[English] 日本語
Yorodumi
- PDB-6n1c: Crystal structure of Inorganic pyrophosphatase from Legionella pn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n1c
TitleCrystal structure of Inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Inorganic Pyrophosphatase / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ALANINE / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase
D: Inorganic pyrophosphatase
E: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,94920
Polymers126,7336
Non-polymers1,21614
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15800 Å2
ΔGint-249 kcal/mol
Surface area37610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.080, 119.940, 74.900
Angle α, β, γ (deg.)90.000, 109.590, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 11 and (name N or name...
21(chain B and ((resid 11 and (name N or name...
31(chain C and (resid 11 or resid 13 through 40...
41(chain D and ((resid 11 and (name N or name...
51(chain E and ((resid 11 and (name N or name...
61(chain F and ((resid 11 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 11 and (name N or name...A11
121(chain A and ((resid 11 and (name N or name...A4 - 178
131(chain A and ((resid 11 and (name N or name...A4 - 178
141(chain A and ((resid 11 and (name N or name...A4 - 178
151(chain A and ((resid 11 and (name N or name...A4 - 178
211(chain B and ((resid 11 and (name N or name...B11
221(chain B and ((resid 11 and (name N or name...B5 - 202
231(chain B and ((resid 11 and (name N or name...B5 - 202
241(chain B and ((resid 11 and (name N or name...B5 - 202
251(chain B and ((resid 11 and (name N or name...B5 - 202
311(chain C and (resid 11 or resid 13 through 40...C11
321(chain C and (resid 11 or resid 13 through 40...C13 - 40
331(chain C and (resid 11 or resid 13 through 40...C42 - 45
341(chain C and (resid 11 or resid 13 through 40...C11 - 177
351(chain C and (resid 11 or resid 13 through 40...C11 - 177
361(chain C and (resid 11 or resid 13 through 40...C119
371(chain C and (resid 11 or resid 13 through 40...C11 - 177
381(chain C and (resid 11 or resid 13 through 40...C11 - 177
391(chain C and (resid 11 or resid 13 through 40...C11 - 177
411(chain D and ((resid 11 and (name N or name...D11
421(chain D and ((resid 11 and (name N or name...D6 - 176
431(chain D and ((resid 11 and (name N or name...D6 - 176
441(chain D and ((resid 11 and (name N or name...D6 - 176
451(chain D and ((resid 11 and (name N or name...D6 - 176
511(chain E and ((resid 11 and (name N or name...E11
521(chain E and ((resid 11 and (name N or name...E4 - 177
531(chain E and ((resid 11 and (name N or name...E4 - 177
541(chain E and ((resid 11 and (name N or name...E4 - 177
551(chain E and ((resid 11 and (name N or name...E4 - 177
611(chain F and ((resid 11 and (name N or name...F11
621(chain F and ((resid 11 and (name N or name...F6 - 203
631(chain F and ((resid 11 and (name N or name...F6 - 203
641(chain F and ((resid 11 and (name N or name...F6 - 203
651(chain F and ((resid 11 and (name N or name...F6 - 203

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Inorganic pyrophosphatase / / Pyrophosphate phospho-hydrolase / PPase


Mass: 21122.242 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: ppa, lpg2764 / Plasmid: LepnA.00023.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZRW2, inorganic diphosphatase

-
Non-polymers , 5 types, 494 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Molecular dimensions Morpheus screen, H12: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD: 20mM of each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM Bicine/Trizma base ...Details: Molecular dimensions Morpheus screen, H12: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD: 20mM of each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM Bicine/Trizma base pH 8.5: LepnA.00023.a.B1.PS38421 at 21.3mg/ml: cryo: direct: tray 299905h12: puck hgu1-7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 11, 2018
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40.967 Å / Num. obs: 71673 / % possible obs: 99.5 % / Redundancy: 6.018 % / Biso Wilson estimate: 43.609 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.053 / Χ2: 0.989 / Net I/σ(I): 19.31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.053.9940.6232.2552770.7850.71399.9
2.05-2.114.4090.4963.0851670.8720.56199.9
2.11-2.174.8140.3914.1349950.9250.43899.8
2.17-2.245.0860.2945.6448800.9570.32799.5
2.24-2.315.3940.2486.8247330.9720.27599.4
2.31-2.395.890.2088.4645570.9810.22899.4
2.39-2.486.6450.17210.7144160.9890.18799.4
2.48-2.586.8560.15711.4942380.9910.1799.5
2.58-2.76.8760.13213.3540430.9940.14399.5
2.7-2.836.9060.09617.3839000.9960.10399.6
2.83-2.986.920.06922.8236950.9980.07599.3
2.98-3.166.9330.05926.2534860.9980.06399.6
3.16-3.386.9240.04732.1133420.9990.05199.7
3.38-3.656.8540.03939.2330400.9990.04299.5
3.65-46.7160.03545.5128440.9990.03899.4
4-4.476.6960.0350.6625410.9990.03299.5
4.47-5.166.6680.02854.1622730.9990.0399.5
5.16-6.326.6990.02852.6719180.9990.03199.5
6.32-8.946.6930.02656.9315030.9990.02999.7
8.94-40.9676.2910.02460.18250.9990.02697.6

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3304)refinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
ARP/wARPmodel building
BUCCANEERmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4xel as per Morda

4xel


Resolution: 2→40.967 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.18
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 1980 2.76 %0
Rwork0.1934 ---
obs0.1945 71619 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.38 Å2 / Biso mean: 49.0626 Å2 / Biso min: 20.22 Å2
Refinement stepCycle: final / Resolution: 2→40.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7826 0 80 480 8386
Biso mean--61.22 46.77 -
Num. residues----1029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078186
X-RAY DIFFRACTIONf_angle_d0.8811213
X-RAY DIFFRACTIONf_dihedral_angle_d12.3214888
X-RAY DIFFRACTIONf_chiral_restr0.0631297
X-RAY DIFFRACTIONf_plane_restr0.0071435
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4229X-RAY DIFFRACTION8.287TORSIONAL
12B4229X-RAY DIFFRACTION8.287TORSIONAL
13C4229X-RAY DIFFRACTION8.287TORSIONAL
14D4229X-RAY DIFFRACTION8.287TORSIONAL
15E4229X-RAY DIFFRACTION8.287TORSIONAL
16F4229X-RAY DIFFRACTION8.287TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.2991230.260249565079100
2.05-2.10550.27561420.251649645106100
2.1055-2.16740.32631450.238649685113100
2.1674-2.23740.28341230.222949825105100
2.2374-2.31730.26531220.219750005122100
2.3173-2.41010.26491350.21749485083100
2.4101-2.51980.3191480.22074956510499
2.5198-2.65260.31121410.24054955509699
2.6526-2.81880.23331430.228449545097100
2.8188-3.03630.24741610.21574957511899
3.0363-3.34180.2681390.202349925131100
3.3418-3.8250.20851480.181749735121100
3.825-4.81790.17731670.149149695136100
4.8179-40.97540.21411430.171550655208100
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)
15.5295-2.7881-0.67326.1218-0.36712.6360.54-0.11780.79890.4025-0.3618-0.6911-1.1350.5824-0.12030.7836-0.16490.1890.7413-0.10680.468316.162434.380750.7932
25.4178-2.2693-2.5297.66093.38323.59030.10190.0438-0.22810.35740.1525-0.64240.35290.133-0.27160.1969-0.008-0.02670.217-0.00170.366925.21325.421735.3976
31.75311.0354-0.05922.93160.65442.88230.08450.10630.09310.2031-0.15210.24870.1901-0.21030.07540.1653-0.0110.06050.23180.0080.226513.021128.908734.2326
43.0919-0.23960.042.1703-0.00466.24140.53-0.649-0.1011.0317-0.25570.7690.6988-0.7732-0.27160.5114-0.12970.13260.30540.02810.33748.76224.191146.8031
52222-6.078920.5902-1.93542.66441.1895-1.30591.1677-2.282-3.99760.71610.86910.0795-0.21120.9563-0.23460.429420.49440.763224.2258
61.2189-0.1150.66915.88593.37242.3737-0.08240.19470.1826-1.0665-0.31790.1401-0.49790.4662-0.00421.3303-0.17260.0830.8784-0.30980.308928.475326.9412-9.7944
72.1857-0.957-1.38481.8221.72131.7604-0.10350.18450.0301-0.86080.04360.276-0.3585-0.08730.08060.5311-0.0461-0.07240.4091-0.08050.245218.426134.10647.6624
82.4524-2.6482-0.9524.2976-1.1053.5715-0.28311.1547-0.1574-0.81010.29540.7441-0.0715-0.5361-0.06690.927-0.1603-0.29280.7854-0.03770.376815.372529.018-6.2391
91.23850.7266-0.82412.20790.35892.2902-0.32130.4522-0.5517-0.64720.24140.09910.0746-0.26720.00050.4802-0.0939-0.02340.4886-0.15140.278420.546221.30753.3573
102.81752.3741-1.71235.2866-3.36712.171-0.12210.60450.2804-0.29650.1748-0.1226-1.27640.4726-0.07661.013-0.30550.02390.48060.05420.19641.819853.44882.2124
116.07720.11370.92416.5392-1.13975.6214-0.19120.7688-0.0097-1.22280.18910.14480.31050.107-0.07240.5749-0.20950.11550.4403-0.03540.385836.737738.83254.2955
121.94151.4497-0.12021.0411-0.05780.0663-0.36560.5217-0.5279-0.66310.3769-0.4626-0.05350.1193-0.03630.453-0.11760.13690.4075-0.10780.333841.198336.52346.6858
133.94192.1259-2.28454.71932.73089.3292-0.08561.001-0.4741-1.41710.0775-0.80210.37990.48070.06631.0331-0.27980.22090.9011-0.09260.396745.474546.6625-6.2009
141.56870.2455-0.53050.0633-0.23252.4725-0.32560.83110.07-1.0460.4218-0.2014-0.72630.6101-0.19240.7236-0.33050.27690.5743-0.10610.224745.962448.72946.7783
152.86841.5952-0.03414.1725-0.03440.92130.02350.19490.5043-0.44940.371-0.3816-0.81340.7332-0.34920.7504-0.30440.12020.5987-0.1170.37451.525856.747415.3278
161.7185-1.9468-1.24093.65740.23971.8918-0.03740.5758-0.4768-0.99270.3722-0.9234-0.21830.6255-0.18290.3522-0.02850.16310.6332-0.17620.612252.624336.176910.3179
170.87220.1504-0.04861.1096-0.12410.13260.0790.72710.3119-0.9210.1958-0.0075-0.71040.21330.06130.884-0.75480.75531.175-0.09220.269352.626451.0793-2.9769
18228.58972-7.221120.6933-2.8624.22141.8584-0.4516-1.6857-2.32910.6562-0.25991.03060.2328-0.19280.6578-0.15440.731938.151244.877822.2334
190.4501-0.35120.11771.34130.15274.9151-0.3108-0.08020.1208-0.3255-0.1404-0.0323-0.4701-0.22420.17081.0185-0.037-0.50470.65470.13360.92024.896252.81844.1854
206.9573-0.07251.10030.33890.35260.8605-0.22460.62970.2075-1.12230.11810.306-0.2399-0.02110.04360.67990.0048-0.16080.30690.00110.329623.980252.334610.263
213.50190.50330.87070.41530.27792.42760.09330.30950.1414-0.615-0.09690.0677-0.5031-0.02630.02610.53560.0185-0.10440.2401-0.00240.257626.906155.245615.7231
222.2336-1.65060.14492.1196-0.20313.4517-0.10090.23050.6315-1.1353-0.24970.1712-0.66320.07850.28420.65430.0022-0.23040.3279-0.01390.416516.506454.380810.3077
231.45351.59560.18923.93582.15681.75450.16350.12210.2706-1.0182-0.25091.1262-0.6584-0.33680.3190.66130.1306-0.32690.3199-0.04660.44212.993459.69715.6542
241.3546-1.3947-0.76671.63121.35062.16080.01550.24810.0142-0.3868-0.71131.4733-0.1064-0.5790.49520.35510.0696-0.19670.5464-0.15291.00573.904944.960418.1092
251.63930.64870.52985.24490.97411.7024-0.0851-0.31720.0897-0.5738-0.22260.6677-0.3922-0.16030.21110.45710.0659-0.07540.2843-0.03230.32418.860960.17124.9414
261.1320.04240.8902-0.0112-0.06891.4635-0.15620.2170.6583-1.1306-0.08961.2163-0.5073-0.15280.07561.01460.1846-0.55870.42210.06120.87278.896764.146310.8239
278.16391.70080.87272.4718-0.3043.120.0129-0.4997-0.63220.6072-0.0089-0.822-0.04840.2084-0.05420.319-0.0361-0.10580.2321-0.00430.41635.256343.115141.8772
282.57160.10610.26323.2863-0.21941.3977-0.0169-0.2305-0.0180.24720.0339-0.5213-0.20680.1261-0.00230.2252-0.047-0.05760.236-0.04480.316339.45153.721339.8489
295.72982.77461.73992.01771.99012.4664-0.0641-0.14561.2654-0.9175-0.4761-0.2305-0.35170.00230.3890.83890.1828-0.09670.4190.17831.326439.35669.705637.5401
300.3701-0.0029-0.79022.57090.2231.710.16760.014-0.44520.27650.1673-0.63720.07740.4648-0.26880.27180.0329-0.12460.3156-0.05310.806745.223328.065232.0661
311.7510.3259-0.58811.49750.36741.0339-0.00650.1142-0.61520.08510.0531-0.85540.10520.3290.00550.2960.0459-0.07530.3115-0.03820.869546.681618.119825.9143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 15 )A4 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 45 )A16 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 150 )A46 - 150
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 178 )A151 - 178
5X-RAY DIFFRACTION5chain 'A' and (resid 301 through 301 )A301
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 15 )B5 - 15
7X-RAY DIFFRACTION7chain 'B' and (resid 16 through 58 )B16 - 58
8X-RAY DIFFRACTION8chain 'B' and (resid 59 through 70 )B59 - 70
9X-RAY DIFFRACTION9chain 'B' and (resid 71 through 175 )B71 - 175
10X-RAY DIFFRACTION10chain 'C' and (resid 11 through 22 )C11 - 22
11X-RAY DIFFRACTION11chain 'C' and (resid 23 through 39 )C23 - 39
12X-RAY DIFFRACTION12chain 'C' and (resid 40 through 58 )C40 - 58
13X-RAY DIFFRACTION13chain 'C' and (resid 59 through 70 )C59 - 70
14X-RAY DIFFRACTION14chain 'C' and (resid 71 through 115 )C71 - 115
15X-RAY DIFFRACTION15chain 'C' and (resid 116 through 128 )C116 - 128
16X-RAY DIFFRACTION16chain 'C' and (resid 129 through 150 )C129 - 150
17X-RAY DIFFRACTION17chain 'C' and (resid 151 through 177 )C151 - 177
18X-RAY DIFFRACTION18chain 'C' and (resid 301 through 301 )C301
19X-RAY DIFFRACTION19chain 'D' and (resid 6 through 15 )D6 - 15
20X-RAY DIFFRACTION20chain 'D' and (resid 16 through 39 )D16 - 39
21X-RAY DIFFRACTION21chain 'D' and (resid 40 through 58 )D40 - 58
22X-RAY DIFFRACTION22chain 'D' and (resid 59 through 84 )D59 - 84
23X-RAY DIFFRACTION23chain 'D' and (resid 85 through 110 )D85 - 110
24X-RAY DIFFRACTION24chain 'D' and (resid 111 through 123 )D111 - 123
25X-RAY DIFFRACTION25chain 'D' and (resid 124 through 150 )D124 - 150
26X-RAY DIFFRACTION26chain 'D' and (resid 151 through 176 )D151 - 176
27X-RAY DIFFRACTION27chain 'E' and (resid 4 through 45 )E4 - 45
28X-RAY DIFFRACTION28chain 'E' and (resid 46 through 177 )E46 - 177
29X-RAY DIFFRACTION29chain 'F' and (resid 6 through 15 )F6 - 15
30X-RAY DIFFRACTION30chain 'F' and (resid 16 through 70 )F16 - 70
31X-RAY DIFFRACTION31chain 'F' and (resid 71 through 176 )F71 - 176

+
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