[English] 日本語
Yorodumi
- PDB-5ts2: Crystal structure of a phosphopantetheine adenylyltransferase (Co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ts2
TitleCrystal structure of a phosphopantetheine adenylyltransferase (CoaD, PPAT) from Pseudomonas aeruginosa bound to dephospho coenzyme A
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / structural genomics / coenzyme A biosynthesis / PPAT / CoaD / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


[citrate (pro-3S)-lyase] ligase activity / pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Citrate lyase ligase, C-terminal / Citrate lyase ligase C-terminal domain / Phosphopantetheine adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DEPHOSPHO COENZYME A / Phosphopantetheine adenylyltransferase / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a phosphopantetheine adenylyltransferase (CoaD, PPAT) from Pseudomonas aeruginosa bound to dephospho coenzyme A
Authors: Edwards, T.E. / Davies, D.R. / Fairman, J.W. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionOct 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 4, 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 / struct_ncs_dom_lim
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
E: Phosphopantetheine adenylyltransferase
F: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,55525
Polymers112,9606
Non-polymers4,59519
Water3,405189
1
A: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1758
Polymers37,6532
Non-polymers1,5226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-58 kcal/mol
Surface area15110 Å2
2
B: Phosphopantetheine adenylyltransferase
E: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1758
Polymers37,6532
Non-polymers1,5226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-65 kcal/mol
Surface area15040 Å2
3
C: Phosphopantetheine adenylyltransferase
F: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2069
Polymers37,6532
Non-polymers1,5527
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-79 kcal/mol
Surface area15040 Å2
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25250 Å2
ΔGint-307 kcal/mol
Surface area35950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.380, 101.350, 105.710
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 1 and (name N or name...
21(chain B and ((resid 1 and (name N or name...
31(chain C and ((resid 1 and (name N or name...
41(chain D and ((resid 1 and (name N or name...
51(chain E and ((resid 1 and (name N or name...
61(chain F and (resid 1 through 29 or resid 31...

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
11METMETMETMET(chain A and ((resid 1 and (name N or name...AA19
12ALAALALYSLYS(chain A and ((resid 1 and (name N or name...AA-6 - 1582 - 166
13ALAALALYSLYS(chain A and ((resid 1 and (name N or name...AA-6 - 1582 - 166
14ALAALALYSLYS(chain A and ((resid 1 and (name N or name...AA-6 - 1582 - 166
15ALAALALYSLYS(chain A and ((resid 1 and (name N or name...AA-6 - 1582 - 166
21METMETMETMET(chain B and ((resid 1 and (name N or name...BB19
22METMETLYSLYS(chain B and ((resid 1 and (name N or name...BB1 - 1589 - 166
23METMETLYSLYS(chain B and ((resid 1 and (name N or name...BB1 - 1589 - 166
24METMETLYSLYS(chain B and ((resid 1 and (name N or name...BB1 - 1589 - 166
25METMETLYSLYS(chain B and ((resid 1 and (name N or name...BB1 - 1589 - 166
31METMETMETMET(chain C and ((resid 1 and (name N or name...CC19
32ALAALALYSLYS(chain C and ((resid 1 and (name N or name...CC-6 - 1582 - 166
33ALAALALYSLYS(chain C and ((resid 1 and (name N or name...CC-6 - 1582 - 166
34ALAALALYSLYS(chain C and ((resid 1 and (name N or name...CC-6 - 1582 - 166
35ALAALALYSLYS(chain C and ((resid 1 and (name N or name...CC-6 - 1582 - 166
41METMETMETMET(chain D and ((resid 1 and (name N or name...DD19
42HISHISPHEPHE(chain D and ((resid 1 and (name N or name...DD-1 - 1577 - 165
43HISHISPHEPHE(chain D and ((resid 1 and (name N or name...DD-1 - 1577 - 165
44HISHISPHEPHE(chain D and ((resid 1 and (name N or name...DD-1 - 1577 - 165
45HISHISPHEPHE(chain D and ((resid 1 and (name N or name...DD-1 - 1577 - 165
51METMETMETMET(chain E and ((resid 1 and (name N or name...EE19
52ALAALACODCOD(chain E and ((resid 1 and (name N or name...EE - T-6 - 2012
53ALAALACODCOD(chain E and ((resid 1 and (name N or name...EE - T-6 - 2012
54ALAALACODCOD(chain E and ((resid 1 and (name N or name...EE - T-6 - 2012
55ALAALACODCOD(chain E and ((resid 1 and (name N or name...EE - T-6 - 2012
61METMETASPASP(chain F and (resid 1 through 29 or resid 31...FF1 - 299 - 37
62VALVALILEILE(chain F and (resid 1 through 29 or resid 31...FF31 - 3239 - 40
63ALAALAPROPRO(chain F and (resid 1 through 29 or resid 31...FF34 - 3942 - 47
64LYSLYSASNASN(chain F and (resid 1 through 29 or resid 31...FF40 - 4248 - 50
65HISHISLYSLYS(chain F and (resid 1 through 29 or resid 31...FF0 - 1588 - 166
66HISHISLYSLYS(chain F and (resid 1 through 29 or resid 31...FF0 - 1588 - 166
67HISHISLYSLYS(chain F and (resid 1 through 29 or resid 31...FF0 - 1588 - 166
68HISHISLYSLYS(chain F and (resid 1 through 29 or resid 31...FF0 - 1588 - 166

-
Components

#1: Protein
Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT


Mass: 18826.633 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain LESB58) (bacteria)
Strain: LESB58 / Gene: coaD, PLES_03601 / Production host: Escherichia coli (E. coli)
References: UniProt: B7V2S6, UniProt: Q9I6D1*PLUS, pantetheine-phosphate adenylyltransferase
#2: Chemical
ChemComp-COD / DEPHOSPHO COENZYME A


Mass: 687.554 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H35N7O13P2S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PsaeA.00960.a.B1 batch PS02167 at 18.6 against MCSG1 screen condition E9 0.2 M CaCl2, 20% PEG 3350 supplemented with 20% ethylene glycol, 2 mM MgCl, and 2 mM ATP in the cryo-protectant, ...Details: PsaeA.00960.a.B1 batch PS02167 at 18.6 against MCSG1 screen condition E9 0.2 M CaCl2, 20% PEG 3350 supplemented with 20% ethylene glycol, 2 mM MgCl, and 2 mM ATP in the cryo-protectant, crystal tracking ID 259488e9, unique puck ID sls7-3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→46.865 Å / Num. obs: 46486 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 43.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.63
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.3-2.360.5073.020.824199
2.36-2.420.4113.70.867198.8
2.42-2.490.364.30.9198.7
2.49-2.570.2795.380.927198.4
2.57-2.660.2276.550.951198
2.66-2.750.1877.80.969198.5
2.75-2.850.13910.250.984198.3
2.85-2.970.1112.60.989197.6
2.97-3.10.08315.90.993198
3.1-3.250.07217.970.995197.6
3.25-3.430.05622.340.997197.5
3.43-3.640.04626.080.998196.8
3.64-3.890.04229.340.998197.2
3.89-4.20.03732.660.998196.8
4.2-4.60.03535.170.998196.4
4.6-5.140.03436.760.998195.6
5.14-5.940.03634.970.998195.6
5.94-7.270.03236.170.999194.9
7.27-10.290.02941.560.999193.7
10.290.02740.410.998188.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3k9w
Resolution: 2.3→46.865 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.4
RfactorNum. reflection% reflection
Rfree0.2444 2158 4.65 %
Rwork0.1804 --
obs0.1834 46437 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.28 Å2 / Biso mean: 51.2273 Å2 / Biso min: 20.98 Å2
Refinement stepCycle: final / Resolution: 2.3→46.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7501 0 277 189 7967
Biso mean--69.12 47.07 -
Num. residues----971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087988
X-RAY DIFFRACTIONf_angle_d1.01410896
X-RAY DIFFRACTIONf_chiral_restr0.0571231
X-RAY DIFFRACTIONf_plane_restr0.0071388
X-RAY DIFFRACTIONf_dihedral_angle_d14.394652
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4085X-RAY DIFFRACTION11.1TORSIONAL
12B4085X-RAY DIFFRACTION11.1TORSIONAL
13C4085X-RAY DIFFRACTION11.1TORSIONAL
14D4085X-RAY DIFFRACTION11.1TORSIONAL
15E4085X-RAY DIFFRACTION11.1TORSIONAL
16F4085X-RAY DIFFRACTION11.1TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3002-2.35370.30231830.22852921310499
2.3537-2.41260.3251470.23582931307899
2.4126-2.47780.30131380.2252953309199
2.4778-2.55070.30281340.22312925305999
2.5507-2.6330.2971340.22992971310599
2.633-2.72710.31081440.23722950309498
2.7271-2.83630.31881170.22352965308298
2.8363-2.96530.29291240.222953307798
2.9653-3.12170.30541360.21252955309198
3.1217-3.31720.26571060.21692988309498
3.3172-3.57320.25331490.1932929307897
3.5732-3.93270.22611920.16482913310597
3.9327-4.50130.18291620.14222940310297
4.5013-5.66960.19751700.13572936310696
5.6696-46.87460.23321220.14993049317194
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)
19.26254.18624.10741.75431.12052.98220.07070.4236-0.24540.03180.1986-0.10490.1647-0.054-0.28540.3868-0.04140.05660.4032-0.0940.4234-1.824435.3518-22.3685
23.55552.06334.14812.39811.6435.29980.01580.3093-0.15380.26470.0865-0.26690.98810.5347-0.18380.3928-0.01190.15610.407-0.12010.54547.260831.9384-14.4447
36.85441.80742.00316.90683.16855.671-0.39960.08850.678-1.18260.23270.2021-0.84310.21850.13490.5116-0.08440.15670.3761-0.07360.47478.722544.4644-21.6425
45.0594-0.21430.04254.527-1.34511.66610.00040.6752-0.1651-0.67830.1312-0.7616-0.31590.4158-0.14750.4623-0.09610.14510.4399-0.16540.37178.792841.4847-25.2597
56.2106-0.52714.75457.5004-3.29626.7544-0.5061-0.47040.44860.1324-0.107-0.8416-0.88990.30640.5980.35260.02280.07210.513-0.03970.4608-0.116241.5098-14.9697
64.62540.00214.47716.5940.30154.44690.3863-0.79480.0208-0.1453-0.1981-0.6897-0.087-1.0178-0.20140.52550.0142-0.0050.4242-0.04030.5258-6.11249.5697-12.4775
74.8705-1.98683.77825.9054-4.53844.61580.142-0.1214-0.4641-0.59940.06850.36840.3532-0.2874-0.16560.4740.0382-0.03640.4027-0.04970.334-7.304740.6856-17.42
83.18072.30882.11293.158-1.18326.57930.3496-0.37340.8043-0.3172-0.3081-0.6917-0.3334-0.4567-0.19230.5409-0.04170.01360.4091-0.0470.630710.090136.2255-4.8767
96.1549-4.32143.23233.2726-1.1868.8961-0.47450.2454-0.16990.03560.7278-0.2309-0.7465-0.4491-0.10360.4458-0.04870.11690.253-0.03260.581419.404348.2323-7.7518
104.3096-2.32442.81163.03662.11489.19980.03650.5436-0.7823-0.35320.4672-0.75910.10960.2814-0.51810.3599-0.08130.0980.4748-0.07870.713124.691942.2516-12.3432
117.03142.0489-2.97623.2912.83516.4311-0.4716-0.25940.6793-0.29610.0061-0.5502-0.2021-0.13120.36810.42120.1187-0.01480.2808-0.11530.4382-22.884557.722217.1733
126.035-2.28392.02052.67931.13752.6936-0.0802-0.22010.61770.62550.0545-0.8154-0.55870.48520.05420.47490.1441-0.04260.4636-0.06850.3327-15.494464.1319.1757
134.1219-0.64291.80576.65-4.37095.4745-0.1552-0.4924-0.52780.04240.16560.42980.1923-0.1717-0.04790.4280.16330.09820.4256-0.03820.4211-24.985352.929322.7203
144.87320.4681.83052.52331.13363.5216-0.1841-0.0094-0.10280.1913-0.00540.0937-0.00740.02980.25910.34680.13650.02040.3554-0.01280.3907-24.891157.252313.7128
156.63221.58463.70854.43922.87165.7169-0.23660.0321-0.2792-0.12410.2579-0.1359-0.10840.2233-0.04880.41890.05090.08050.39240.00370.3832-16.593754.4447.037
166.5213-2.74393.57685.2826-0.77136.643-0.7071-0.9074-0.00771.05120.5518-0.09840.106-0.080.14840.51490.1850.03350.55990.02510.3614-12.695248.515231.5559
170.4165-1.23250.60845.2872-6.7417.1644-0.1683-0.00620.14440.262-0.2396-1.1917-0.50290.36360.44090.5506-0.0152-0.10120.30640.02510.507222.787947.374416.9719
183.5228-0.9882-0.95857.6387-1.76692.0075-0.0749-0.01180.0095-0.0209-0.041-0.3932-0.686-0.14920.16650.5454-0.0485-0.12610.2916-0.04310.362419.425357.806912.5167
191.19360.4272-0.56223.18571.40573.87610.0147-0.1034-0.0999-0.15590.0812-0.4418-0.5920.2182-0.13380.5109-0.0838-0.09050.3589-0.00330.603126.450357.974811.46
208.787-1.4048-0.79023.36483.08587.9271-0.13820.24170.04560.0245-0.02430.1076-0.2274-0.53190.15060.3239-0.0664-0.01710.26750.1040.417215.518645.48977.7439
213.7065-1.01421.83218.1325-2.92883.614-0.4059-0.22020.29610.00240.2157-0.3378-0.4928-0.14240.19320.68020.04330.02120.3547-0.04480.357310.672269.702410.3962
224.056-0.4399-2.00644.9045-0.58958.5862-0.2906-0.0049-0.5758-0.0961-0.0864-0.00650.48810.63960.34740.19210.0207-0.03190.2949-0.06890.3644-15.153427.3895-9.2135
235.8198-0.6586-4.60135.53651.2313.76770.1541-0.0340.1169-0.2526-0.12810.1372-0.9763-0.26170.00460.31250.0288-0.07950.3339-0.04570.3364-17.332335.7746-14.0217
244.3865-0.3573-2.55624.79340.35732.8106-0.13710.0343-0.21420.3814-0.10650.68860.3598-0.23760.29020.2847-0.01920.01080.273-0.07480.3479-21.592426.2893-3.7956
253.0715-1.90812.17471.5614-1.17463.61750.0348-0.0961-0.3842-0.1654-0.08630.15690.2608-0.4697-0.02840.2857-0.0569-0.01230.2938-0.03490.3783-15.356921.5213-7.7863
261.80190.72260.9612.3038-0.26642.7637-0.1658-0.06540.35140.93310.35570.118-0.06010.17650.02030.31980.0297-0.0150.3409-0.0040.3966-8.841731.628-6.4853
274.2101-0.76881.40967.4532-2.48054.036-0.1490.02520.11840.4306-0.0287-0.4921-0.22460.03760.1980.2262-0.0564-0.05330.40980.01170.4188-1.932230.4547-2.6049
287.9272-1.1532-0.11364.15150.68144.27470.1141-0.024-0.1216-0.0241-0.46620.4045-0.4209-0.37530.3560.30380.0201-0.03480.313-0.1040.4342-26.905440.1245-1.1332
291.3494-0.0856-1.36491.58711.1454.78470.1490.0393-0.1038-0.4474-0.08560.0582-0.6236-0.2033-0.12930.52240.08380.00380.2748-0.01310.3487-13.42571.4616-1.5723
302.47690.09890.35160.5497-0.32653.01830.06120.18920.0916-0.25-0.0554-0.0556-0.3348-0.0190.01020.7730.0894-0.00850.2936-0.00680.3824-9.673173.5296-3.4978
317.7722.31954.27893.5925-1.07083.94420.03090.0592-0.37770.2446-0.2058-0.0137-0.1160.2170.01230.48880.07990.01510.36920.01960.3496-5.040265.08518.2539
325.3318-1.8923-3.03492.0929-0.48727.74760.07660.00230.1066-0.0711-0.44280.2244-0.71310.27140.39710.7192-0.0613-0.08570.3663-0.0160.3126-8.104361.9908-18.5305
336.03982.9099-0.15744.97460.57685.63770.2511-0.1052-0.02730.2021-0.1639-0.01480.077-0.4203-0.09680.25710.0822-0.04890.36420.01940.26996.947630.892522.505
346.4104-1.57641.74443.5762-2.06013.86490.109-0.5172-0.43950.6270.1038-0.0746-0.1636-0.0301-0.19740.4170.0333-0.10920.55320.08440.32227.333334.03530.0085
354.3162-0.86934.22462.8061-0.95394.30050.74410.7409-0.6216-0.6841-0.21970.23970.597-0.6549-0.47820.5530.0857-0.09530.5933-0.00570.46456.308340.821919.3677
364.81984.30594.65494.12294.35094.8327-0.69260.44380.3454-0.70360.43440.024-1.731-0.49130.37970.71390.1694-0.06840.6072-0.02630.5202-0.524848.298920.4685
374.6614-0.4636-2.12987.03545.77925.908-0.22910.46230.2369-0.42030.40190.0417-0.21380.2772-0.13260.39490.0528-0.02870.40210.13050.28978.286239.631615.1251
388.7755-1.9835.06696.5419-1.45375.72930.4694-0.2651-0.86220.27910.11570.34530.6679-0.2587-0.5530.4463-0.1139-0.01290.40170.00410.3911-1.076519.345412.1541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -6 through 14 )A-6 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 27 )A15 - 27
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 46 )A28 - 46
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 79 )A47 - 79
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 94 )A80 - 94
6X-RAY DIFFRACTION6chain 'A' and (resid 95 through 108 )A95 - 108
7X-RAY DIFFRACTION7chain 'A' and (resid 109 through 117 )A109 - 117
8X-RAY DIFFRACTION8chain 'A' and (resid 118 through 127 )A118 - 127
9X-RAY DIFFRACTION9chain 'A' and (resid 128 through 136 )A128 - 136
10X-RAY DIFFRACTION10chain 'A' and (resid 137 through 158 )A137 - 158
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 14 )B1 - 14
12X-RAY DIFFRACTION12chain 'B' and (resid 15 through 27 )B15 - 27
13X-RAY DIFFRACTION13chain 'B' and (resid 28 through 58 )B28 - 58
14X-RAY DIFFRACTION14chain 'B' and (resid 59 through 94 )B59 - 94
15X-RAY DIFFRACTION15chain 'B' and (resid 95 through 127 )B95 - 127
16X-RAY DIFFRACTION16chain 'B' and (resid 128 through 158 )B128 - 158
17X-RAY DIFFRACTION17chain 'C' and (resid -6 through 14 )C-6 - 14
18X-RAY DIFFRACTION18chain 'C' and (resid 15 through 46 )C15 - 46
19X-RAY DIFFRACTION19chain 'C' and (resid 47 through 79 )C47 - 79
20X-RAY DIFFRACTION20chain 'C' and (resid 80 through 117 )C80 - 117
21X-RAY DIFFRACTION21chain 'C' and (resid 118 through 158 )C118 - 158
22X-RAY DIFFRACTION22chain 'D' and (resid -1 through 14 )D-1 - 14
23X-RAY DIFFRACTION23chain 'D' and (resid 15 through 27 )D15 - 27
24X-RAY DIFFRACTION24chain 'D' and (resid 28 through 58 )D28 - 58
25X-RAY DIFFRACTION25chain 'D' and (resid 59 through 79 )D59 - 79
26X-RAY DIFFRACTION26chain 'D' and (resid 80 through 94 )D80 - 94
27X-RAY DIFFRACTION27chain 'D' and (resid 95 through 117 )D95 - 117
28X-RAY DIFFRACTION28chain 'D' and (resid 118 through 157 )D118 - 157
29X-RAY DIFFRACTION29chain 'E' and (resid -6 through 46 )E-6 - 46
30X-RAY DIFFRACTION30chain 'E' and (resid 47 through 94 )E47 - 94
31X-RAY DIFFRACTION31chain 'E' and (resid 95 through 118 )E95 - 118
32X-RAY DIFFRACTION32chain 'E' and (resid 119 through 158 )E119 - 158
33X-RAY DIFFRACTION33chain 'F' and (resid 0 through 58 )F0 - 58
34X-RAY DIFFRACTION34chain 'F' and (resid 59 through 79 )F59 - 79
35X-RAY DIFFRACTION35chain 'F' and (resid 80 through 94 )F80 - 94
36X-RAY DIFFRACTION36chain 'F' and (resid 95 through 108 )F95 - 108
37X-RAY DIFFRACTION37chain 'F' and (resid 109 through 127 )F109 - 127
38X-RAY DIFFRACTION38chain 'F' and (resid 128 through 158 )F128 - 158

+
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