[English] 日本語
Yorodumi
- PDB-7kto: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56A mutant w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kto
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, H56A mutant with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE
Function / homology
Function and homology information


(R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-3VN / ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsSaran, S. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: ALLOSTERIC SITE RESIDUE 'H56' CAPS THE INHIBITOR AT THE TIGHT DIMER INTERFACE FOR TRANSMITTING THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS
Authors: Saran, S. / Skovpen, Y. / Yazdi, M.M. / Palmer, D.R.J. / Sanders, D.A.R.
History
DepositionNov 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.2Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,93549
Polymers204,7096
Non-polymers4,22643
Water19,9431107
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,44133
Polymers136,4734
Non-polymers2,96829
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16530 Å2
ΔGint-12 kcal/mol
Surface area39400 Å2
MethodPISA
2
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules

E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,98832
Polymers136,4734
Non-polymers2,51528
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area15200 Å2
ΔGint-7 kcal/mol
Surface area40270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.080, 225.150, 200.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-489-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 20 or (resid 21...
21(chain B and (resid 3 through 20 or (resid 21...
31(chain C and (resid 3 through 31 or (resid 32...
41(chain D and (resid 3 through 20 or (resid 21...
51(chain E and (resid 3 through 20 or (resid 21...
61(chain F and (resid 3 through 20 or (resid 21...

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
11LYSLYSGLYGLY(chain A and (resid 3 through 20 or (resid 21...AA3 - 2015 - 32
12LYSLYSLYSLYS(chain A and (resid 3 through 20 or (resid 21...AA2133
13LYSLYSPHEPHE(chain A and (resid 3 through 20 or (resid 21...AA3 - 29815 - 310
14LYSLYSPHEPHE(chain A and (resid 3 through 20 or (resid 21...AA3 - 29815 - 310
15LYSLYSPHEPHE(chain A and (resid 3 through 20 or (resid 21...AA3 - 29815 - 310
16LYSLYSPHEPHE(chain A and (resid 3 through 20 or (resid 21...AA3 - 29815 - 310
21LYSLYSGLYGLY(chain B and (resid 3 through 20 or (resid 21...BB3 - 2015 - 32
22LYSLYSLYSLYS(chain B and (resid 3 through 20 or (resid 21...BB2133
23LYSLYSPHEPHE(chain B and (resid 3 through 20 or (resid 21...BB3 - 29815 - 310
24LYSLYSPHEPHE(chain B and (resid 3 through 20 or (resid 21...BB3 - 29815 - 310
25LYSLYSPHEPHE(chain B and (resid 3 through 20 or (resid 21...BB3 - 29815 - 310
26LYSLYSPHEPHE(chain B and (resid 3 through 20 or (resid 21...BB3 - 29815 - 310
31LYSLYSILEILE(chain C and (resid 3 through 31 or (resid 32...CC3 - 3115 - 43
32LYSLYSLYSLYS(chain C and (resid 3 through 31 or (resid 32...CC3244
33HISHISPHEPHE(chain C and (resid 3 through 31 or (resid 32...CC-7 - 2985 - 310
34HISHISPHEPHE(chain C and (resid 3 through 31 or (resid 32...CC-7 - 2985 - 310
35HISHISPHEPHE(chain C and (resid 3 through 31 or (resid 32...CC-7 - 2985 - 310
36HISHISPHEPHE(chain C and (resid 3 through 31 or (resid 32...CC-7 - 2985 - 310
41LYSLYSGLYGLY(chain D and (resid 3 through 20 or (resid 21...DD3 - 2015 - 32
42LYSLYSLYSLYS(chain D and (resid 3 through 20 or (resid 21...DD2133
43LYSLYSPHEPHE(chain D and (resid 3 through 20 or (resid 21...DD3 - 29815 - 310
44LYSLYSPHEPHE(chain D and (resid 3 through 20 or (resid 21...DD3 - 29815 - 310
45LYSLYSPHEPHE(chain D and (resid 3 through 20 or (resid 21...DD3 - 29815 - 310
46LYSLYSPHEPHE(chain D and (resid 3 through 20 or (resid 21...DD3 - 29815 - 310
51LYSLYSGLYGLY(chain E and (resid 3 through 20 or (resid 21...EE3 - 2015 - 32
52LYSLYSLYSLYS(chain E and (resid 3 through 20 or (resid 21...EE2133
53LYSLYSPHEPHE(chain E and (resid 3 through 20 or (resid 21...EE3 - 29815 - 310
54LYSLYSPHEPHE(chain E and (resid 3 through 20 or (resid 21...EE3 - 29815 - 310
55LYSLYSPHEPHE(chain E and (resid 3 through 20 or (resid 21...EE3 - 29815 - 310
56LYSLYSPHEPHE(chain E and (resid 3 through 20 or (resid 21...EE3 - 29815 - 310
61LYSLYSGLYGLY(chain F and (resid 3 through 20 or (resid 21...FF3 - 2015 - 32
62LYSLYSLYSLYS(chain F and (resid 3 through 20 or (resid 21...FF2133
63HISHISPHEPHE(chain F and (resid 3 through 20 or (resid 21...FF-7 - 2985 - 310
64HISHISPHEPHE(chain F and (resid 3 through 20 or (resid 21...FF-7 - 2985 - 310
65HISHISPHEPHE(chain F and (resid 3 through 20 or (resid 21...FF-7 - 2985 - 310
66HISHISPHEPHE(chain F and (resid 3 through 20 or (resid 21...FF-7 - 2985 - 310

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


Mass: 34118.191 Da / Num. of mol.: 6 / Mutation: H56A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: dapA, Cj0806 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase

-
Non-polymers , 8 types, 1150 molecules

#2: Chemical ChemComp-3VN / (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid / bis-Lysine


Mass: 318.412 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H30N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1107 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.3 M Magnesium acetate, 12 % PEG 8000, 0.1 M Sodium acetate (pH 7.4), 120 mM R,R-bislysine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 22, 2019
RadiationMonochromator: double beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.13→45.83 Å / Num. obs: 107327 / % possible obs: 99.66 % / Redundancy: 15 % / CC1/2: 0.99 / Net I/σ(I): 10.2
Reflection shellResolution: 2.13→2.15 Å / Rmerge(I) obs: 0.93 / Num. unique obs: 10622 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 2.13→45.83 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 5367 5 %
Rwork0.2023 101940 -
obs0.2045 107307 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.56 Å2 / Biso mean: 30.8276 Å2 / Biso min: 14.69 Å2
Refinement stepCycle: final / Resolution: 2.13→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13763 0 281 1107 15151
Biso mean--55.96 34.98 -
Num. residues----1796
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5322X-RAY DIFFRACTION1.106TORSIONAL
12B5322X-RAY DIFFRACTION1.106TORSIONAL
13C5322X-RAY DIFFRACTION1.106TORSIONAL
14D5322X-RAY DIFFRACTION1.106TORSIONAL
15E5322X-RAY DIFFRACTION1.106TORSIONAL
16F5322X-RAY DIFFRACTION1.106TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.13-2.150.3051770.28233355100
2.15-2.180.35361770.26483369100
2.18-2.210.32571770.26573368100
2.21-2.230.31941770.25583355100
2.23-2.260.30731750.25423316100
2.26-2.290.27981810.25363443100
2.29-2.330.30391750.25023324100
2.33-2.360.33581790.25553410100
2.36-2.40.32111760.26373332100
2.4-2.440.31661780.2623389100
2.44-2.480.31911770.25613363100
2.48-2.530.3151790.26143397100
2.53-2.570.29391780.25583379100
2.57-2.630.28631770.2486336199
2.63-2.680.29021780.2501337999
2.68-2.750.30071800.24433422100
2.75-2.810.27621750.24023324100
2.81-2.890.27681780.2378338999
2.89-2.980.32591780.24163372100
2.98-3.070.23631790.2303340299
3.07-3.180.26121790.19773402100
3.18-3.310.27491790.19593406100
3.31-3.460.23481800.19023406100
3.46-3.640.21041800.17583422100
3.64-3.870.20251810.16443447100
3.87-4.170.20891800.14833411100
4.17-4.590.16651810.13713441100
4.59-5.250.18871810.14543450100
5.25-6.610.20911840.17083489100
6.61-100.1711910.1568361799
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)
12.4789-0.39912.46121.1708-1.64947.6980.1986-0.1619-0.1534-0.03650.18830.2418-0.0905-0.451-0.37470.30230.04480.0190.21530.04190.3597-33.6919-46.8979-18.6572
22.949-0.0951-0.59682.8257-1.83832.96480.02040.0931-0.0851-0.02020.19380.3887-0.1625-0.3316-0.23510.25180.01160.02620.27060.01870.2718-36.7607-48.2486-19.7884
31.28530.41960.36778.10191.11040.5644-0.03770.10670.0326-0.0866-0.0750.5863-0.0569-0.22380.12470.24740.02250.03650.3550.04510.289-39.507-39.8066-10.7056
41.3581-0.36980.40811.27560.35160.9656-0.05880.0218-0.06840.09210.06140.1116-0.1008-0.10660.01690.27790.01190.0360.25190.01260.223-26.4559-34.9676-4.8423
51.70950.10871.03640.55390.6341.73180.1103-0.3285-0.07290.0263-0.0485-0.07610.1123-0.25-0.07510.258-0.01470.04160.20910.03530.2891-19.0452-52.6301-10.5415
61.283-1.12321.33051.15-1.75676.0743-0.02210.2340.0322-0.08950.0276-0.0346-0.0279-0.01190.01940.1942-0.02480.04110.2134-0.01870.2728-12.4532-52.7171-16.6167
71.8666-0.56370.13244.5583-0.39661.34460.05280.0007-0.0434-0.32620.0881-0.060.01490.1142-0.15080.2533-0.0345-0.00240.213-0.00020.2165-22.8104-48.4471-31.2449
82.19240.5432-1.30652.302-1.08314.58340.02640.08660.0241-0.00160.18380.33080.1369-0.55-0.21730.23510.0085-0.03150.28790.04590.2901-36.1552-8.0756-21.9621
94.8354-1.0355-1.89086.2414-1.28645.48110.26730.0218-0.291-0.6316-0.29240.50490.6335-0.9132-0.04050.2193-0.0856-0.08090.51730.08270.3218-43.6539-12.3115-25.5456
101.3966-2.2809-0.33867.32140.32611.5812-0.10340.20590.06060.04120.11630.4224-0.0739-0.3963-0.06340.20170.0117-0.00380.34690.06770.2882-38.2507-17.2929-31.9876
110.52180.4069-0.1812.53890.59220.4611-0.07330.06680.01-0.06680.04910.0876-0.0066-0.00410.02780.25710.0065-0.01730.22570.02480.2209-22.3177-15.8774-31.8633
121.10410.3251-0.39343.0096-4.02895.3451-0.1892-0.04790.14620.31630.1576-0.235-0.2692-0.28360.03620.29610.03-0.04450.1844-0.01810.2986-15.4405-0.4833-21.0782
132.17440.3845-0.28634.2186-1.00321.4905-0.0668-0.24930.19030.36680.13180.22-0.2258-0.0587-0.07390.34990.03450.04740.2868-0.01310.2241-28.9676-7.1963-7.9894
142.11360.60820.58561.1086-0.91992.4160.2018-0.1389-0.02520.4691-0.3373-0.4732-0.0378-0.08940.06370.19670.065-0.02750.27340.01190.312514.2889-36.45621.3103
152.37191.025-0.94596.8475-2.16033.0234-0.1493-0.02880.01370.31970.2577-0.3355-0.2133-0.0904-0.10860.2630.0426-0.04120.29970.01220.296214.7774-35.92984.7698
163.73621.9459-1.66674.0236-5.41578.3270.1201-0.29650.1906-0.3557-0.3474-0.95150.31180.4270.26680.21160.00540.03940.22-0.0040.401723.3854-35.55440.1095
172.6802-0.8457-0.45484.4321-3.22856.2866-0.21830.4923-0.1812-0.15610.2071-0.3669-0.0134-0.31540.13760.1468-0.02-0.00110.0908-0.01920.300520.2052-39.6547-8.3535
181.18820.04570.89951.46-0.02482.26890.1081-0.0135-0.1274-0.0158-0.1225-0.06410.05090.08170.02310.22250.00150.03040.22580.02650.285911.583-37.759-16.6429
193.7791-0.5397-1.40623.62050.74254.1727-0.05160.0250.097-0.09780.1069-0.1092-0.04360.0593-0.0910.2962-0.02760.00510.17630.01220.21926.2584-45.42-17.0309
200.95580.04470.37210.22530.05671.2084-0.0887-0.0107-0.02460.00230.0172-0.0158-0.0519-0.05630.06290.1870.01080.02620.21370.03470.2361-0.3511-45.7652-3.8764
212.060.5540.19337.98540.54522.0885-0.0748-0.1847-0.17320.63650.12610.46260.0687-0.2223-0.06060.28740.04340.00510.32360.03970.2551-6.3603-42.61834.8476
220.91120.4841-1.14354.5618-2.543.2381-0.16410.03780.06620.4655-0.0134-0.4614-0.36550.10750.18050.3384-0.0075-0.02540.2255-0.02750.27457.2553-23.94976.0712
234.6318-0.42220.65234.9454-1.79723.8456-0.2223-0.59910.10580.81460.5450.4335-0.3675-0.4359-0.27650.31740.090.02680.31760.01230.2301-1.551-28.622113.1023
241.8587-0.4706-0.86352.28980.61582.32550.0406-0.0449-0.0073-0.1202-0.0107-0.39740.18560.15240.00580.2761-0.0463-0.0010.25440.04460.345118.042-13.7271-30.2701
250.38660.4732-0.86840.7579-0.56313.15850.0219-0.0340.2650.0770.15540.0517-0.088-0.0651-0.08920.1793-0.026-0.02580.23510.0380.34221.6955-10.848-20.1933
261.7891-0.30880.28362.3897-0.91462.5477-0.05770.03680.16870.02290.07970.0353-0.27250.1139-0.01710.2265-0.0052-0.02080.17920.02480.21129.2532-12.8357-11.9101
273.57710.94620.93862.86540.32765.3121-0.0314-0.10380.09340.0946-0.1960.0021-0.12570.06660.24020.2350.02650.02030.14370.02970.26983.1331-5.9872-13.2615
280.7435-0.0945-1.16291.35380.092.2076-0.01910.07350.0686-0.06890.0037-0.0198-0.0561-0.04260.0090.2196-0.0052-0.01170.21620.01940.22930.2945-5.7181-28.1316
294.3509-2.9050.6743.0995-1.85671.97340.10150.27980.1157-0.667-0.04940.07690.0876-0.0771-0.12170.2931-0.02860.00410.3354-0.02040.2378-2.4137-12.208-37.9918
301.7379-0.4955-0.02183.0695-1.55362.6954-0.02570.1195-0.0802-0.34210.0345-0.07280.3217-0.15510.02220.3002-0.00380.03050.2271-0.01320.206710.5193-25.2659-38.4335
313.21713.3429-2.03157.7499-3.41553.40470.0988-0.33440.0227-0.4845-0.3744-0.37930.01870.4750.19780.26670.0005-0.02180.2707-0.0010.264420.8007-76.9825-27.5696
322.55110.1399-0.35262.3545-1.36034.26460.03920.08940.1506-0.0303-0.1986-0.35620.07190.51990.11870.2112-0.0133-0.0220.2910.02050.274723.9085-75.8628-26.3527
331.42810.47340.88013.60862.92863.747-0.1067-0.1877-0.02940.25280.1299-0.2540.05650.2779-0.09620.21210.0013-0.01220.25770.060.287525.4262-87.9534-28.2622
340.2878-0.2198-0.20220.67590.77670.71710.0403-0.0655-0.01170.0335-0.0213-0.0444-0.03710.0029-0.01080.2176-0.0053-0.00560.18150.0230.1919.8945-89.719-30.7586
354.13272.4119-2.88513.7068-3.15886.22670.1739-0.17670.28020.3185-0.11340.181-0.3992-0.0745-0.0360.2739-0.0013-0.05240.2515-0.02180.2974-0.9564-74.0529-24.9221
361.6788-0.1576-1.38432.17440.77514.4182-0.01680.11810.2468-0.08090.01330.0038-0.3299-0.0485-0.00090.23350.0068-0.02440.19080.00990.247513.3806-63.8321-34.4949
371.43320.09010.0723.2775-1.46613.16470.0057-0.0084-0.08710.125-0.1038-0.32240.07620.25930.13110.19770.00480.00230.2523-0.02360.23531.0704-93.0456-60.6991
382.9043-1.2963-1.44152.29360.88362.4767-0.04450.14340.09030.07230.0692-0.1425-0.05410.1042-0.07320.2232-0.0116-0.01610.20940.01720.223725.1414-77.9056-56.0309
390.16090.31490.09772.3551-0.17071.0469-0.02110.07410.03860.01470.0063-0.171-0.0540.06640.02120.20930.00180.00880.19120.00540.175214.9222-79.3812-66.5519
403.77830.6032-0.4312.2531-0.96913.5836-0.03750.4565-0.2007-0.21730.0761-0.02970.11850.0439-0.06230.1950.0291-0.0120.213-0.05370.2113.3175-94.4109-74.2057
411.7045-0.10310.27922.36561.23374.46150.0341-0.0538-0.24910.1086-0.01550.12560.27770.180.0050.20270.0127-0.00330.1810.00450.230918.6396-105.306-57.9756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 23 )A3 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 70 )A24 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 98 )A71 - 98
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 191 )A99 - 191
5X-RAY DIFFRACTION5chain 'A' and (resid 192 through 229 )A192 - 229
6X-RAY DIFFRACTION6chain 'A' and (resid 230 through 248 )A230 - 248
7X-RAY DIFFRACTION7chain 'A' and (resid 249 through 298 )A249 - 298
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 55 )B3 - 55
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 70 )B56 - 70
10X-RAY DIFFRACTION10chain 'B' and (resid 71 through 99 )B71 - 99
11X-RAY DIFFRACTION11chain 'B' and (resid 100 through 226 )B100 - 226
12X-RAY DIFFRACTION12chain 'B' and (resid 227 through 248 )B227 - 248
13X-RAY DIFFRACTION13chain 'B' and (resid 249 through 298 )B249 - 298
14X-RAY DIFFRACTION14chain 'C' and (resid 3 through 23 )C3 - 23
15X-RAY DIFFRACTION15chain 'C' and (resid 24 through 55 )C24 - 55
16X-RAY DIFFRACTION16chain 'C' and (resid 56 through 70 )C56 - 70
17X-RAY DIFFRACTION17chain 'C' and (resid 71 through 98 )C71 - 98
18X-RAY DIFFRACTION18chain 'C' and (resid 99 through 148 )C99 - 148
19X-RAY DIFFRACTION19chain 'C' and (resid 149 through 171 )C149 - 171
20X-RAY DIFFRACTION20chain 'C' and (resid 172 through 226 )C172 - 226
21X-RAY DIFFRACTION21chain 'C' and (resid 227 through 248 )C227 - 248
22X-RAY DIFFRACTION22chain 'C' and (resid 249 through 279 )C249 - 279
23X-RAY DIFFRACTION23chain 'C' and (resid 280 through 298 )C280 - 298
24X-RAY DIFFRACTION24chain 'D' and (resid 3 through 55 )D3 - 55
25X-RAY DIFFRACTION25chain 'D' and (resid 56 through 98 )D56 - 98
26X-RAY DIFFRACTION26chain 'D' and (resid 99 through 148 )D99 - 148
27X-RAY DIFFRACTION27chain 'D' and (resid 149 through 171 )D149 - 171
28X-RAY DIFFRACTION28chain 'D' and (resid 172 through 229 )D172 - 229
29X-RAY DIFFRACTION29chain 'D' and (resid 230 through 248 )D230 - 248
30X-RAY DIFFRACTION30chain 'D' and (resid 249 through 298 )D249 - 298
31X-RAY DIFFRACTION31chain 'E' and (resid 3 through 23 )E3 - 23
32X-RAY DIFFRACTION32chain 'E' and (resid 24 through 70 )E24 - 70
33X-RAY DIFFRACTION33chain 'E' and (resid 71 through 99 )E71 - 99
34X-RAY DIFFRACTION34chain 'E' and (resid 100 through 226 )E100 - 226
35X-RAY DIFFRACTION35chain 'E' and (resid 227 through 248 )E227 - 248
36X-RAY DIFFRACTION36chain 'E' and (resid 249 through 298 )E249 - 298
37X-RAY DIFFRACTION37chain 'F' and (resid 3 through 70 )F3 - 70
38X-RAY DIFFRACTION38chain 'F' and (resid 71 through 148 )F71 - 148
39X-RAY DIFFRACTION39chain 'F' and (resid 149 through 214 )F149 - 214
40X-RAY DIFFRACTION40chain 'F' and (resid 215 through 248 )F215 - 248
41X-RAY DIFFRACTION41chain 'F' and (resid 249 through 298 )F249 - 298

+
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://pdbjlc1.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