[English] 日本語
Yorodumi
- PDB-3myf: The Crystal Structure of the HPT domain from the Hpt Sensor Hybri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3myf
TitleThe Crystal Structure of the HPT domain from the Hpt Sensor Hybrid Histidine Kinase from Shewanella to 1.80A
ComponentsSensor protein
KeywordsTRANSFERASE / HPT / histidine kinase / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor / histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020
Similarity search - Function
Histidine kinase BarA, N-terminal / Single cache domain 4 / HPT domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain ...Histidine kinase BarA, N-terminal / Single cache domain 4 / HPT domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histidine kinase / Hpt sensor hybrid histidine kinase
Similarity search - Component
Biological speciesShewanella sp. W3-18-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsStein, A.J. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of the HPT domain from the Hpt Sensor Hybrid Histidine Kinase from Shewanella to 1.80A
Authors: Stein, A.J. / Tesar, C. / Clancy, S. / Joachimiak, A.
History
DepositionMay 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sensor protein
B: Sensor protein
C: Sensor protein
D: Sensor protein


Theoretical massNumber of molelcules
Total (without water)53,8204
Polymers53,8204
Non-polymers00
Water3,909217
1
A: Sensor protein
B: Sensor protein


Theoretical massNumber of molelcules
Total (without water)26,9102
Polymers26,9102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-14 kcal/mol
Surface area11350 Å2
MethodPISA
2
C: Sensor protein
D: Sensor protein


Theoretical massNumber of molelcules
Total (without water)26,9102
Polymers26,9102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-15 kcal/mol
Surface area11320 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.889, 71.188, 95.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Sensor protein


Mass: 13454.894 Da / Num. of mol.: 4 / Fragment: residues 805-923
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella sp. W3-18-1 (bacteria) / Strain: W3 / Gene: Sputw3181_1245 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A1RHE3, UniProt: A0A6N3J2V7*PLUS, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 8% PEG 4000, 0.1M Sodium acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 43778 / % possible obs: 99.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.075 / Χ2: 2.43 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.865.30.57943250.93100
1.86-1.945.30.39643180.992100
1.94-2.035.30.2643401.162100
2.03-2.135.30.18243271.349100
2.13-2.275.30.12843631.617100
2.27-2.445.30.10443551.868100
2.44-2.695.30.08843812.333100
2.69-3.085.20.08144273.424100
3.08-3.885.10.06444314.46100
3.88-504.90.05645116.43296.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
Cootmodel building
RefinementResolution: 1.8→32.42 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.565 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2208 5.1 %RANDOM
Rwork0.222 ---
obs0.225 43658 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.553 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 0 217 3701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223617
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.9994947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.285493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29527.174138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81915683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.279159
X-RAY DIFFRACTIONr_chiral_restr0.0870.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212591
X-RAY DIFFRACTIONr_mcbond_it0.5121.52359
X-RAY DIFFRACTIONr_mcangle_it0.86923824
X-RAY DIFFRACTIONr_scbond_it1.77131258
X-RAY DIFFRACTIONr_scangle_it2.5764.51105
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 138 -
Rwork0.286 2707 -
all-2845 -
obs--88.6 %
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)
135.4396-8.98018.06798.2327-9.963112.3838-0.5939-0.94031.10670.95370.4239-0.273-1.2345-0.46250.170.2857-0.1182-0.02370.22890.09810.354827.2781-26.5278-15.3564
20.3050.642-1.48626.9198-10.583717.25850.3550.03110.07120.1026-0.2740.0754-0.79430.4564-0.0810.4165-0.1284-0.04710.65740.29940.385730.0732-26.1028-24.5744
322.5659-0.7584-11.653319.1437-14.743818.00280.28280.73750.5239-0.8693-1.0226-1.31520.54740.4260.73980.19820.03910.02060.86940.1580.309331.3486-29.2498-30.6199
49.98432.7414-10.010812.433-5.09610.51040.193-0.4229-0.4431-1.0643-0.671-0.28870.02640.56410.4780.3746-0.045-0.08770.69930.14730.295525.1002-24.5887-33.5736
534.25242.52557.19870.58251.85136.0308-0.19250.7182-1.747-0.2893-0.1512-0.39770.45930.7580.34380.51940.17220.14520.36480.25260.435418.136-26.9813-30.1343
68.64391.1716-6.78892.6757-5.041612.17210.31760.7162-0.18110.09420.04180.3671-0.434-0.4719-0.35940.14430.0257-0.13430.12070.02340.325810.9176-29.7484-22.6085
719.64031.7108-4.629116.1599-6.80773.65340.29490.1385-0.04510.1679-0.02850.6572-0.1298-0.0291-0.26640.0829-0.0109-0.04710.20020.09890.24237.0942-35.2272-14.9458
80.8557-2.87130.505410.2972-0.90111.2744-0.0619-0.122-0.1420.448800.61980.1473-0.63090.06180.1142-0.07240.01880.4030.07390.38084.5985-42.6517-10.7946
911.90215.1351-4.62112.3803-2.98557.8247-0.09620.17290.3012-0.0590.07850.12750.161-0.11120.01770.113-0.0005-0.07670.14480.10550.35059.4881-44.4094-18.2428
1021.46858.3358-10.18986.5477-6.22686.5050.36630.2144-0.4835-0.5114-0.21630.4130.19220.3935-0.150.2065-0.1418-0.14680.6635-0.08690.241117.4665-39.34-22.7701
117.7756-0.4751-2.75042.63420.14118.52720.30670.6241-0.1203-0.2194-0.2323-0.18470.23810.5919-0.07450.1136-0.0035-0.06110.25290.09790.174724.6328-33.5723-21.5835
1215.94150.22771.73512.3902-3.1381.0106-0.11980.1926-0.0778-0.08870.0676-0.27810.02790.05210.05210.07750.0055-0.05190.24580.06140.133924.0474-39.3606-15.2314
135.7685-2.0486-2.205815.5986-6.29554.21760.1465-0.3426-0.1046-0.1338-0.14260.0646-0.00240.2681-0.00390.08540.0249-0.07650.21560.00250.266218.7764-46.0197-14.9061
147.3233-6.0591-6.006811.253110.68612.1401-0.02370.0628-0.1042-0.2927-0.0853-0.11470.0940.35470.10910.15040.0272-0.02710.14430.13870.331114.8219-50.8605-12.5151
159.214614.3238-3.545223.9456-1.569110.63650.19730.0540.19630.4102-0.11440.31960.0733-0.5134-0.08290.11360.05270.01160.27280.20390.272113.5045-43.9677-5.1783
168.71090.2181.390511.41912.17821.1048-0.3072-0.3429-0.19160.51480.2841-0.0656-0.03640.5120.02310.062-0.0169-0.02850.13880.13250.174816.8306-37.2768-8.9058
176.38350.9668-8.017111.6701-6.363212.59950.1531-0.56770.36380.49560.23950.3624-0.49010.5401-0.39260.1525-0.0235-0.06170.18510.02140.245917.5093-28.9821-12.7629
182.30342.1085-7.232223.025-18.52729.43310.51890.1073-0.12810.7434-0.48830.7501-1.72570.0166-0.03070.3408-0.1565-0.0610.17340.08450.342518.0831-21.7028-19.2557
1915.740126.655-5.864157.2508-15.32364.61411.1230.5513-0.591.9031-1.2893-0.9173-0.59690.7930.16631.12210.0150.14560.47650.04780.235422.4719-16.8167-25.872
202.6994-0.9912-0.53242.68920.64182.02330.014-0.1181-0.10070.15530.0363-0.21170.22690.3176-0.05030.13310.0067-0.02760.11120.00440.1338.6266-29.0988-39.928
213.07473.242-6.5346.220925.095944.37760.39230.58570.1524-0.9241-0.6232-0.7638-1.66120.08940.2310.35780.08860.13610.96070.40630.492923.41411.0314-42.1579
2211.1544-1.8556-11.647221.0709-0.564612.51760.40790.35550.3790.1595-0.00740.5928-0.6067-0.4492-0.40050.61420.2187-0.01990.19620.00630.389813.698710.591-37.9547
233.02411.86110.43417.73985.82274.75040.1698-0.0620.34150.2147-1.18451.39520.0709-1.01171.01470.58080.2250.09090.3794-0.08480.50179.39368.3413-31.8612
2421.8453-7.4359-19.48795.163-3.625557.39150.4594-0.06690.2256-0.21730.42340.1064-0.2304-1.5165-0.88280.40.11030.07620.12160.03590.250316.64847.8325-27.1039
258.4059-2.5685-2.54461.1199-0.635112.0554-0.4757-1.6958-0.06020.26690.54670.2964-0.66580.6436-0.07110.33760.02620.08690.42-0.04220.488622.2253.7509-25.862
2614.957-1.0606-1.84875.14974.98755.5331-0.0194-1.15570.16940.36090.0233-0.10840.20650.0802-0.0040.1797-0.0148-0.01170.2255-0.03560.124330.8163-1.1015-27.3151
2715.6089-7.29991.989512.03864.84568.73810.0106-0.52680.35710.46880.1016-0.4760.18240.5307-0.11220.0957-0.0233-0.01080.2369-0.02270.106435.0937-7.336-30.5295
2848.708520.75647.572111.17020.95083.5293-0.01430.2091-1.94860.0480.3004-0.99730.1565-0.0687-0.2860.39550.19-0.13110.3043-0.08730.336535.5372-15.0857-32.7727
298.415-5.8081-0.81626.1963.9875.4441-0.1796-0.1148-0.02230.2670.3851-0.12310.25340.5332-0.20550.1387-0.00740.01180.17430.06510.106127.5465-10.8006-32.7805
305.9606-0.51430.403411.57982.04857.7175-0.0186-0.4056-0.11310.093-0.0230.16790.0333-0.57010.04160.104-0.00070.0450.0674-0.00250.095821.2681-6.1387-33.8971
311.9824-0.8025-2.4575.6922-7.004314.97480.26360.1926-0.08950.1182-0.19220.1608-0.7277-0.114-0.07140.31460.1034-0.00120.0982-0.07480.172517.50621.9949-36.0493
320.56431.99821.414213.11230.90536.3358-0.21910.02840.0363-0.30680.15080.1279-0.88830.03330.06830.2795-0.01150.08980.09250.01790.134623.62441.3585-42.5376
330.9857-1.61580.93168.4674-0.60789.78250.0554-0.21460.0729-0.281-0.06180.22-0.31030.25410.00640.0764-0.02220.01690.1235-0.0180.088925.3415-6.4863-42.1142
3412.9689-0.61271.715615.7333.24778.68930.3063-0.0349-0.85230.03-0.2860.38080.7438-0.5615-0.02030.1062-0.03620.01270.10680.02250.124525.7528-16.0517-42.2697
353.50244.67080.062910.5521-1.28684.76510.0668-0.28010.03530.2076-0.1038-0.06220.01360.85320.0370.0887-0.00010.01870.2837-0.00330.062335.4802-11.8174-42.0944
362.3594-5.5647-3.269213.80885.99298.906-0.0072-0.10040.03830.17730.1071-0.0348-0.34770.5104-0.09990.1223-0.13110.05420.2002-0.01130.137733.5673-2.461-40.6941
377.7901-3.70475.633313.804-4.02568.6841-0.03540.41510.86740.3506-0.2643-0.3509-0.34860.25430.29970.2291-0.14010.08110.163-0.05230.219232.11243.9167-36.4358
3821.8643.5023-0.14639.87685.79247.2879-0.2378-0.1191-0.08450.28240.2913-0.5303-0.80750.329-0.05350.3816-0.07960.0370.0736-0.05130.27528.18549.424-34.107
3926.6112-4.043111.55181.4896-3.40939.5725-0.3461-1.39751.68460.0251-0.1584-0.1446-1.3310.35020.50451.066-0.1834-0.0140.2826-0.13070.372422.237415.6325-29.8425
4024.3882-4.5496-6.85295.97033.845719.79830.1169-0.484-0.7350.4473-0.3230.67621.2213-0.84170.20610.2775-0.0664-0.00620.0852-0.04030.18963.407-6.659-13.8449
415.3027-0.5819-0.448213.7234-7.636222.2718-0.13710.6705-0.1825-0.30140.07750.09450.3722-1.18630.05960.112-0.0139-0.02260.2386-0.08770.18242.3487-3.2457-23.4799
425.6475-2.7546-1.315811.088918.268441.08960.150.25390.1852-0.7436-0.40680.0828-2.1789-1.15520.25680.26190.1024-0.04140.2757-0.03680.24562.12862.3565-28.2085
4331.1913-6.76771.95264.0343-3.612311.7432-0.01980.29460.2428-0.261-0.03350.0039-0.0564-0.32480.05340.1490.0160.00770.1186-0.04870.159.4563-3.1984-31.0975
4418.9576-0.8775-5.03043.37323.17520.2880.06020.61661.6624-0.6506-0.15940.329-0.82060.05930.09920.16-0.0652-0.02960.2838-0.09180.268314.9151-2.9613-25.3598
455.7230.60313.55544.789-0.05112.5628-0.0310.54910.0040.12480.2669-0.79170.41331.1117-0.23590.15320.1014-0.03850.2545-0.09090.272922.4027-4.4747-16.9274
4629.9603-2.3509-8.499212.9654-1.29539.2156-0.27360.515-0.14910.76950.6407-0.77070.6721.0578-0.3670.27570.2258-0.16660.3267-0.16910.241625.9507-0.0332-7.2812
478.66531.2470.00538.0842-7.33646.9240.24230.4791-0.04950.4356-0.3933-0.5169-0.18060.52140.15110.43960.1703-0.43550.4145-0.30510.70328.12056.3097-3.6578
482.45342.61592.96384.01655.90489.7504-0.22040.3739-0.2479-0.08410.4321-0.25780.06180.5885-0.21170.14120.01930.0090.22470.02720.266521.97057.1531-11.4143
4913.7863.86460.414413.0502-0.265711.1214-0.24950.30060.3559-0.60410.1007-0.1722-0.00510.43950.14880.11760.03030.01380.1175-0.01690.102115.3974.9121-16.8544
5010.72125.902-5.53698.41511.36489.4429-0.10120.5160.3225-0.540.27150.0816-0.4439-0.1248-0.17030.1520.0272-0.02310.1211-0.01630.11378.08341.8445-19.0998
516.26830.42063.593311.29632.88232.68750.0150.22340.06030.3683-0.08470.3080.10380.09070.06970.1280.0251-0.00090.07670.02880.13879.53233.2593-9.9981
527.26423.2436-1.556313.1471-0.74976.5481-0.0486-0.01050.3364-0.1660.00970.13150.1340.04780.03890.11120.0028-0.02420.0196-0.0060.119814.19.4958-6.3353
536.9252-7.26141.021318.35070.53048.95120.0068-0.27060.27040.84440.0228-0.2425-0.4973-0.2081-0.02960.2028-0.02260.00550.0446-0.00390.155917.447614.3773-3.5327
5410.62990.6554-4.61887.064-0.44289.90830.1021-0.5902-0.2724-0.06070.1352-0.14450.52310.4297-0.23730.1751-0.0002-0.05290.05680.00910.154519.60675.5431.5731
551.84960.189-5.619317.36223.012618.1210.0764-0.0465-0.0250.157-0.1339-0.27430.2589-0.0730.05750.4579-0.1627-0.04860.1487-0.02970.092815.2982-0.5015-1.6953
5614.36757.68663.21694.75590.44193.72820.3226-0.6497-0.31410.0774-0.3156-0.20760.803-0.2038-0.00690.61110.0236-0.0180.0561-0.04460.162414.0306-6.4248-9.7415
575.19-3.816711.78645.6275-3.189637.40850.13180.0677-0.11830.4825-0.15440.22691.4525-0.04540.02260.3338-0.0047-0.02710.0291-0.09540.329112.0518-12.0321-18.8281
5820.601811.012510.128114.2861-0.726839.9422-0.06781.0313-0.28130.04750.1489-0.39261.1375-0.41-0.0810.2843-0.0677-0.00380.1972-0.08810.28818.522-12.8223-27.2776
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A806 - 810
2X-RAY DIFFRACTION2A811 - 815
3X-RAY DIFFRACTION3A816 - 821
4X-RAY DIFFRACTION4A822 - 827
5X-RAY DIFFRACTION5A828 - 832
6X-RAY DIFFRACTION6A833 - 840
7X-RAY DIFFRACTION7A841 - 846
8X-RAY DIFFRACTION8A847 - 852
9X-RAY DIFFRACTION9A853 - 859
10X-RAY DIFFRACTION10A860 - 867
11X-RAY DIFFRACTION11A868 - 875
12X-RAY DIFFRACTION12A876 - 880
13X-RAY DIFFRACTION13A881 - 886
14X-RAY DIFFRACTION14A887 - 892
15X-RAY DIFFRACTION15A893 - 897
16X-RAY DIFFRACTION16A898 - 902
17X-RAY DIFFRACTION17A903 - 909
18X-RAY DIFFRACTION18A910 - 915
19X-RAY DIFFRACTION19A916 - 921
20X-RAY DIFFRACTION20B806 - 919
21X-RAY DIFFRACTION21C806 - 810
22X-RAY DIFFRACTION22C811 - 817
23X-RAY DIFFRACTION23C818 - 826
24X-RAY DIFFRACTION24C827 - 831
25X-RAY DIFFRACTION25C832 - 836
26X-RAY DIFFRACTION26C837 - 842
27X-RAY DIFFRACTION27C843 - 848
28X-RAY DIFFRACTION28C849 - 854
29X-RAY DIFFRACTION29C855 - 860
30X-RAY DIFFRACTION30C861 - 865
31X-RAY DIFFRACTION31C866 - 872
32X-RAY DIFFRACTION32C873 - 877
33X-RAY DIFFRACTION33C878 - 883
34X-RAY DIFFRACTION34C884 - 889
35X-RAY DIFFRACTION35C890 - 897
36X-RAY DIFFRACTION36C898 - 902
37X-RAY DIFFRACTION37C903 - 907
38X-RAY DIFFRACTION38C908 - 912
39X-RAY DIFFRACTION39C913 - 919
40X-RAY DIFFRACTION40D806 - 810
41X-RAY DIFFRACTION41D811 - 816
42X-RAY DIFFRACTION42D817 - 822
43X-RAY DIFFRACTION43D823 - 828
44X-RAY DIFFRACTION44D829 - 833
45X-RAY DIFFRACTION45D834 - 842
46X-RAY DIFFRACTION46D843 - 848
47X-RAY DIFFRACTION47D849 - 854
48X-RAY DIFFRACTION48D855 - 861
49X-RAY DIFFRACTION49D862 - 867
50X-RAY DIFFRACTION50D868 - 873
51X-RAY DIFFRACTION51D874 - 880
52X-RAY DIFFRACTION52D881 - 885
53X-RAY DIFFRACTION53D886 - 890
54X-RAY DIFFRACTION54D891 - 896
55X-RAY DIFFRACTION55D897 - 901
56X-RAY DIFFRACTION56D902 - 909
57X-RAY DIFFRACTION57D910 - 915
58X-RAY DIFFRACTION58D916 - 921

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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

Read more