[English] 日本語
Yorodumi
- PDB-6aqy: Crystal structure of a gdp-l-fucose synthetase from Naegleria fowleri -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6aqy
TitleCrystal structure of a gdp-l-fucose synthetase from Naegleria fowleri
Componentsgdp-l-fucose synthetase
KeywordsOXIDOREDUCTASE / NIAID / structural genomics / brain-eating bacteria / NADP-dependent / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


GDP-L-fucose synthase / GDP-L-fucose synthase activity / 'de novo' GDP-L-fucose biosynthetic process
Similarity search - Function
GDP-L-fucose synthase/GDP-L-colitose synthase / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GDP-L-fucose synthase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a gdp-l-fucose synthetase from Naegleria fowleri
Authors: Edwards, T.E. / Dranow, D.M. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionAug 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: gdp-l-fucose synthetase
B: gdp-l-fucose synthetase
C: gdp-l-fucose synthetase
D: gdp-l-fucose synthetase
E: gdp-l-fucose synthetase
F: gdp-l-fucose synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,61412
Polymers234,1586
Non-polymers4556
Water2,702150
1
A: gdp-l-fucose synthetase
B: gdp-l-fucose synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2805
Polymers78,0532
Non-polymers2283
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-51 kcal/mol
Surface area28300 Å2
MethodPISA
2
C: gdp-l-fucose synthetase
D: gdp-l-fucose synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1493
Polymers78,0532
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-32 kcal/mol
Surface area27590 Å2
MethodPISA
3
E: gdp-l-fucose synthetase
F: gdp-l-fucose synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1844
Polymers78,0532
Non-polymers1322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-41 kcal/mol
Surface area28700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.730, 102.100, 121.820
Angle α, β, γ (deg.)90.000, 107.630, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 or (resid 11 through 13...
21(chain B and (resid 10 or (resid 11 through 13...
31(chain C and (resid 10 or (resid 11 through 13...
41(chain D and (resid 10 through 16 or (resid 17...
51(chain E and (resid 10 or (resid 11 through 13...
61(chain F and (resid 10 through 65 or (resid 66...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPRO(chain A and (resid 10 or (resid 11 through 13...AA1018
12ILEILELEULEU(chain A and (resid 10 or (resid 11 through 13...AA11 - 1319 - 21
13HISHISLYSLYS(chain A and (resid 10 or (resid 11 through 13...AA0 - 3338 - 341
14HISHISLYSLYS(chain A and (resid 10 or (resid 11 through 13...AA0 - 3338 - 341
15HISHISLYSLYS(chain A and (resid 10 or (resid 11 through 13...AA0 - 3338 - 341
16HISHISLYSLYS(chain A and (resid 10 or (resid 11 through 13...AA0 - 3338 - 341
21PROPROPROPRO(chain B and (resid 10 or (resid 11 through 13...BB1018
22ILEILELEULEU(chain B and (resid 10 or (resid 11 through 13...BB11 - 1319 - 21
23ARGARGLYSLYS(chain B and (resid 10 or (resid 11 through 13...BB4 - 33312 - 341
24ARGARGLYSLYS(chain B and (resid 10 or (resid 11 through 13...BB4 - 33312 - 341
25ARGARGLYSLYS(chain B and (resid 10 or (resid 11 through 13...BB4 - 33312 - 341
26ARGARGLYSLYS(chain B and (resid 10 or (resid 11 through 13...BB4 - 33312 - 341
31PROPROPROPRO(chain C and (resid 10 or (resid 11 through 13...CC1018
32ILEILELEULEU(chain C and (resid 10 or (resid 11 through 13...CC11 - 1319 - 21
33GLNGLNLYSLYS(chain C and (resid 10 or (resid 11 through 13...CC3 - 33311 - 341
34GLNGLNLYSLYS(chain C and (resid 10 or (resid 11 through 13...CC3 - 33311 - 341
35GLNGLNLYSLYS(chain C and (resid 10 or (resid 11 through 13...CC3 - 33311 - 341
36GLNGLNLYSLYS(chain C and (resid 10 or (resid 11 through 13...CC3 - 33311 - 341
41PROPROASPASP(chain D and (resid 10 through 16 or (resid 17...DD10 - 1618 - 24
42ASPASPLEULEU(chain D and (resid 10 through 16 or (resid 17...DD17 - 2025 - 28
43GLUGLULYSLYS(chain D and (resid 10 through 16 or (resid 17...DD5 - 33313 - 341
44GLUGLULYSLYS(chain D and (resid 10 through 16 or (resid 17...DD5 - 33313 - 341
45GLUGLULYSLYS(chain D and (resid 10 through 16 or (resid 17...DD5 - 33313 - 341
46GLUGLULYSLYS(chain D and (resid 10 through 16 or (resid 17...DD5 - 33313 - 341
51PROPROPROPRO(chain E and (resid 10 or (resid 11 through 13...EE1018
52ILEILELEULEU(chain E and (resid 10 or (resid 11 through 13...EE11 - 1319 - 21
53METMETLYSLYS(chain E and (resid 10 or (resid 11 through 13...EE1 - 3339 - 341
54METMETLYSLYS(chain E and (resid 10 or (resid 11 through 13...EE1 - 3339 - 341
55METMETLYSLYS(chain E and (resid 10 or (resid 11 through 13...EE1 - 3339 - 341
56METMETLYSLYS(chain E and (resid 10 or (resid 11 through 13...EE1 - 3339 - 341
61PROPROPHEPHE(chain F and (resid 10 through 65 or (resid 66...FF10 - 6518 - 73
62GLUGLULYSLYS(chain F and (resid 10 through 65 or (resid 66...FF66 - 6774 - 75
63PROPROLYSLYS(chain F and (resid 10 through 65 or (resid 66...FF10 - 33318 - 341
64PROPROLYSLYS(chain F and (resid 10 through 65 or (resid 66...FF10 - 33318 - 341
65PROPROLYSLYS(chain F and (resid 10 through 65 or (resid 66...FF10 - 33318 - 341
66PROPROLYSLYS(chain F and (resid 10 through 65 or (resid 66...FF10 - 33318 - 341

-
Components

#1: Protein
gdp-l-fucose synthetase


Mass: 39026.402 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D0TCK0*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NafoA.00085.a.B1.PS38274 at 12 mg/mL against Morpheus screen condition C8 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 30 mM sodium nitrate, 30 mM disodium hydrogen phosphate, 30 mM ammonium ...Details: NafoA.00085.a.B1.PS38274 at 12 mg/mL against Morpheus screen condition C8 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 30 mM sodium nitrate, 30 mM disodium hydrogen phosphate, 30 mM ammonium sulfate, 0.1 M MOPS/HEPES pH 7.5, crystal tracking ID 292647c8, dhq2-1 unique puck ID

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.55→35.558 Å / Num. obs: 75854 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.174 % / Biso Wilson estimate: 57.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.055 / Χ2: 1.036 / Net I/σ(I): 19.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.55-2.624.2760.5672.7755570.820.64699.9
2.62-2.694.2670.4313.6254800.8960.49199.9
2.69-2.774.2780.3434.753120.9260.39199.9
2.77-2.854.2590.2735.7751330.9540.31299.8
2.85-2.944.2470.2077.5749830.9710.23799.6
2.94-3.054.2440.1559.8548070.9840.17699.7
3.05-3.164.2120.11612.7646680.990.13399.7
3.16-3.294.1990.09115.8444980.9930.10499.8
3.29-3.444.170.06919.5943020.9960.07999.7
3.44-3.614.1340.05323.9141000.9970.06199.8
3.61-3.84.1040.04427.8239420.9980.0599.8
3.8-4.034.0760.03931.3737050.9980.04599.8
4.03-4.314.0810.03534.4435120.9980.0499.8
4.31-4.664.0650.03137.3632530.9980.03699.8
4.66-5.14.080.0337.9530180.9990.03499.7
5.1-5.74.0770.0338.0427130.9980.03499.8
5.7-6.584.0860.02937.9624050.9990.03399.9
6.58-8.064.0620.02440.5520460.9990.02799.9
8.06-11.44.0420.0244.1215880.9990.02298.7
11.4-35.5583.7220.0242.228320.9990.02391.5

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(1.12_2829: ???)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4e5y

4e5y


Resolution: 2.55→35.558 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.49
RfactorNum. reflection% reflection
Rfree0.2403 2059 2.72 %
Rwork0.1857 --
obs0.1872 75816 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 193.27 Å2 / Biso mean: 71.423 Å2 / Biso min: 24.49 Å2
Refinement stepCycle: final / Resolution: 2.55→35.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14496 0 22 150 14668
Biso mean--151 53.53 -
Num. residues----1926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814887
X-RAY DIFFRACTIONf_angle_d0.89720281
X-RAY DIFFRACTIONf_chiral_restr0.0522226
X-RAY DIFFRACTIONf_plane_restr0.0062655
X-RAY DIFFRACTIONf_dihedral_angle_d13.3378668
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7009X-RAY DIFFRACTION9.57TORSIONAL
12B7009X-RAY DIFFRACTION9.57TORSIONAL
13C7009X-RAY DIFFRACTION9.57TORSIONAL
14D7009X-RAY DIFFRACTION9.57TORSIONAL
15E7009X-RAY DIFFRACTION9.57TORSIONAL
16F7009X-RAY DIFFRACTION9.57TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.60930.32981340.270348945028100
2.6093-2.67450.30571240.250848785002100
2.6745-2.74680.27591220.236749425064100
2.7468-2.82760.31561350.239449055040100
2.8276-2.91880.29171390.246348795018100
2.9188-3.02310.30531550.240148565011100
3.0231-3.1440.31771550.222648915046100
3.144-3.2870.28741530.227748975050100
3.287-3.46020.27111390.212849135052100
3.4602-3.67680.25351520.192249115063100
3.6768-3.96030.22011630.17348945057100
3.9603-4.35820.20291380.15449255063100
4.3582-4.98740.17511220.147749785100100
4.9874-6.2780.23351150.177549805095100
6.278-35.56150.19841130.15565014512799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2453-0.3671-0.73215.1159-2.60742.35680.0259-0.28010.19140.36420.0855-0.1669-0.65540.0806-0.14080.590.0235-0.03980.336-0.14080.388-43.524821.077333.0725
23.3466-1.369-0.47.37273.45636.2265-0.1056-0.5976-0.40081.04920.19060.17490.71430.0474-0.09530.47250.0236-0.01460.36390.05550.345-48.20167.449135.5013
33.0636-0.4121-1.57193.50281.47193.6956-0.0256-0.0257-0.0715-0.11650.0578-0.2031-0.05810.3445-0.00970.3284-0.0115-0.04660.26910.02830.3144-42.83287.258519.1215
44.0963-1.30491.41771.4666-0.25072.8737-0.0229-0.41350.07010.0670.0742-0.4266-0.06130.7713-0.02220.4597-0.0526-0.0570.6874-0.07110.6005-24.635911.967531.488
51.5661.00111.05992.1679-0.30653.3135-0.0898-0.0283-0.0046-0.01240.02120.11110.6126-0.17470.06490.5258-0.06090.08660.2824-0.02670.4968-57.6407-20.04453.2624
62.90150.3802-0.46655.97081.38034.769-0.3138-0.30180.1090.2890.06580.57530.5414-0.36660.32370.434-0.00410.03990.27590.00220.3965-58.3142-14.662614.1094
72.55040.0214-0.77472.87180.8953.4569-0.01270.09660.2369-0.06010.0984-0.0764-0.11190.1156-0.07370.37210.0081-0.00370.27820.00310.3673-46.8845-4.42038.871
81.57820.05631.06673.8961-1.9664.10580.03450.15190.2908-0.42720.28150.61860.0064-0.3331-0.29610.5558-0.01840.06430.34520.07440.563-57.4154-5.2218-9.6237
92.9785-0.2909-0.03494.2741-1.82262.734-0.0674-0.00740.3145-0.3730.42280.6905-0.2522-0.448-0.32780.6235-0.0320.01040.44050.11660.5558-58.9139-4.3378-14.4372
105.6402-0.01471.58044.6162-1.2426.0130.10090.4913-0.1272-0.7341-0.2619-0.64010.55610.45310.14710.45850.11130.08390.52730.00890.4809-8.424612.2172-35.7593
110.3359-1.0150.61564.8411-1.00674.52030.0108-0.11690.13020.2031-0.1388-0.4517-0.0914-0.21440.12730.33140.0303-0.1120.4889-0.02080.566-8.47069.9838-18.5427
126.33030.8981-0.43752.334-0.141.50840.01530.0987-0.09030.3561-0.038-0.16320.18540.07250.02010.56330.0202-0.02970.29730.00330.3388-26.982418.9536-26.9529
133.4505-2.00151.46595.2873-1.51246.62410.1446-0.6786-0.77140.10850.1496-0.0030.9746-0.6748-0.1580.7645-0.1562-0.17750.69430.28710.81-0.6882-18.78071.759
142.6327-2.04272.462.6104-0.15367.16230.7021-0.2281-0.5705-0.7229-0.4782-0.34921.96870.8003-0.0230.79680.0105-0.08780.52130.15380.92782.3495-18.743-10.6825
153.4226-2.96122.28795.2694-3.0047.8025-0.0242-0.377-0.0504-0.2996-0.3052-0.63280.4785-0.09540.0420.45230.0002-0.11960.53730.02990.652-1.4066-7.2904-12.5204
162.3671-3.28090.19516.1898-2.59485.8129-0.5988-1.23440.35620.5850.6741-0.102-0.5865-0.6163-0.09660.53820.113-0.17770.9989-0.01160.73-7.23090.553-4.4864
177.5267-1.72972.75953.7925-1.65914.7134-0.4662-0.80610.35870.22940.0723-0.98370.01060.02270.30220.64840.053-0.20180.56320.04260.819710.0605-4.81692.8297
182.87030.18691.85230.9165-0.61782.46-0.7579-1.41761.63220.333-0.022-1.2399-0.7434-0.58440.63581.00820.2451-0.42080.6419-0.25021.4913.95614.445412.1261
198.9356-0.53894.1943.5543-1.24875.6561-0.4184-1.88720.26140.78680.4484-0.0548-0.1861-1.26730.08980.73520.1621-0.06671.07720.04440.62411.5933-6.367210.6073
206.7233-1.41760.4632.61310.50793.0678-0.3547-1.48120.83380.58730.053-0.4291-0.5192-0.41730.23910.87070.2758-0.25991.0243-0.01230.84885.83270.77514.1646
214.6639-1.76482.18781.4277-0.51991.1447-0.1231-0.4888-0.18860.0541-0.1286-0.7148-0.20250.01390.23110.7482-0.0425-0.26750.68980.28611.033919.2929-10.11717.8807
221.8566-0.40711.92995.45372.65796.6289-0.25370.32260.1308-0.41290.261-0.3143-0.64210.55040.02290.4109-0.12430.18520.5131-0.08380.4955-33.7346-4.4689-70.1282
235.10241.02-0.39154.3602-0.28783.8899-0.0032-0.4080.25810.15520.0903-0.0897-0.3629-0.3835-0.14030.42360.0121-0.00180.4727-0.06710.3316-47.2864-4.178-61.1519
243.25540.39410.83732.2012-0.16664.07850.1521-0.5799-0.24020.44550.0728-0.4240.21550.4074-0.21380.45150.0232-0.00270.6131-0.0610.52-29.8691-12.2176-51.3347
251.17130.0308-1.3550.47510.42812.01670.05690.1195-0.0365-0.1221-0.27550.8137-0.112-1.6048-0.29130.60550.23630.31882.565-0.28780.8857-85.039-0.4911-51.171
260.90570.046-1.54311.70631.42394.03770.0522-0.90251.2668-0.02320.09410.0942-1.1893-1.2223-0.25440.80740.5686-0.04451.923-0.31450.8713-71.55544.2831-56.6831
272.9008-0.5367-0.11222.1699-0.61085.07730.245-1.2359-0.2660.16130.00870.41850.137-1.7946-0.18210.4921-0.0258-0.01321.39340.08640.4755-65.008-9.7145-54.221
280.0735-0.48380.39873.1502-1.10054.21510.4296-1.6920.3081-0.51530.37880.50590.5383-1.6785-0.01170.5625-0.25150.081.67570.07210.6573-79.0406-10.9386-58.5878
292.8562-0.4157-0.25314.1707-0.6453.79050.5166-0.7905-1.0432-0.93230.21330.93650.0292-0.29-0.29741.175-0.524-0.31641.08390.53281.231-87.9222-21.8101-70.9275
300.5741-0.57440.84730.7547-0.56251.51370.625-1.6051-0.6004-0.00970.24240.5460.8103-0.69240.40270.7443-0.6719-0.07182.33120.57631.1352-82.3824-21.0083-53.5506
310.03990.2574-0.26416.8837-1.40621.6779-0.4572-0.9363-0.1024-0.5240.04780.50750.2272-1.3706-0.21130.567-0.4412-0.15571.61730.2370.9662-94.5951-11.9165-66.8571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 38 )A0 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 89 )A39 - 89
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 170 )A90 - 170
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 333 )A171 - 333
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 57 )B4 - 57
6X-RAY DIFFRACTION6chain 'B' and (resid 58 through 89 )B58 - 89
7X-RAY DIFFRACTION7chain 'B' and (resid 90 through 171 )B90 - 171
8X-RAY DIFFRACTION8chain 'B' and (resid 172 through 275 )B172 - 275
9X-RAY DIFFRACTION9chain 'B' and (resid 276 through 333 )B276 - 333
10X-RAY DIFFRACTION10chain 'C' and (resid 3 through 89 )C3 - 89
11X-RAY DIFFRACTION11chain 'C' and (resid 90 through 170 )C90 - 170
12X-RAY DIFFRACTION12chain 'C' and (resid 171 through 333 )C171 - 333
13X-RAY DIFFRACTION13chain 'D' and (resid 5 through 38 )D5 - 38
14X-RAY DIFFRACTION14chain 'D' and (resid 39 through 68 )D39 - 68
15X-RAY DIFFRACTION15chain 'D' and (resid 69 through 110 )D69 - 110
16X-RAY DIFFRACTION16chain 'D' and (resid 111 through 170 )D111 - 170
17X-RAY DIFFRACTION17chain 'D' and (resid 171 through 213 )D171 - 213
18X-RAY DIFFRACTION18chain 'D' and (resid 214 through 231 )D214 - 231
19X-RAY DIFFRACTION19chain 'D' and (resid 232 through 275 )D232 - 275
20X-RAY DIFFRACTION20chain 'D' and (resid 276 through 312 )D276 - 312
21X-RAY DIFFRACTION21chain 'D' and (resid 313 through 333 )D313 - 333
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 38 )E1 - 38
23X-RAY DIFFRACTION23chain 'E' and (resid 39 through 170 )E39 - 170
24X-RAY DIFFRACTION24chain 'E' and (resid 171 through 333 )E171 - 333
25X-RAY DIFFRACTION25chain 'F' and (resid 10 through 52 )F10 - 52
26X-RAY DIFFRACTION26chain 'F' and (resid 53 through 89 )F53 - 89
27X-RAY DIFFRACTION27chain 'F' and (resid 90 through 171 )F90 - 171
28X-RAY DIFFRACTION28chain 'F' and (resid 172 through 198 )F172 - 198
29X-RAY DIFFRACTION29chain 'F' and (resid 199 through 231 )F199 - 231
30X-RAY DIFFRACTION30chain 'F' and (resid 232 through 312 )F232 - 312
31X-RAY DIFFRACTION31chain 'F' and (resid 313 through 333 )F313 - 333

+
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://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