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- PDB-5bmz: Crystal Structure of Putative MarR Family Transcriptional Regulat... -

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Basic information

Entry
Database: PDB / ID: 5bmz
TitleCrystal Structure of Putative MarR Family Transcriptional Regulator HcaR from Acinetobacter sp. ADP complexed with 24mer DNA.
Components
  • DNA (5'-D(P*GP*AP*AP*TP*AP*TP*CP*AP*GP*TP*TP*AP*AP*AP*CP*TP*GP*AP*TP*AP*TP*TP*C)-3')
  • HcaR protein
KeywordsTRANSCRIPTION / MarR / transcription factor / wHTH / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity
Similarity search - Function
MarR family / : / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Repressor protein
Similarity search - Component
Biological speciesAcinetobacter baylyi (bacteria)
Acinetobacter sp. ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.001 Å
AuthorsKim, Y. / Joachimiak, G. / Biglow, L. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of Putative MarR Family Transcriptional Regulator HcaR from Acinetobacter sp. ADP complexed with 24mer DNA.
Authors: Kim, Y. / Joachimiak, G. / Biglow, L. / Cobb, G. / Joachimiak, A.
History
DepositionMay 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HcaR protein
B: HcaR protein
E: DNA (5'-D(P*GP*AP*AP*TP*AP*TP*CP*AP*GP*TP*TP*AP*AP*AP*CP*TP*GP*AP*TP*AP*TP*TP*C)-3')
F: DNA (5'-D(P*GP*AP*AP*TP*AP*TP*CP*AP*GP*TP*TP*AP*AP*AP*CP*TP*GP*AP*TP*AP*TP*TP*C)-3')
C: HcaR protein
D: HcaR protein
G: DNA (5'-D(P*GP*AP*AP*TP*AP*TP*CP*AP*GP*TP*TP*AP*AP*AP*CP*TP*GP*AP*TP*AP*TP*TP*C)-3')
H: DNA (5'-D(P*GP*AP*AP*TP*AP*TP*CP*AP*GP*TP*TP*AP*AP*AP*CP*TP*GP*AP*TP*AP*TP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)102,8738
Polymers102,8738
Non-polymers00
Water00
1
A: HcaR protein
B: HcaR protein
E: DNA (5'-D(P*GP*AP*AP*TP*AP*TP*CP*AP*GP*TP*TP*AP*AP*AP*CP*TP*GP*AP*TP*AP*TP*TP*C)-3')
F: DNA (5'-D(P*GP*AP*AP*TP*AP*TP*CP*AP*GP*TP*TP*AP*AP*AP*CP*TP*GP*AP*TP*AP*TP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)51,4374
Polymers51,4374
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10540 Å2
ΔGint-79 kcal/mol
Surface area19870 Å2
MethodPISA
2
C: HcaR protein
D: HcaR protein
G: DNA (5'-D(P*GP*AP*AP*TP*AP*TP*CP*AP*GP*TP*TP*AP*AP*AP*CP*TP*GP*AP*TP*AP*TP*TP*C)-3')
H: DNA (5'-D(P*GP*AP*AP*TP*AP*TP*CP*AP*GP*TP*TP*AP*AP*AP*CP*TP*GP*AP*TP*AP*TP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)51,4374
Polymers51,4374
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-80 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.965, 161.965, 73.827
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
HcaR protein / Repressor protein


Mass: 18366.490 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1) (bacteria)
Strain: ATCC 33305 / BD413 / ADP1 / Gene: hcaR, ACIAD1728 / Plasmid: pMCSG19C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q7X0D9
#2: DNA chain
DNA (5'-D(P*GP*AP*AP*TP*AP*TP*CP*AP*GP*TP*TP*AP*AP*AP*CP*TP*GP*AP*TP*AP*TP*TP*C)-3')


Mass: 7351.791 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Acinetobacter sp. ADP1 (bacteria)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 5.5, 40 % v/v (+/-)-2-Methyl-2,4-pentanediol, 0.02 M Hexammine cobalt(III) chloride

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97924
SYNCHROTRONAPS 19-ID20.9794
SYNCHROTRONAPS 19-ID30.97159
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJun 2, 2013
ADSC QUANTUM 315r2CCDJun 2, 2013
ADSC QUANTUM 315r3CCDJun 2, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorMADMx-ray1
2double crystal monochromatorMADMx-ray2
3double crystal monochromatorMADMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.97941
30.971591
ReflectionResolution: 3→50 Å / Num. all: 22173 / Num. obs: 22173 / % possible obs: 99 % / Redundancy: 6.9 % / Biso Wilson estimate: 90.18 Å2 / Rsym value: 0.076 / Net I/σ(I): 31.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 2.36 / % possible all: 98.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
PHENIXphasing
Cootmodel building
PHENIXdev_1839refinement
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 3.001→38.903 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 42.32 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2939 992 4.72 %random
Rwork0.2524 ---
obs0.2545 21002 94.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 173.4 Å2
Refinement stepCycle: LAST / Resolution: 3.001→38.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4364 1888 0 0 6252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046540
X-RAY DIFFRACTIONf_angle_d0.6969252
X-RAY DIFFRACTIONf_dihedral_angle_d21.6562612
X-RAY DIFFRACTIONf_chiral_restr0.0271092
X-RAY DIFFRACTIONf_plane_restr0.004864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0007-3.15880.44671330.45972383X-RAY DIFFRACTION80
3.1588-3.35660.3471390.34462676X-RAY DIFFRACTION88
3.3566-3.61560.36881410.31262785X-RAY DIFFRACTION93
3.6156-3.97910.3151420.2772978X-RAY DIFFRACTION98
3.9791-4.55410.28621310.24883050X-RAY DIFFRACTION99
4.5541-5.73480.29431340.27533058X-RAY DIFFRACTION100
5.7348-38.9060.26771720.21063080X-RAY DIFFRACTION100
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)
10.04540.0549-0.04210.0812-0.04720.0485-1.2136-0.5029-0.550.5531-1.3793-0.8862-0.14140.70550.00911.0748-0.1630.08581.6346-0.02331.392740.882837.360911.7789
23.0856-0.67861.93170.7118-0.5571.17590.5581-2.15220.140.2574-0.294-0.2453-0.9166-1.18690.00251.7571-0.93910.07820.025-0.36540.500920.289839.641110.5763
30.9158-0.2087-0.65340.4250.29112.150.02160.32620.2289-0.0863-0.68411.3317-0.9664-1.9495-0.02741.6065-0.40610.07150.95270.02480.754511.384341.8028-5.1649
40.285-0.25110.22860.65180.24320.56620.8843-0.45770.4798-0.9591-0.55560.2675-0.51650.27-0.00111.0174-0.222-0.03760.927-0.13530.719512.644133.2117-8.4319
50.01380.01090.02010.0379-0.01280.06320.23170.90830.5707-1.3378-0.56791.5428-0.0968-0.604-0.00541.38480.1047-0.43511.14580.22881.50772.340640.3115-10.0734
60.750.52940.76430.38370.5520.77740.36843.04680.24240.1114-0.5991-2.0967-0.0311.2147-0.03811.57780.3281-0.1871.70730.01931.10398.165338.3812-19.694
71.08230.8595-0.3920.6888-0.33980.17731.7068-0.09511.80760.8556-1.04441.8671-2.0336-0.50710.1291.67890.02890.10661.0399-0.10230.759412.788150.24544.5546
80.8176-0.73670.29831.08140.41071.2756-0.43980.1819-0.5971-1.2163-1.83460.838-0.37940.1473-0.18761.548-0.54770.47011.22450.29841.402832.06447.3739-0.1701
93.50471.2745-0.93211.5630.90321.886-0.2922-0.2509-0.6149-0.17770.0904-0.946-0.18640.1761-0.00041.3271-0.1506-0.03770.75070.07670.966727.825629.541910.7788
100.0153-0.3751-0.13314.53611.12020.9241-0.5542-0.48570.64581.99870.5086-0.6973-0.4583-0.1025-0.03121.30290.1409-0.33532.14740.56861.855332.564418.937327.9851
110.9178-0.190.74511.6349-0.4710.63260.6471-0.63670.20991.77890.6497-1.0721-1.6846-0.94170.1020.9137-0.22430.23181.15430.58231.511637.224424.135415.9579
123.023-0.50160.49640.2070.09282.8431-1.54210.07830.72580.4912-0.7854-0.60240.9782-0.6413-0.51491.9724-0.4970.59610.24650.02491.211635.490644.38528.2431
13-0.0283-0.0264-0.0352-0.00720.0155-0.0026-0.49220.8562-0.6550.00680.4668-0.43480.82360.2034-0.00131.60430.06780.20511.6409-0.00210.956415.549225.3607-22.345
140.0886-0.10020.11810.0746-0.09360.0944-0.07760.1578-1.2270.0620.08360.92260.8327-0.4235-0.00361.5324-0.3994-0.00041.56340.45491.42237.578820.0554-6.9291
150.07590.12230.050.15020.03340.0194-0.0499-0.0609-0.6436-0.90671.79330.48540.25520.78980.00791.3011-0.0361-0.27681.011-0.28311.056117.365122.74968.5609
160.0152-0.04140.08480.1782-0.09760.15580.85240.7471-0.33851.59380.02840.57050.3952-1.79750.00371.7118-0.60180.15131.66460.11571.02369.147120.807525.2358
170.00510.0060.00820.02780.07140.17790.5690.8183-1.5357-0.55090.2763-0.5183-0.4853-0.05810.00121.58390.0239-0.14281.6298-0.47871.434418.351718.855538.6179
180.1873-0.5343-0.1521.32020.25920.366-0.9226-0.40531.33750.7035-0.2481-1.004-1.08820.1468-0.01262.5022-0.0337-0.47691.170.12950.991815.799926.263434.3533
190.0509-0.11-0.00840.2450.04190.0010.6332-1.036-1.3810.8149-0.3851.1254-0.0030.1255-0.01091.5992-0.6551-0.26561.31390.15041.013312.424617.001719.1267
200.76260.3263-0.03620.7882-0.15670.68740.74890.6632-0.23-0.68920.29360.47950.9046-2.20330.05431.6112-0.198-0.08341.0297-0.09030.892712.331721.8752-5.4719
210.0139-0.03120.01470.0835-0.07210.15960.7825-0.5813-0.6438-0.08920.29931.0155-0.2828-0.3226-0.00162.2945-0.4263-0.76651.89060.35311.67318.429426.0274-27.1987
220.84980.2939-0.49680.0985-0.16850.29110.16150.2656-0.3363-0.02750.3402-0.05730.2315-0.09340.69960.423-1.2311-0.24531.4415-0.89353.271824.750587.284444.1329
230.24130.03230.04560.0222-0.0240.06670.26090.2170.0766-0.1548-0.21960.63850.07220.1711-0.0365-0.8689-1.7155-0.11231.0896-0.73062.415927.215272.274330.002
240.0336-0.0030.05870.00160.01210.1011-0.00960.0605-0.0716-0.46820.30220.44940.05840.2166-0.07751.9478-1.90580.38490.3838-0.50971.801635.039458.993230.7477
250.0410.0007-0.00650.01950.01410.01450.4396-0.0765-0.08250.1445-0.1601-0.03190.4468-0.3961-0.00141.73030.1394-0.77383.02340.47381.159643.337352.651440.1796
260.0039-0.00570.010.02190.00010.0097-0.1224-0.2971-0.54060.3121-0.0262-0.0656-0.31320.28640.00031.7126-0.4661-0.10312.2318-0.03190.984633.412256.573144.1795
270.17290.0077-0.01710.03330.01670.00850.2663-0.3146-0.1360.2672-0.1928-0.02690.1424-0.1023-0.21182.0774-1.81010.11881.9112-0.8211.144629.470650.5535.3026
280.69130.29770.0520.186-0.13210.3517-0.07750.01120.3772-0.12160.23910.5883-0.1810.05540.23591.933-0.26030.46510.5452-0.78332.868137.738247.197530.1763
290.6192-0.31450.56680.16-0.29070.5096-0.6764-0.1338-0.04-0.1364-0.49360.2981-0.0006-0.0466-0.46173.07570.297-0.75760.49670.3552.482141.893142.808246.0872
300.13490.33890.13640.77290.3110.17020.25061.2526-0.0302-1.6766-0.1247-0.5296-2.15842.25360.07032.7283-0.0664-0.25780.9953-0.14452.35240.191461.5526.4647
315.3148-2.65130.03171.6089-0.02290.0105-0.6001-0.463-1.10050.51020.61831.0283-0.21780.2736-0.88962.6015-1.0893-1.01730.5322-0.42431.676839.203777.452940.5893
321.21130.1301-0.17020.01450.07741.5291-0.48740.45260.0101-0.6954-0.16980.51-0.20560.5081-1.04642.2494-1.51040.2292-0.6486-1.381.899730.226669.963443.3152
330.0390.057-0.03140.19610.15780.21760.22680.05670.5186-0.21960.20320.3635-0.06180.00031.14640.8755-2.4311-0.93810.3154-0.56342.779410.717976.785236.1714
340.01330.0318-0.00210.0556-0.010.0013-0.04840.0570.1337-0.07140.0463-0.1477-0.15890.20140.14171.3664-0.79970.13662.5418-0.56832.8641.766879.19541.872
350.2257-0.1250.07450.1141-0.22742.48850.3366-0.2144-0.06540.5479-0.41790.22530.00230.3105-0.50771.4929-0.4732-0.02420.561-0.46382.096920.356683.114441.2914
360.02730.010.0264-0.00290.0020.02380.2483-0.7257-0.3474-0.24360.5083-0.3735-0.59740.53490.00442.0425-0.50880.20851.7868-0.05253.051131.476544.073253.2217
370.804-0.0852-0.50860.6134-0.7421.2401-0.3369-0.66940.29450.4384-1.33381.03891.3461-1.0648-2.09952.2936-0.81540.23281.4516-0.66553.295716.602454.330937.8874
381.59550.14070.52390.2572-0.11181.9619-0.1734-0.11720.2613-0.4413-0.1650.0114-0.0466-0.73970.53962.0844-0.2418-0.98261.7966-0.4812.70134.234466.26220.2021
390.00820.0075-0.00370.0069-0.0043-0.0010.34240.2328-0.5184-0.0323-0.01290.33650.6174-0.2943-0.02742.80241.3425-0.54243.17430.23624.2846-4.201980.520718.9533
400.03290.01540.01050.0036-0.01940.0574-0.2629-0.18420.2984-0.6559-0.1739-0.1987-0.3137-0.80370.00022.4439-0.1406-0.42431.80330.73813.53163.84578.069917.3913
410.92390.1501-0.20770.2263-0.19610.15880.1670.12240.5624-0.34890.24650.28220.2885-0.54290.72731.8533-0.918-0.6140.8237-0.41073.095111.796260.414131.5078
420.63220.06470.50450.19220.0960.3575-0.5736-0.0785-0.15560.889-0.6305-0.18580.7798-0.1173-0.0622.6932-0.72030.59031.29830.24692.216325.937941.375949.3853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 83 )
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 91 )
6X-RAY DIFFRACTION6chain 'A' and (resid 92 through 104 )
7X-RAY DIFFRACTION7chain 'A' and (resid 105 through 126 )
8X-RAY DIFFRACTION8chain 'A' and (resid 127 through 150 )
9X-RAY DIFFRACTION9chain 'B' and (resid 12 through 84 )
10X-RAY DIFFRACTION10chain 'B' and (resid 85 through 94 )
11X-RAY DIFFRACTION11chain 'B' and (resid 95 through 123 )
12X-RAY DIFFRACTION12chain 'B' and (resid 124 through 150 )
13X-RAY DIFFRACTION13chain 'E' and (resid -11 through -7 )
14X-RAY DIFFRACTION14chain 'E' and (resid -6 through -2 )
15X-RAY DIFFRACTION15chain 'E' and (resid -1 through 3 )
16X-RAY DIFFRACTION16chain 'E' and (resid 4 through 8 )
17X-RAY DIFFRACTION17chain 'E' and (resid 9 through 11 )
18X-RAY DIFFRACTION18chain 'F' and (resid -11 through -7 )
19X-RAY DIFFRACTION19chain 'F' and (resid -6 through -2 )
20X-RAY DIFFRACTION20chain 'F' and (resid -1 through 8 )
21X-RAY DIFFRACTION21chain 'F' and (resid 9 through 11 )
22X-RAY DIFFRACTION22chain 'C' and (resid 12 through 17 )
23X-RAY DIFFRACTION23chain 'C' and (resid 18 through 39 )
24X-RAY DIFFRACTION24chain 'C' and (resid 40 through 54 )
25X-RAY DIFFRACTION25chain 'C' and (resid 55 through 59 )
26X-RAY DIFFRACTION26chain 'C' and (resid 60 through 70 )
27X-RAY DIFFRACTION27chain 'C' and (resid 71 through 82 )
28X-RAY DIFFRACTION28chain 'C' and (resid 83 through 91 )
29X-RAY DIFFRACTION29chain 'C' and (resid 92 through 98 )
30X-RAY DIFFRACTION30chain 'C' and (resid 99 through 124 )
31X-RAY DIFFRACTION31chain 'C' and (resid 125 through 150 )
32X-RAY DIFFRACTION32chain 'D' and (resid 12 through 39 )
33X-RAY DIFFRACTION33chain 'D' and (resid 40 through 83 )
34X-RAY DIFFRACTION34chain 'D' and (resid 84 through 90 )
35X-RAY DIFFRACTION35chain 'D' and (resid 91 through 150 )
36X-RAY DIFFRACTION36chain 'G' and (resid -11 through -7 )
37X-RAY DIFFRACTION37chain 'G' and (resid -6 through 3 )
38X-RAY DIFFRACTION38chain 'G' and (resid 4 through 8 )
39X-RAY DIFFRACTION39chain 'G' and (resid 9 through 11 )
40X-RAY DIFFRACTION40chain 'H' and (resid -11 through -7 )
41X-RAY DIFFRACTION41chain 'H' and (resid -6 through 3 )
42X-RAY DIFFRACTION42chain 'H' and (resid 4 through 11 )

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