.9206
281.8803-1.00230.04381.33850.32540.4519-0.06130.09430.2130.03090.0095-0.1586-0.26910.22240.05190.1028-0.0613-0.103-0.06370.0572-0.0582-25.2289-24.11978.7634
291.0944-0.2280.12971.4443-0.51340.25340.12790.3495-0.2312-0.256-0.048-0.0271-0.00040.1129-0.0799-0.01340.0353-0.0282-0.0017-0.0569-0.00444.6228-59.686231.9289
301.17020.16250.16710.83620.4846-0.05270.02270.019-0.0975-0.11740.08990.1431-0.0473-0.1285-0.1126-0.05340.0261-0.0578-0.0379-0.00630.0578-13.4199-62.010545.8749
311.54540.619-0.35281.1656-0.81640.54860.02450.1146-0.0547-0.06140.01490.0115-0.0477-0.0154-0.0394-0.01350.0106-0.0472-0.045-0.0139-0.0046-4.8193-51.731442.2381
321.4266-0.5454-0.11460.01560.80870.2830.1250.1319-0.273-0.090.00480.10170.00290.1339-0.1298-0.0640.0067-0.0762-0.0821-0.02960.1494-4.8025-76.266745.5721
332.8672-0.4949-0.49632.42440.81822.21220.0451-0.1778-0.50560.22070.0720.12480.12830.0144-0.1171-0.07040.0285-0.0899-0.10950.05540.09280.9122-78.180458.2591
341.9468-0.20360.14481.5233-0.26421.233-0.0694-0.3584-0.2290.28240.10460.0432-0.1174-0.1151-0.0352-0.07010.0309-0.0195-0.0370.03710.0337-8.3626-67.372759.7052
350.52620.09820.26861.6534-1.32030.22250.13610.2653-0.3294-0.27430.00930.07280.04210.1713-0.1454-0.02670.046-0.0682-0.0534-0.0680.09378.0796-68.478137.3793
361.4642-3.71850.91751.84181.07340.59010.00220.12970.0538-0.1529-0.1857-0.0787-0.16750.20440.18350.0229-0.0496-0.0493-0.10.0790.06419.1887-19.44538.3154
372.1187-0.51610.32110.486-0.16392.7062-0.20750.26180.3417-0.2881-0.0339-0.2076-0.230.23630.2414-0.0406-0.0578-0.0465-0.09620.05690.111611.3564-22.901144.4601
381.7386-0.46351.26911.40751.79580.8110.10240.1768-0.0861-0.1828-0.0037-0.2314-0.04680.2011-0.0987-0.0328-0.00150.0054-0.03330.01570.045913.2971-36.83936.9369
390.89230.5578-0.63740.5466-0.44530.0151-0.0035-0.07940.24360.0727-0.0098-0.1533-0.0480.01860.0133-0.01590.0008-0.0643-0.0445-0.01390.04080.4156-27.11456.0629
401.7146-0.0051-0.40980.07130.15190.89920.0459-0.15870.22120.0497-0.0146-0.1392-0.00720.0667-0.0312-0.0073-0.0096-0.0348-0.07690.01350.04937.2559-32.540256.2144
411.87721.123-0.13570.6057-0.05861.24490.05950.13840.22190.02680.0088-0.0071-0.1812-0.0644-0.06820.02320.029-0.032-0.08670.03240.0205-14.7576-23.388444.6828
423.1749-0.8268-0.43150.9257-0.54620.7856-0.05510.1567-0.0759-0.06250.0150.0590.0094-0.10560.04010.00410.0024-0.0591-0.0192-0.022-0.0005-18.7846-35.382842.8095
43-0.67951.90710.65221.1582-0.33480.76750.00970.0149-0.01480.0512-0.0378-0.0522-0.0618-0.01140.02810.0065-0.0033-0.0187-0.0163-0.01620.0215-13.1805-28.999552.619
442.105-1.1811-0.78161.23330.09011.6470.0437-0.19760.01340.0677-0.0794-0.02790.0627-0.09570.0357-0.0352-0.0049-0.02460.0094-0.0059-0.0032-14.9595-32.622458.1332
451.0681-0.0077-0.42942.45550.01271.1620.0283-0.048-0.21910.1456-0.1330.00530.0232-0.07890.10470.00230.0013-0.0371-0.04110.0198-0.014-15.8847-40.64857.4438
461.55770.1127-0.31280.4583-0.115-0.1851-0.02620.14540.2208-0.277-0.0320.0837-0.0734-0.11630.05820.03140.0116-0.0357-0.0280.03270.03061.6731-29.204335.1678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|0 - A|73}A0 - 73
2X-RAY DIFFRACTION2{A|74 - A|133}A74 - 133
3X-RAY DIFFRACTION3{A|134 - A|152}A134 - 152
4X-RAY DIFFRACTION4{A|153 - A|205}A153 - 205
5X-RAY DIFFRACTION5{A|206 - A|246}A206 - 246
6X-RAY DIFFRACTION6{A|247 - A|275}A247 - 275
7X-RAY DIFFRACTION7{B|0 - B|62}B0 - 62
8X-RAY DIFFRACTION8{B|63 - B|87}B63 - 87
9X-RAY DIFFRACTION9{B|88 - B|133}B88 - 133
10X-RAY DIFFRACTION10{B|134 - B|158}B134 - 158
11X-RAY DIFFRACTION11{B|159 - B|227}B159 - 227
12X-RAY DIFFRACTION12{B|228 - B|246}B228 - 246
13X-RAY DIFFRACTION13{B|247 - B|275}B247 - 275
14X-RAY DIFFRACTION14{C|1 - C|54}C1 - 54
15X-RAY DIFFRACTION15{C|55 - C|88}C55 - 88
16X-RAY DIFFRACTION16{C|89 - C|158}C89 - 158
17X-RAY DIFFRACTION17{C|159 - C|190}C159 - 190
18X-RAY DIFFRACTION18{C|191 - C|205}C191 - 205
19X-RAY DIFFRACTION19{C|206 - C|227}C206 - 227
20X-RAY DIFFRACTION20{C|228 - C|246}C228 - 246
21X-RAY DIFFRACTION21{C|247 - C|275}C247 - 275
22X-RAY DIFFRACTION22{D|1 - D|62}D1 - 62
23X-RAY DIFFRACTION23{D|63 - D|91}D63 - 91
24X-RAY DIFFRACTION24{D|92 - D|133}D92 - 133
25X-RAY DIFFRACTION25{D|134 - D|153}D134 - 153
26X-RAY DIFFRACTION26{D|154 - D|190}D154 - 190
27X-RAY DIFFRACTION27{D|191 - D|246}D191 - 246
28X-RAY DIFFRACTION28{D|247 - D|275}D247 - 275
29X-RAY DIFFRACTION29{E|1 - E|67}E1 - 67
30X-RAY DIFFRACTION30{E|68 - E|91}E68 - 91
31X-RAY DIFFRACTION31{E|92 - E|133}E92 - 133
32X-RAY DIFFRACTION32{E|134 - E|153}E134 - 153
33X-RAY DIFFRACTION33{E|154 - E|190}E154 - 190
34X-RAY DIFFRACTION34{E|191 - E|246}E191 - 246
35X-RAY DIFFRACTION35{E|247 - E|275}E247 - 275
36X-RAY DIFFRACTION36{F|1 - F|17}F1 - 17
37X-RAY DIFFRACTION37{F|18 - F|36}F18 - 36
38X-RAY DIFFRACTION38{F|37 - F|62}F37 - 62
39X-RAY DIFFRACTION39{F|63 - F|88}F63 - 88
40X-RAY DIFFRACTION40{F|89 - F|133}F89 - 133
41X-RAY DIFFRACTION41{F|134 - F|158}F134 - 158
42X-RAY DIFFRACTION42{F|159 - F|190}F159 - 190
43X-RAY DIFFRACTION43{F|191 - F|205}F191 - 205
44X-RAY DIFFRACTION44{F|206 - F|227}F206 - 227
45X-RAY DIFFRACTION45{F|228 - F|246}F228 - 246
46X-RAY DIFFRACTION46{F|247 - F|275}F247 - 275

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