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- PDB-2w7n: Crystal Structure of KorA Bound to Operator DNA: Insight into Rep... -

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Basic information

Entry
Database: PDB / ID: 2w7n
TitleCrystal Structure of KorA Bound to Operator DNA: Insight into Repressor Cooperation in RP4 Gene Regulation
Components
  • 5'-D(*AP*AP*TP*GP*TP*TP*TP*AP*GP*CP *TP*AP*AP*AP*CP*AP*AP*G)-3'
  • 5'-D(*CP*BRUP*BRUP*GP*TP*TP*TP*AP*GP*CP*TP*AP *AP*AP*CP*AP*BRUP*T)-3'
  • TRFB TRANSCRIPTIONAL REPRESSOR PROTEIN
KeywordsTRANSCRIPTION/DNA / INCP / PLASMID / REPRESSOR / DNA-BINDING / PROTEIN-DNA COMPLEX / TRANSCRIPTION FACTOR / HELIX-TURN-HELIX MOTIF / TRANSCRIPTION REGULATION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


Arc Repressor Mutant, subunit A - #2690 / TrfB transcriptional repressor protein / TrfB plasmid transcriptional repressor / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / TrfB transcriptional repressor protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsKoenig, B. / Mueller, J.J. / Lanka, E. / Heinemann, U.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Crystal Structure of Kora Bound to Operator DNA: Insight Into Repressor Cooperation in Rp4 Gene Regulation
Authors: Koenig, B. / Mueller, J.J. / Lanka, E. / Heinemann, U.
History
DepositionDec 23, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4May 22, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRFB TRANSCRIPTIONAL REPRESSOR PROTEIN
B: TRFB TRANSCRIPTIONAL REPRESSOR PROTEIN
E: 5'-D(*AP*AP*TP*GP*TP*TP*TP*AP*GP*CP *TP*AP*AP*AP*CP*AP*AP*G)-3'
F: 5'-D(*CP*BRUP*BRUP*GP*TP*TP*TP*AP*GP*CP*TP*AP *AP*AP*CP*AP*BRUP*T)-3'
G: 5'-D(*AP*AP*TP*GP*TP*TP*TP*AP*GP*CP *TP*AP*AP*AP*CP*AP*AP*G)-3'
H: 5'-D(*CP*BRUP*BRUP*GP*TP*TP*TP*AP*GP*CP*TP*AP *AP*AP*CP*AP*BRUP*T)-3'


Theoretical massNumber of molelcules
Total (without water)45,0936
Polymers45,0936
Non-polymers00
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-25.6 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.830, 115.450, 49.880
Angle α, β, γ (deg.)90.00, 114.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A3 - 95
2116B3 - 95

NCS oper: (Code: given
Matrix: (-0.2408, 0.1716, 0.9553), (0.179, -0.9595, 0.2175), (0.9539, 0.2234, 0.2004)
Vector: -76.88, 65.43, 48.02)

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Components

#1: Protein TRFB TRANSCRIPTIONAL REPRESSOR PROTEIN / TRANSCRIPTIONAL REPRESSOR PROTEIN KORA / REGULATORY PROTEIN KORA


Mass: 11323.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PMS51-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03052
#2: DNA chain 5'-D(*AP*AP*TP*GP*TP*TP*TP*AP*GP*CP *TP*AP*AP*AP*CP*AP*AP*G)-3' / KORA OPERATOR


Mass: 5547.642 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
#3: DNA chain 5'-D(*CP*BRUP*BRUP*GP*TP*TP*TP*AP*GP*CP*TP*AP *AP*AP*CP*AP*BRUP*T)-3' / KORA OPERATOR


Mass: 5675.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 3.6 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.5M (NH4)2SO4, 0.1M C6H5NA3O7 2H2O (PH 5.6), 1.0M LI2SO4 H2O, VAPOR DIFFUSION, HANGING DROP, 291 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91991
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 27, 2006 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91991 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 31085 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 42.5
Reflection shellResolution: 1.96→2.08 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 17.4 / % possible all: 70.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
XDSphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.85→57.74 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.935 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1753 5.1 %RANDOM
Rwork0.17 ---
obs0.172 32666 87.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.79 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å2-0.18 Å2
2--2.52 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.85→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1479 1464 0 317 3260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223163
X-RAY DIFFRACTIONr_bond_other_d0.0010.021704
X-RAY DIFFRACTIONr_angle_refined_deg1.5222.5254543
X-RAY DIFFRACTIONr_angle_other_deg0.9053.0054138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6695187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70524.475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33615271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6361512
X-RAY DIFFRACTIONr_chiral_restr0.1360.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02421
X-RAY DIFFRACTIONr_nbd_refined0.1990.2355
X-RAY DIFFRACTIONr_nbd_other0.1730.21114
X-RAY DIFFRACTIONr_nbtor_refined0.210.21227
X-RAY DIFFRACTIONr_nbtor_other0.0810.2754
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.23221233
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57731504
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.45153102
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.84163039
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1218 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional1.085
2Bloose positional1.085
1Aloose thermal1.1210
2Bloose thermal1.1210
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.208 69
Rwork0.174 1272
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)
113.0972-0.01320.802913.3036-0.55088.4329-0.3286-0.33660.9290.33810.30380.3073-0.91630.27140.0248-0.0782-0.0422-0.02390.03980.0093-0.03670.208950.715940.5742
215.83287.4378-3.057115.0959-4.30538.7186-0.2283-0.0669-0.86320.11190.1557-0.65790.35790.60470.0727-0.10070.05180.0185-0.0111-0.0066-0.12820.306738.006241.0913
38.58740.46154.51623.007-4.80934.6889-0.12440.677-0.4203-1.40510.0265-0.4630.67550.7210.0979-0.0420.01950.0256-0.062-0.0155-0.1521-8.321538.625734.6952
411.491-0.76211.42893.4702-2.09921.3526-0.02120.76620.4266-0.5275-0.0501-0.2212-0.26450.42390.0713-0.0806-0.0301-0.0089-0.05930.0255-0.1421-7.186949.758734.8152
53.0789-0.80621.43932.0972-0.66535.8625-0.03120.13260.1429-0.0891-0.00040.1585-0.2397-0.11340.0316-0.13970.0019-0.0358-0.17470-0.1419-16.835546.901737.0258
626.679-3.897611.74311.43211.182914.9075-0.3343-0.620.42320.0051-0.0266-0.0587-0.37360.28240.3608-0.1192-0.0026-0.0278-0.08880.0161-0.1663-5.041844.156746.3331
721.31975.668221.67276.32984.625.37080.1510.7934-0.55590.0479-0.07960.04270.10230.453-0.0714-0.14440.0389-0.01080.06320.0107-0.10464.612242.747353.2289
814.86023.7532-9.7511.3924-3.35568.9264-0.02990.4162-0.0337-0.0717-0.00870.1501-0.1302-0.63080.0386-0.16220.0229-0.0080.072-0.0299-0.0919-2.769239.787967.0843
915.44334.153-2.717912.1736-5.517811.751-0.1415-0.40450.95270.41370.10410.8954-0.9688-0.94790.0374-0.09740.1148-0.03220.0581-0.0631-0.071-3.813146.571973.8142
1021.756619.9593.867959.47717.76315.5959-0.18810.77162.0142-2.1847-0.23870.9287-1.0863-1.30870.42680.20290.1492-0.10370.18840.13050.1158-1.009852.984365.38
116.009-0.21392.067617.4855-2.5376.7426-0.2477-0.5107-0.6250.33160.4907-0.57250.3337-0.1831-0.243-0.09250.0540.00570.04590.0426-0.0859-29.365528.780769.2422
128.37394.9247-4.856323.1692-16.29926.1518-0.1083-0.32980.46871.00340.0711-0.2876-1.07850.2520.0372-0.1420.04-0.0294-0.0191-0.0962-0.098-27.58440.231864.8545
132.0207-0.2033-2.8519.0514-1.42014.3449-0.07160.0324-0.1384-0.0225-0.09420.21990.1856-0.59250.1658-0.1704-0.0187-0.0167-0.0575-0.0067-0.12-33.763833.026358.8504
140.0134-0.1474-0.36963.581.472213.6396-0.1127-0.3143-0.66420.09920.18810.43190.5181-0.6966-0.0754-0.046-0.03470.0724-0.10010.05310.0393-32.083122.290259.8829
154.4150.8682-0.35671.89870.77877.8954-0.16280.2348-0.3101-0.15830.10880.25380.301-0.29720.0539-0.0776-0.03030.0057-0.174-0.0353-0.0612-29.42326.249150.7052
168.81982.31989.56640.87143.6515.29760.0015-0.4669-0.32790.05030.1481-0.20770.03650.1866-0.1496-0.11960.0328-0.007-0.0776-0.0178-0.0717-21.473832.838765.6026
1726.544311.7523-25.44985.2991-11.883228.3531-0.22830.44970.0883-0.20420.4371-0.31790.7054-0.0808-0.2088-0.110.04590.01220.1491-0.0291-0.0424-11.601738.214272.3138
186.34681.0751-5.63312.4893-1.25639.5665-0.272-0.0275-0.4446-0.032-0.0192-0.1860.3015-0.08120.2912-0.17840.0173-0.0114-0.0474-0.0261-0.14874.870539.284868.1926
1916.0797-2.12050.461517.0228-5.40139.1564-0.4036-0.0429-1.53470.01970.5489-0.26260.9709-0.0027-0.1453-0.073200.0724-0.03260.01560.0212-0.317534.506775.1609
2044.9929-8.07525.404922.1572-25.304335.12650.2282-0.7861-2.8575-0.49650.65680.61352.4997-0.6758-0.88510.2007-0.04690.01230.34210.17580.4683-6.946729.502778.9776
213.3432-2.40350.05122.45282.902411.9187-0.20.505-0.1789-0.1935-0.23660.93660.92670.15810.43660.0406-0.02610.0302-0.2576-0.01820.0389-25.291214.38149.3155
2212.81296.5797-4.03229.1809-7.2555.9014-0.0612-1.2676-0.59230.0515-0.5728-0.5723-0.03170.54510.6341-0.09130.01580.0853-0.0534-0.0635-0.2213-15.504728.358349.2255
232.7541-0.3838-1.02385.2182.69636.43690.0812-0.25860.0982-0.1958-0.09620.7193-0.2371-0.53320.015-0.1674-0.0349-0.0034-0.13530.0311-0.0643-24.002243.822344.038
246.30310.8763.0130.1444-0.131414.80590.6453-0.5310.29290.4416-0.39450.4244-0.9848-0.1638-0.25080.14670.02030.0666-0.2344-0.06590.0285-18.951259.107448.2447
253.7736-5.0603-5.85816.78597.85579.09420.35570.92030.5283-1.1151-0.59421.0957-1.816-0.32630.23850.13240.04950.0208-0.17380.06990.3905-19.973159.037139.576
264.84526.137-1.65968.2337-2.1690.5782-0.0743-0.2127-0.0471-0.05440.1169-0.0152-0.15240.0207-0.0427-0.1749-0.0063-0.0181-0.2047-0.0478-0.0734-21.272844.601450.7167
278.5993-7.1959-4.359210.38265.34082.86710.3530.74610.0611-0.6659-0.4353-0.41850.2818-0.44480.08220.0404-0.01810.0489-0.08880.0159-0.1167-21.163627.657642.8018
2811.7006-0.30127.42010.0078-0.1914.70551.4832-1.0391-1.3733-0.332-1.4571-0.6632.3721.6214-0.02610.4525-0.07470.04390.15860.06460.1818-15.615615.082850.8412
299.2689-1.49366.677613.9604-0.888113.37020.3902-0.27370.4749-0.544-0.29630.6579-0.4613-0.2306-0.0939-0.01580.0162-0.0291-0.1162-0.032-0.1676-19.787259.085739.4882
304.63372.0254-0.46236.1628-3.39582.38170.3271-0.20160.50960.1392-0.44080.1054-0.02670.34620.1137-0.1430.04770.0125-0.1370.0228-0.1417-19.601346.230350.8677
311.92521.06070.17141.4135-2.7279.61620.2860.3171-0.2717-0.4007-0.1697-0.18640.25010.1396-0.1164-0.0577-0.0018-0.0102-0.1865-0.0569-0.11-22.168629.757743.7736
3214.776915.0652-9.115223.0662-14.279524.12830.9254-0.16790.06150.5022-0.5228-0.32980.05820.0542-0.40260.11270.1090.0969-0.21-0.0880.1308-15.877614.808550.6737
336.4058-3.0479-3.06911.45021.46031.47040.6973-0.0253-0.5204-1.0012-0.48390.34930.4177-1.1332-0.21340.2128-0.0629-0.01990.0057-0.07020.2281-24.767514.629849.2229
340.51741.588-2.72796.8203-8.692914.43440.17370.2936-0.1992-0.13920.02350.40050.08880.1422-0.1972-0.1017-0.0235-0.0635-0.17980.07030.0669-15.84130.008847.5558
353.05692.1786-1.28141.5805-1.3948.82810.06170.52060.0509-0.029-0.39091.1018-0.4365-1.08830.3292-0.07870.0449-0.0365-0.0883-0.04310.011-25.756645.60644.4349
363.5423-2.6306-4.25123.69160.6228.79910.2044-0.60871.04430.9786-0.4081-0.0884-1.18410.66210.20370.1523-0.0594-0.05860.01370.02910.0128-18.790459.070348.6872
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 9
2X-RAY DIFFRACTION2A10 - 18
3X-RAY DIFFRACTION3A19 - 25
4X-RAY DIFFRACTION4A26 - 39
5X-RAY DIFFRACTION5A40 - 55
6X-RAY DIFFRACTION6A56 - 63
7X-RAY DIFFRACTION7A64 - 69
8X-RAY DIFFRACTION8A70 - 80
9X-RAY DIFFRACTION9A81 - 89
10X-RAY DIFFRACTION10A90 - 95
11X-RAY DIFFRACTION11B3 - 12
12X-RAY DIFFRACTION12B13 - 18
13X-RAY DIFFRACTION13B19 - 28
14X-RAY DIFFRACTION14B29 - 39
15X-RAY DIFFRACTION15B40 - 55
16X-RAY DIFFRACTION16B56 - 67
17X-RAY DIFFRACTION17B68 - 76
18X-RAY DIFFRACTION18B77 - 87
19X-RAY DIFFRACTION19B88 - 92
20X-RAY DIFFRACTION20B93 - 97
21X-RAY DIFFRACTION21E1 - 4
22X-RAY DIFFRACTION22E5 - 8
23X-RAY DIFFRACTION23E9 - 14
24X-RAY DIFFRACTION24E15 - 18
25X-RAY DIFFRACTION25F1 - 4
26X-RAY DIFFRACTION26F5 - 9
27X-RAY DIFFRACTION27F10 - 14
28X-RAY DIFFRACTION28F15 - 18
29X-RAY DIFFRACTION29G1 - 4
30X-RAY DIFFRACTION30G5 - 8
31X-RAY DIFFRACTION31G9 - 14
32X-RAY DIFFRACTION32G15 - 18
33X-RAY DIFFRACTION33H1 - 4
34X-RAY DIFFRACTION34H5 - 9
35X-RAY DIFFRACTION35H10 - 14
36X-RAY DIFFRACTION36H15 - 18

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