[English] 日本語
Yorodumi
- PDB-6esz: Crystal structure of PqsBC from Pseudomonas aeruginosa (crystal f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6esz
TitleCrystal structure of PqsBC from Pseudomonas aeruginosa (crystal form 1)
Components
  • PqsB
  • PqsC
KeywordsTRANSFERASE / Pseudomonas Quinolone Signal / FabH / HHQ
Function / homology
Function and homology information


2-heptyl-4(1H)-quinolone synthase / secondary metabolite biosynthetic process / acyltransferase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 2-heptyl-4(1H)-quinolone synthase subunit PqsC / 2-heptyl-4(1H)-quinolone synthase subunit PqsB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsWitzgall, F. / Blankenfeldt, W.
CitationJournal: Chembiochem / Year: 2018
Title: The Alkylquinolone Repertoire of Pseudomonas aeruginosa is Linked to Structural Flexibility of the FabH-like 2-Heptyl-3-hydroxy-4(1H)-quinolone (PQS) Biosynthesis Enzyme PqsBC.
Authors: Witzgall, F. / Depke, T. / Hoffmann, M. / Empting, M. / Bronstrup, M. / Muller, R. / Blankenfeldt, W.
History
DepositionOct 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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: PqsC
B: PqsB
C: PqsC
D: PqsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,58921
Polymers141,8354
Non-polymers1,75417
Water21,8341212
1
A: PqsC
B: PqsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,93312
Polymers70,9182
Non-polymers1,01510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-133 kcal/mol
Surface area23460 Å2
MethodPISA
2
C: PqsC
D: PqsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6569
Polymers70,9182
Non-polymers7397
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-94 kcal/mol
Surface area22990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.989, 142.384, 171.121
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid -5 and (name N or name...
21(chain C and (resid -5 through -3 or resid -1...
12(chain B and (resid 1 through 15 or resid 17...
22(chain D and (resid 1 through 15 or resid 17...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEULEULEU(chain A and ((resid -5 and (name N or name...AA-512
121HISHISCYSCYS(chain A and ((resid -5 and (name N or name...AA-10 - 3487 - 365
131HISHISCYSCYS(chain A and ((resid -5 and (name N or name...AA-10 - 3487 - 365
141HISHISCYSCYS(chain A and ((resid -5 and (name N or name...AA-10 - 3487 - 365
151HISHISCYSCYS(chain A and ((resid -5 and (name N or name...AA-10 - 3487 - 365
161HISHISCYSCYS(chain A and ((resid -5 and (name N or name...AA-10 - 3487 - 365
211LEULEUPHEPHE(chain C and (resid -5 through -3 or resid -1...CC-5 - -312 - 14
221GLYGLYPROPRO(chain C and (resid -5 through -3 or resid -1...CC-1 - 2316 - 40
231PHEPHEARGARG(chain C and (resid -5 through -3 or resid -1...CC25 - 6842 - 85
241SERSERTHRTHR(chain C and (resid -5 through -3 or resid -1...CC70 - 9087 - 107
251ALAALAASNASN(chain C and (resid -5 through -3 or resid -1...CC92 - 109109 - 126
261LEULEUSERSER(chain C and (resid -5 through -3 or resid -1...CC111 - 112128 - 129
271GLNGLNSERSER(chain C and (resid -5 through -3 or resid -1...CC114 - 125131 - 142
281METMETGLUGLU(chain C and (resid -5 through -3 or resid -1...CC127 - 128144 - 145
291ALAALASERSER(chain C and (resid -5 through -3 or resid -1...CC130 - 141147 - 158
2101ILEILEGLYGLY(chain C and (resid -5 through -3 or resid -1...CC143 - 176160 - 193
2111ALAALASERSER(chain C and (resid -5 through -3 or resid -1...CC178 - 228195 - 245
2121PHEPHESERSER(chain C and (resid -5 through -3 or resid -1...CC230 - 231247 - 248
2131LYSLYSPROPRO(chain C and (resid -5 through -3 or resid -1...CC236 - 242253 - 259
2141ASNASNALAALA(chain C and (resid -5 through -3 or resid -1...CC244 - 248261 - 265
2151ARGARGGLUGLU(chain C and (resid -5 through -3 or resid -1...CC250 - 254267 - 271
2161ALAALAVALVAL(chain C and (resid -5 through -3 or resid -1...CC256 - 276273 - 293
2171ALAALAPROPRO(chain C and (resid -5 through -3 or resid -1...CC278 - 287295 - 304
2181GLNGLNMETMET(chain C and (resid -5 through -3 or resid -1...CC289 - 310306 - 327
2191GLYGLYLEULEU(chain C and (resid -5 through -3 or resid -1...CC312 - 313329 - 330
2201GLUGLUASPASP(chain C and (resid -5 through -3 or resid -1...CC315 - 322332 - 339
2211ILEILECYSCYS(chain C and (resid -5 through -3 or resid -1...CC324 - 348341 - 365
112METMETVALVAL(chain B and (resid 1 through 15 or resid 17...BB1 - 151 - 15
122LEULEULEULEU(chain B and (resid 1 through 15 or resid 17...BB1717
132GLYGLYASPASP(chain B and (resid 1 through 15 or resid 17...BB19 - 3119 - 31
142METMETLEULEU(chain B and (resid 1 through 15 or resid 17...BB33 - 4633 - 46
152GLUGLUVALVAL(chain B and (resid 1 through 15 or resid 17...BB48 - 5148 - 51
162PROPROPROPRO(chain B and (resid 1 through 15 or resid 17...BB5353
172GLUGLUGLUGLU(chain B and (resid 1 through 15 or resid 17...BB5555
182ASPASPILEILE(chain B and (resid 1 through 15 or resid 17...BB57 - 7057 - 70
192ASNASNALAALA(chain B and (resid 1 through 15 or resid 17...BB72 - 7772 - 77
1102LYSLYSSERSER(chain B and (resid 1 through 15 or resid 17...BB79 - 10279 - 102
1112ALAALAASPASP(chain B and (resid 1 through 15 or resid 17...BB104 - 116104 - 116
1122GLYGLYASNASN(chain B and (resid 1 through 15 or resid 17...BB118 - 121118 - 121
1132VALVALVALVAL(chain B and (resid 1 through 15 or resid 17...BB124 - 125124 - 125
1142GLYGLYASPASP(chain B and (resid 1 through 15 or resid 17...BB127 - 136127 - 136
1152SERSERGLYGLY(chain B and (resid 1 through 15 or resid 17...BB139 - 156139 - 156
1162ALAALAILEILE(chain B and (resid 1 through 15 or resid 17...BB158 - 184158 - 184
1172GLNGLNPROPRO(chain B and (resid 1 through 15 or resid 17...BB186 - 203186 - 203
1182ALAALAVALVAL(chain B and (resid 1 through 15 or resid 17...BB205 - 206205 - 206
1192ALAALAVALVAL(chain B and (resid 1 through 15 or resid 17...BB208 - 223208 - 223
1202GLUGLUGLUGLU(chain B and (resid 1 through 15 or resid 17...BB225225
1212TRPTRPGLYGLY(chain B and (resid 1 through 15 or resid 17...BB227 - 239227 - 239
1222PHEPHEALAALA(chain B and (resid 1 through 15 or resid 17...BB241 - 250241 - 250
1232ARGARGGLYGLY(chain B and (resid 1 through 15 or resid 17...BB252 - 279252 - 279
212METMETVALVAL(chain D and (resid 1 through 15 or resid 17...DD1 - 151 - 15
222LEULEULEULEU(chain D and (resid 1 through 15 or resid 17...DD1717
232GLYGLYASPASP(chain D and (resid 1 through 15 or resid 17...DD19 - 3119 - 31
242METMETLEULEU(chain D and (resid 1 through 15 or resid 17...DD33 - 4633 - 46
252GLUGLUVALVAL(chain D and (resid 1 through 15 or resid 17...DD48 - 5148 - 51
262PROPROPROPRO(chain D and (resid 1 through 15 or resid 17...DD5353
272GLUGLUGLUGLU(chain D and (resid 1 through 15 or resid 17...DD5555
282ASPASPILEILE(chain D and (resid 1 through 15 or resid 17...DD57 - 7057 - 70
292ASNASNALAALA(chain D and (resid 1 through 15 or resid 17...DD72 - 7772 - 77
2102LYSLYSSERSER(chain D and (resid 1 through 15 or resid 17...DD79 - 10279 - 102
2112ALAALAASPASP(chain D and (resid 1 through 15 or resid 17...DD104 - 116104 - 116
2122GLYGLYTYRTYR(chain D and (resid 1 through 15 or resid 17...DD118 - 119118 - 119
2132ARGARGARGARG(chain D and (resid 1 through 15 or resid 17...DD120120
2142METMETALAALA(chain D and (resid 1 through 15 or resid 17...DD1 - 2831 - 283
2152METMETALAALA(chain D and (resid 1 through 15 or resid 17...DD1 - 2831 - 283
2162METMETALAALA(chain D and (resid 1 through 15 or resid 17...DD1 - 2831 - 283
2172METMETALAALA(chain D and (resid 1 through 15 or resid 17...DD1 - 2831 - 283
2182METMETALAALA(chain D and (resid 1 through 15 or resid 17...DD1 - 2831 - 283
2192METMETALAALA(chain D and (resid 1 through 15 or resid 17...DD1 - 2831 - 283

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein PqsC


Mass: 40385.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pqsC, PA0998 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4X1
#2: Protein PqsB


Mass: 30531.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pqsB, PA0997 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4X2

-
Non-polymers , 4 types, 1229 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1212 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.1 M Bis-Tris (pH 6.6), 0.2 M Lithium sulfate, 16% PEG 3350, 5% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→47.46 Å / Num. obs: 132059 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 19.37 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.044 / Rrim(I) all: 0.128 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.84-1.877.91.06665390.8060.4041.142100
10.08-47.467.30.0279290.9990.0110.02999.2

-
Processing

Software
NameVersionClassification
PHENIXdev_2875refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.22data extraction
Cootmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ET1
Resolution: 1.84→47.343 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.34
RfactorNum. reflection% reflection
Rfree0.1786 6454 4.89 %
Rwork0.1495 --
obs0.151 131871 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.54 Å2 / Biso mean: 33.2446 Å2 / Biso min: 11.56 Å2
Refinement stepCycle: final / Resolution: 1.84→47.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9721 0 182 1212 11115
Biso mean--62.39 39.87 -
Num. residues----1271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710400
X-RAY DIFFRACTIONf_angle_d0.82914225
X-RAY DIFFRACTIONf_chiral_restr0.0541578
X-RAY DIFFRACTIONf_plane_restr0.0061875
X-RAY DIFFRACTIONf_dihedral_angle_d14.4526391
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3788X-RAY DIFFRACTION5.264TORSIONAL
12C3788X-RAY DIFFRACTION5.264TORSIONAL
21B2818X-RAY DIFFRACTION5.264TORSIONAL
22D2818X-RAY DIFFRACTION5.264TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.86090.32332310.263541364367100
1.8609-1.88280.29412050.245741494354100
1.8828-1.90580.27662390.25674067430699
1.9058-1.92990.31542120.27574121433399
1.9299-1.95530.25761670.23441694336100
1.9553-1.98210.2481960.199641354331100
1.9821-2.01040.2282230.184941834406100
2.0104-2.04040.22462080.182941144322100
2.0404-2.07230.25092030.197941834386100
2.0723-2.10630.22292200.170240844304100
2.1063-2.14260.20831970.152641934390100
2.1426-2.18150.17222510.152140734324100
2.1815-2.22350.1742140.150142034417100
2.2235-2.26890.25512320.187740754307100
2.2689-2.31820.19422420.146341544396100
2.3182-2.37210.18152080.138241364344100
2.3721-2.43150.16662130.137841854398100
2.4315-2.49720.18722060.136541814387100
2.4972-2.57070.19652220.134641554377100
2.5707-2.65360.19431910.136341924383100
2.6536-2.74850.1552030.13341964399100
2.7485-2.85850.16312330.130341684401100
2.8585-2.98860.1432190.138341954414100
2.9886-3.14610.17381960.136342224418100
3.1461-3.34320.15662180.135941864404100
3.3432-3.60120.15831960.128642584454100
3.6012-3.96350.13862330.120542254458100
3.9635-4.53660.11952370.105142424479100
4.5366-5.71410.13452170.118543394556100
5.7141-47.35830.1922220.184444984720100
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)
10.80081.0653-0.58334.2978-2.36071.9303-0.04630.10520.022-0.06310.28550.33230.1689-0.1736-0.27860.1695-0.0334-0.01930.2305-0.02020.1517-32.9912-33.333315.3655
20.89310.09730.18290.86420.24010.9856-0.0230.0619-0.0552-0.01950.03150.03670.1080.0106-0.01280.1728-0.0260.00630.1697-0.02270.1454-29.4226-29.245517.6636
31.0127-0.80370.51621.4224-0.12392.422-0.1407-0.03570.11450.11390.086-0.0833-0.24110.19780.06850.1442-0.07860.01680.1733-0.02950.1564-15.9492-5.389939.2403
43.2789-3.31473.90133.7541-4.68056.323-0.154-0.15570.22190.26360.0462-0.0529-0.3396-0.15630.08690.2177-0.01490.0260.189-0.05630.1724-29.1175-5.991839.1899
50.76810.31220.67331.9862-1.48633.39710.0377-0.0980.07230.08180.10820.2614-0.0615-0.2178-0.15310.1771-0.01540.0230.2032-0.02450.1919-31.7527-14.0133.0734
61.9709-1.8758-2.20873.21591.58273.86270.0811-0.0341-0.02-0.0085-0.14750.257-0.1671-0.31330.07630.1511-0.02850.00180.1387-0.02650.1413-32.538-13.768727.1752
70.43270.31180.21971.0213-0.12372.2465-0.053-0.00330.0781-0.02150.02410.0036-0.15480.09960.02930.1521-0.0360.00570.1865-0.02020.1564-22.1798-11.606527.0226
84.74590.0412.19110.37781.11373.9594-0.2132-0.10230.06440.13230.09090.0193-0.4445-0.05260.17660.1266-0.07280.03390.1212-0.03120.1243-19.6969-7.888633.2121
91.93980.3847-0.3231.7249-0.89932.7616-0.08590.16610.0943-0.2496-0.03-0.36680.16320.57170.12860.2217-0.0480.0550.3121-0.08270.1801-6.9115-11.673621.3127
108.48283.387-3.09253.8084-0.6442.90660.0058-0.5461-0.26450.1686-0.1887-0.15180.36170.41270.18690.20670.0265-0.03690.241-0.00130.1215-13.4338-25.778341.8348
113.4258-3.54133.50399.0048-7.48356.3346-0.04580.19250.28630.0541-0.1398-0.38-0.35490.59040.2890.1781-0.12290.05230.402-0.05740.2251-3.146-4.98624.5825
121.8806-0.0210.20232.1134-2.25544.38730.0454-0.13740.17050.1233-0.0382-0.0297-0.47780.52480.03210.2225-0.10440.02550.29-0.04160.2018-8.283-1.71832.477
133.9288-2.3594-0.09819.4514-1.34294.75510.07870.02980.404-0.04930.08260.2232-0.6118-0.0804-0.16450.1983-0.0930.01070.2021-0.00920.1941-16.252.043827.632
146.3306-4.98513.15057.8065-5.37296.3524-0.10750.17360.3439-0.15310.0167-0.191-0.15010.11440.09340.1462-0.1057-0.01030.2142-0.050.1267-14.1151-6.702522.8018
152.69160.8525-2.1960.9363-0.74482.61740.2678-0.21520.08590.0892-0.2008-0.1349-0.26750.1583-0.03880.1696-0.0805-0.03520.28860.02520.22220.765615.7873-6.1305
162.8756-1.0981.71145.9147-1.85468.15990.1453-0.2807-0.6412-0.084-0.195-0.39420.09750.5070.09260.1182-0.0352-0.04540.24560.05920.333519.9009-0.6498-9.3354
172.18760.57860.02150.7144-0.06581.29040.1381-0.3901-0.09660.1059-0.1647-0.1134-0.04920.0690.0280.1356-0.0544-0.01190.2380.02410.18768.86548.3768-6.7586
184.17871.05910.38072.62260.79691.99620.17430.26930.9765-0.4991-0.1736-0.5203-0.8464-0.0354-0.0280.391-0.07350.04590.35970.09290.505613.649426.0173-23.6749
191.50480.36460.29440.82120.17081.86830.2336-0.76060.25190.2023-0.2042-0.1376-0.24040.12940.00510.2639-0.1684-0.01260.5217-0.08330.264716.72620.6925.038
201.67380.44630.1880.60910.16631.20820.0493-0.20190.30050.0185-0.05050.0761-0.2106-0.0780.00550.1534-0.0110.01410.1509-0.02660.1789-9.230816.9627-13.8239
211.85470.75460.75541.29960.16720.72830.0728-0.19270.17370.0216-0.03050.0433-0.0989-0.0597-0.01640.1054-0.01970.00170.15140.00920.1422-8.816611.5749-14.9721
222.27850.4618-0.81381.1408-0.26342.2609-0.04360.0137-0.1878-0.09030.0032-0.02660.21370.02990.04680.1098-0.0014-0.02770.11210.01850.1633-6.0767-1.7792-17.7669
231.24810.4724-1.52722.4268-1.5294.20580.0308-0.091-0.0403-0.1830.10360.18690.1471-0.5527-0.1430.1263-0.0643-0.02790.22770.04150.1957-19.8509-0.0442-15.8559
245.0229-1.7239-0.84782.8170.27391.48820.0038-0.43160.15270.09560.10240.1601-0.0568-0.1492-0.11010.1293-0.0341-0.00810.23650.00350.1623-21.0766.7392-8.061
252.798-0.0633-0.16253.8063-0.70863.5426-0.1215-0.50350.0530.4443-0.03030.4796-0.1992-0.27870.16010.1052-0.0605-0.04130.234-0.02760.1945-15.27014.99-4.0669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -10 through 45 )A-10 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 348 )A46 - 348
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 26 )B1 - 26
4X-RAY DIFFRACTION4chain 'B' and (resid 27 through 49 )B27 - 49
5X-RAY DIFFRACTION5chain 'B' and (resid 50 through 80 )B50 - 80
6X-RAY DIFFRACTION6chain 'B' and (resid 81 through 102 )B81 - 102
7X-RAY DIFFRACTION7chain 'B' and (resid 103 through 138 )B103 - 138
8X-RAY DIFFRACTION8chain 'B' and (resid 139 through 153 )B139 - 153
9X-RAY DIFFRACTION9chain 'B' and (resid 154 through 176 )B154 - 176
10X-RAY DIFFRACTION10chain 'B' and (resid 177 through 201 )B177 - 201
11X-RAY DIFFRACTION11chain 'B' and (resid 202 through 217 )B202 - 217
12X-RAY DIFFRACTION12chain 'B' and (resid 218 through 238 )B218 - 238
13X-RAY DIFFRACTION13chain 'B' and (resid 239 through 264 )B239 - 264
14X-RAY DIFFRACTION14chain 'B' and (resid 265 through 279 )B265 - 279
15X-RAY DIFFRACTION15chain 'C' and (resid -5 through 48 )C-5 - 48
16X-RAY DIFFRACTION16chain 'C' and (resid 49 through 69 )C49 - 69
17X-RAY DIFFRACTION17chain 'C' and (resid 70 through 212 )C70 - 212
18X-RAY DIFFRACTION18chain 'C' and (resid 213 through 239 )C213 - 239
19X-RAY DIFFRACTION19chain 'C' and (resid 240 through 348 )C240 - 348
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 116 )D1 - 116
21X-RAY DIFFRACTION21chain 'D' and (resid 117 through 153 )D117 - 153
22X-RAY DIFFRACTION22chain 'D' and (resid 154 through 217 )D154 - 217
23X-RAY DIFFRACTION23chain 'D' and (resid 218 through 238 )D218 - 238
24X-RAY DIFFRACTION24chain 'D' and (resid 239 through 264 )D239 - 264
25X-RAY DIFFRACTION25chain 'D' and (resid 265 through 283 )D265 - 283

+
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