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- PDB-4qht: Crystal structure of AAA+/ sigma 54 activator domain of the flage... -

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Basic information

Entry
Database: PDB / ID: 4qht
TitleCrystal structure of AAA+/ sigma 54 activator domain of the flagellar regulatory protein FlrC from Vibrio cholerae in ATP analog bound state
ComponentsFlagellar regulatory protein C
KeywordsTRANSCRIPTION / AAA+ ATPase domain / ATP hydrolysis
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Transcriptional regulators FlbD/FleR/FlgR / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family ...Transcriptional regulators FlbD/FleR/FlgR / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Helicase, Ruva Protein; domain 3 - #60 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Helicase, Ruva Protein; domain 3 / Homeobox-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Flagellar regulatory protein C / Flagellar regulatory protein C
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.559 Å
AuthorsDey, S. / Biswas, M. / Sen, U. / Dasgupta, J.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Unique ATPase site architecture triggers cis-mediated synchronized ATP binding in heptameric AAA+-ATPase domain of flagellar regulatory protein FlrC
Authors: Dey, S. / Biswas, M. / Sen, U. / Dasgupta, J.
History
DepositionMay 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_dist_value / _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_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: Flagellar regulatory protein C
B: Flagellar regulatory protein C
C: Flagellar regulatory protein C
D: Flagellar regulatory protein C
E: Flagellar regulatory protein C
F: Flagellar regulatory protein C
G: Flagellar regulatory protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,28433
Polymers208,8267
Non-polymers4,45826
Water7,116395
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.959, 152.560, 193.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Flagellar regulatory protein C


Mass: 29832.258 Da / Num. of mol.: 7 / Fragment: UNP residues 132-381
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O395 / Gene: flrC / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5F6D4, UniProt: A0A0H3AHP1*PLUS
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% PEG 6000, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 6, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.559→49.387 Å / Num. all: 77804 / Num. obs: 77495 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 49.49 Å2
Reflection shellResolution: 2.56→2.6 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.559→49.199 Å / FOM work R set: 0.7938 / SU ML: 0.36 / σ(F): 1.35 / Phase error: 27.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2474 3899 5.03 %
Rwork0.1822 --
obs0.1856 77495 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.24 Å2 / Biso mean: 54.7 Å2 / Biso min: 19.86 Å2
Refinement stepCycle: LAST / Resolution: 2.559→49.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13469 0 272 395 14136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113968
X-RAY DIFFRACTIONf_angle_d1.30118892
X-RAY DIFFRACTIONf_chiral_restr0.0562163
X-RAY DIFFRACTIONf_plane_restr0.0062408
X-RAY DIFFRACTIONf_dihedral_angle_d19.075298
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5591-2.59030.35911290.26842406253592
2.5903-2.62310.37771350.257126172752100
2.6231-2.65760.29321320.248125962728100
2.6576-2.6940.29561370.22926182755100
2.694-2.73250.29491460.228625792725100
2.7325-2.77330.33791520.226926152767100
2.7733-2.81660.31441310.220926172748100
2.8166-2.86280.29411330.225926172750100
2.8628-2.91210.30351440.218326102754100
2.9121-2.96510.28491310.218626342765100
2.9651-3.02210.2551440.209125982742100
3.0221-3.08380.29851570.215326112768100
3.0838-3.15080.31681350.222426092744100
3.1508-3.22410.28041340.221826452779100
3.2241-3.30470.29631810.222625612742100
3.3047-3.3940.29241360.206726602796100
3.394-3.49390.25921300.202226322762100
3.4939-3.60660.29951260.197226212747100
3.6066-3.73550.25891550.178726362791100
3.7355-3.8850.29661390.177926552794100
3.885-4.06170.22061260.170126522778100
4.0617-4.27570.20911370.155526502787100
4.2757-4.54350.2091330.141426632796100
4.5435-4.8940.18511320.138426452777100
4.894-5.38590.2121470.152626862833100
5.3859-6.1640.25921400.169727062846100
6.164-7.76110.1981340.170627172851100
7.7611-49.20790.16011430.14592740288396
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)
15.8365-2.6716-2.03512.69641.31123.1828-0.0581-0.22440.10220.15950.1965-0.21030.10180.2549-0.08930.4175-0.0622-0.05260.2833-0.01450.3411-25.870534.820348.2
27.688-1.4845-2.7110.75521.16982.20780.0640.55091.0935-0.29570.3434-0.3238-0.44410.2055-0.5080.4655-0.1615-0.00140.46390.00550.6119-11.879236.333436.2943
35.93660.90420.69642.49450.75215.0464-0.25230.5891-0.0088-0.28830.2015-0.1717-0.09940.51570.05210.3412-0.032-0.03070.36810.01570.3653-14.52528.429930.3071
40.50010.74290.20295.3121.0227-0.00460.1327-0.0416-0.12250.0009-0.15760.19430.1089-0.08110.03490.3079-0.0204-0.01370.2896-0.01070.2549-29.154752.172847.3294
57.7151.7414-4.26122.4565-0.10116.27530.4750.9857-0.2892-1.1527-0.11610.6468-0.3345-0.92840.03690.54730.0574-0.11060.3683-0.07920.3528-33.268264.358345.6832
622.00011.99992220.9308-0.3198-3.5012.97182.46112.63287.8024-0.6497-3.39020.97240.2770.14521.09360.24111.2218-35.950868.80639.28
75.6459-2.8093-1.23832.3581.10051.91110.14920.74820.1463-0.2504-0.0425-0.4672-0.0158-0.1655-0.11430.4413-0.08260.02090.436-0.03160.4152-15.440467.665226.7329
86.85881.4271-0.48244.39451.43572.5768-0.09640.1738-0.3785-0.31960.0887-0.03770.2089-0.1733-0.00610.4179-0.0444-0.0130.3450.05960.3131-17.215756.176728.1904
90.67210.3095-0.59774.5816-3.2034.850.31080.00880.1240.3318-0.1149-0.0362-0.59280.0865-0.19980.4590.02150.03940.34870.01630.308-29.286684.774818.8084
106.0716-1.9552-3.51239.402-1.93543.25090.49460.3322-0.1077-0.48190.15370.2731-0.9386-1.3266-0.57490.67040.0565-0.09160.58170.10720.3482-33.082790.97277.8853
113.7608-1.02391.88381.0036-1.97983.3904-0.07280.4526-0.2047-0.0282-0.118-0.17580.02190.4180.26470.4155-0.00170.05720.60020.01750.4236-19.166481.0072-7.0444
125.14170.8757-1.22372.22460.02251.1834-0.1108-0.1259-0.3050.1168-0.024-0.10120.16130.03060.11620.4444-0.0360.02840.57130.06460.378-13.723370.12132.5916
130.49250.3688-0.81090.6475-0.69785.7616-0.0292-0.1812-0.07090.06020.0040.054-0.1015-0.4473-0.00980.30320.03190.01950.29110.05420.2913-29.647480.6659-25.9243
140.71010.6506-0.34161.3588-0.79630.46880.05720.0409-0.26470.0449-0.05830.150.232-0.0873-0.0391.4218-0.78440.01050.7163-0.31021.271-35.426468.8284-38.9167
154.58181.21971.94752.28961.09973.3796-0.02380.1848-0.53290.04930.16-0.02810.27730.5614-0.10620.38140.05250.05320.31880.0160.3571-19.28958.9993-37.615
166.657-0.5691-1.09831.793-1.07373.2265-0.1489-0.3685-0.16320.15690.0051-0.06320.26860.42490.1270.38310.0190.05120.3512-0.00570.355-13.769759.8208-23.0502
170.49790.1050.28425.99613.51572.35460.16440.15920.0682-0.3593-0.09380.032-0.29120.1399-0.03560.4302-0.0052-0.01020.3470.02350.3804-29.268446.0749-48.8898
188.2158-2.96931.20578.78025.02484.68480.21610.3768-0.4797-0.0548-0.0720.6581.2409-1.18380.27170.6385-0.033-0.08440.3227-0.01080.3365-33.32633.9067-52.4978
194.5283-1.21120.9022.00018.30585.7917-0.2073-0.18390.03990.40340.0736-0.36920.25820.2529-0.18051.80370.53230.36810.8490.04910.8715-32.047829.6704-45.254
204.80782.54930.68713.49911.57341.69360.0808-0.1644-0.34420.12160.1207-0.49710.16730.1859-0.21760.34220.06920.01040.346-0.03070.4659-19.220721.6674-39.8314
216.1202-0.8097-1.65311.07251.232.304-0.1007-0.41190.11780.24640.2881-0.15150.00980.164-0.18220.44120.04110.05210.3857-0.03010.5078-13.71833.3605-31.2096
220.8523-1.13280.01783.5623-1.54320.9660.09570.11640.0366-0.2101-0.03640.04030.0499-0.0559-0.05470.35120.00120.01440.3764-0.05140.3069-29.13134.8962-36.6199
234.17420.13775.12282.8323-0.52876.444-0.0777-0.549-0.41010.31610.33720.4779-0.0824-1.0597-0.11660.652-0.0880.0750.4694-0.01240.3905-33.1993-5.455-29.7576
2422-9.71932-0.58011.9999-0.12880.4268-1.0357-0.1281-0.5056-0.2061-0.9627-2.21110.74591.5244-0.231-0.3261.6279-0.28260.8221-37.7263-6.8856-18.8742
255.27481.8835-0.69582.6462-0.96321.3717-0.002-0.66810.13940.3313-0.2632-0.2245-0.010.21510.2610.42680.0327-0.02660.4741-0.01220.3551-19.3386-3.6689-11.9624
265.2253-1.47650.24733.75520.64571.7591-0.1049-0.01450.49440.2589-0.0752-0.4241-0.20480.09080.17460.40310.0163-0.01670.38370.04450.3632-13.839310.3981-15.8713
271.6233-0.80561.14841.6783-1.73145.04930.03620.0656-0.08540.10350.04530.01050.1898-0.1237-0.0890.3855-0.0406-0.00020.3272-0.04380.2784-29.9089-11.87855.194
282.4748-0.3328-1.37715.03521.1737.5087-0.02650.26390.00630.0467-0.10930.09760.49030.34950.15240.30.0325-0.02020.34460.02770.393-25.9176-2.219127.4842
298.25931.924-2.70912.7842-0.39163.26650.0768-0.7651.21880.20590.03520.4553-0.44290.5930.06160.3593-0.0196-0.05250.5309-0.03050.4411-13.526.826122.7848
309.25633.321-3.03472.7769-1.11144.0019-0.16040.04741.2062-0.01390.05880.2887-0.9682-0.2369-0.18580.5784-0.0576-0.150.57820.0990.6688-1.26815.44913.6839
318.6863-2.92331.87466.7477-3.20287.87120.36190.51480.3754-0.2851-0.2912-0.0174-0.57040.5478-0.07260.32260.0128-0.04750.48670.03610.4035-15.29517.503611.928
327.30350.2761-0.37353.9582-0.55920.3951-0.43210.12740.1541-0.43910.0763-0.35470.14830.47720.37860.5371-0.0472-0.06440.74840.0280.3342-7.36864.060511.2167
335.5661.74883.84956.5548-3.46789.4451-0.1520.24950.1938-0.4753-0.09670.4703-0.39640.22790.26980.39270.0719-0.05820.5763-0.08310.4332-27.54627.71639.373
340.46950.27781.0672.06762.32913.406-0.06010.25650.20070.1431-0.10440.13550.05370.0557-0.10030.3721-0.0103-0.01860.28610.03590.3071-27.36295.636.4678
351.73310.53360.99862.09522.30012.51890.0875-0.1563-0.25470.111-0.0260.0831-0.0336-0.43170.1160.2807-0.0173-0.01880.25240.0460.3042-30.721313.915943.9755
366.70971.74231.48496.522-0.04062.5747-0.30330.1677-0.40061.27870.1831.2844-1.3843-0.8920.180.49620.12440.08510.46940.03610.2808-33.548618.865448.4794
371.761.02461.0734.28924.25184.21731.2549-0.55712.36460.44520.0473-0.1981-3.0408-0.4581-1.31641.14750.49180.65630.92820.15330.833-34.98726.23743.0375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 130 THROUGH 164 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 165 THROUGH 206 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 207 THROUGH 292 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 293 THROUGH 361 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 362 THROUGH 374 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 375 THROUGH 375 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 130 THROUGH 221 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 222 THROUGH 293 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 294 THROUGH 360 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 361 THROUGH 374 )
11X-RAY DIFFRACTION11CHAIN C AND (RESID 130 THROUGH 201 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 202 THROUGH 292 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 293 THROUGH 374 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 375 THROUGH 377 )
15X-RAY DIFFRACTION15CHAIN D AND (RESID 130 THROUGH 201 )
16X-RAY DIFFRACTION16CHAIN D AND (RESID 202 THROUGH 292 )
17X-RAY DIFFRACTION17CHAIN D AND (RESID 293 THROUGH 361 )
18X-RAY DIFFRACTION18CHAIN D AND (RESID 362 THROUGH 374 )
19X-RAY DIFFRACTION19CHAIN D AND (RESID 375 THROUGH 375 )
20X-RAY DIFFRACTION20CHAIN E AND (RESID 130 THROUGH 201 )
21X-RAY DIFFRACTION21CHAIN E AND (RESID 202 THROUGH 292 )
22X-RAY DIFFRACTION22CHAIN E AND (RESID 293 THROUGH 361 )
23X-RAY DIFFRACTION23CHAIN E AND (RESID 362 THROUGH 374 )
24X-RAY DIFFRACTION24CHAIN E AND (RESID 375 THROUGH 375 )
25X-RAY DIFFRACTION25CHAIN F AND (RESID 130 THROUGH 201 )
26X-RAY DIFFRACTION26CHAIN F AND (RESID 202 THROUGH 292 )
27X-RAY DIFFRACTION27CHAIN F AND (RESID 293 THROUGH 374 )
28X-RAY DIFFRACTION28CHAIN G AND (RESID 130 THROUGH 164 )
29X-RAY DIFFRACTION29CHAIN G AND (RESID 165 THROUGH 201 )
30X-RAY DIFFRACTION30CHAIN G AND (RESID 202 THROUGH 221 )
31X-RAY DIFFRACTION31CHAIN G AND (RESID 222 THROUGH 249 )
32X-RAY DIFFRACTION32CHAIN G AND (RESID 250 THROUGH 271 )
33X-RAY DIFFRACTION33CHAIN G AND (RESID 272 THROUGH 292 )
34X-RAY DIFFRACTION34CHAIN G AND (RESID 293 THROUGH 324 )
35X-RAY DIFFRACTION35CHAIN G AND (RESID 325 THROUGH 361 )
36X-RAY DIFFRACTION36CHAIN G AND (RESID 362 THROUGH 374 )
37X-RAY DIFFRACTION37CHAIN G AND (RESID 375 THROUGH 375 )

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