[English] 日本語
Yorodumi
- PDB-7l4b: Dihydrodipicolinate synthase (DHDPS) from C.jejuni with pyruvate ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l4b
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni with pyruvate bound in the active site in P1211 space group
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytoplasm
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
ACETATE ION / 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: 2.42 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: B-FACTOR ANALYSIS SUGGEST THAT L-LYSINE AND R, R-BISLYSINE ALLOSTERICALLY INHIBIT Cj.DHDPS ENZYME BY DECREASING PROTEIN DYNAMICS.
Authors: Saran, S. / Sanders, D.A.R.
History
DepositionDec 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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
G: 4-hydroxy-tetrahydrodipicolinate synthase
H: 4-hydroxy-tetrahydrodipicolinate synthase
I: 4-hydroxy-tetrahydrodipicolinate synthase
J: 4-hydroxy-tetrahydrodipicolinate synthase
K: 4-hydroxy-tetrahydrodipicolinate synthase
L: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)412,73537
Polymers410,22312
Non-polymers2,51225
Water9,854547
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
G: 4-hydroxy-tetrahydrodipicolinate synthase
H: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,44911
Polymers136,7414
Non-polymers7087
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-61 kcal/mol
Surface area39950 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
I: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,62413
Polymers136,7414
Non-polymers8839
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-63 kcal/mol
Surface area39350 Å2
MethodPISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
J: 4-hydroxy-tetrahydrodipicolinate synthase
K: 4-hydroxy-tetrahydrodipicolinate synthase
L: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,66213
Polymers136,7414
Non-polymers9219
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-63 kcal/mol
Surface area39600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.510, 200.360, 122.240
Angle α, β, γ (deg.)90.000, 109.830, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 75 or (resid 76...
21(chain B and (resid 3 through 75 or (resid 76...
31(chain C and (resid 3 through 75 or (resid 76...
41(chain D and (resid 3 through 165 or (resid 166...
51(chain E and (resid 3 through 75 or (resid 76...
61(chain F and (resid 3 through 75 or (resid 76...
71(chain G and (resid 3 through 75 or (resid 76...
81(chain H and (resid 3 through 75 or (resid 76...
91(chain I and (resid 3 through 75 or (resid 76...
101(chain J and (resid 3 through 75 or (resid 76...
111(chain K and (resid 3 through 75 or (resid 76...
121(chain L and (resid 3 through 75 or (resid 76...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 75 or (resid 76...A3 - 75
121(chain A and (resid 3 through 75 or (resid 76...A76
131(chain A and (resid 3 through 75 or (resid 76...A3 - 298
141(chain A and (resid 3 through 75 or (resid 76...A3 - 298
151(chain A and (resid 3 through 75 or (resid 76...A3 - 298
161(chain A and (resid 3 through 75 or (resid 76...A3 - 298
211(chain B and (resid 3 through 75 or (resid 76...B3 - 75
221(chain B and (resid 3 through 75 or (resid 76...B76
231(chain B and (resid 3 through 75 or (resid 76...B3 - 298
241(chain B and (resid 3 through 75 or (resid 76...B3 - 298
251(chain B and (resid 3 through 75 or (resid 76...B3 - 298
261(chain B and (resid 3 through 75 or (resid 76...B3 - 298
271(chain B and (resid 3 through 75 or (resid 76...B3 - 298
311(chain C and (resid 3 through 75 or (resid 76...C3 - 75
321(chain C and (resid 3 through 75 or (resid 76...C76
331(chain C and (resid 3 through 75 or (resid 76...C3 - 298
341(chain C and (resid 3 through 75 or (resid 76...C3 - 298
351(chain C and (resid 3 through 75 or (resid 76...C3 - 298
361(chain C and (resid 3 through 75 or (resid 76...C3 - 298
371(chain C and (resid 3 through 75 or (resid 76...C3 - 298
411(chain D and (resid 3 through 165 or (resid 166...D3 - 165
421(chain D and (resid 3 through 165 or (resid 166...D166
431(chain D and (resid 3 through 165 or (resid 166...D3 - 298
441(chain D and (resid 3 through 165 or (resid 166...D3 - 298
451(chain D and (resid 3 through 165 or (resid 166...D3 - 298
461(chain D and (resid 3 through 165 or (resid 166...D3 - 298
471(chain D and (resid 3 through 165 or (resid 166...D3 - 298
481(chain D and (resid 3 through 165 or (resid 166...D3 - 298
491(chain D and (resid 3 through 165 or (resid 166...D3 - 298
4101(chain D and (resid 3 through 165 or (resid 166...D3 - 298
4111(chain D and (resid 3 through 165 or (resid 166...D3 - 298
4121(chain D and (resid 3 through 165 or (resid 166...D3 - 298
511(chain E and (resid 3 through 75 or (resid 76...E3 - 75
521(chain E and (resid 3 through 75 or (resid 76...E76
531(chain E and (resid 3 through 75 or (resid 76...E5 - 298
541(chain E and (resid 3 through 75 or (resid 76...E5 - 298
551(chain E and (resid 3 through 75 or (resid 76...E5 - 298
561(chain E and (resid 3 through 75 or (resid 76...E5 - 298
571(chain E and (resid 3 through 75 or (resid 76...E5 - 298
611(chain F and (resid 3 through 75 or (resid 76...F3 - 75
621(chain F and (resid 3 through 75 or (resid 76...F76
631(chain F and (resid 3 through 75 or (resid 76...F3 - 298
641(chain F and (resid 3 through 75 or (resid 76...F3 - 298
651(chain F and (resid 3 through 75 or (resid 76...F3 - 298
661(chain F and (resid 3 through 75 or (resid 76...F3 - 298
711(chain G and (resid 3 through 75 or (resid 76...G3 - 75
721(chain G and (resid 3 through 75 or (resid 76...G76
731(chain G and (resid 3 through 75 or (resid 76...G3 - 298
741(chain G and (resid 3 through 75 or (resid 76...G3 - 298
751(chain G and (resid 3 through 75 or (resid 76...G3 - 298
761(chain G and (resid 3 through 75 or (resid 76...G3 - 298
771(chain G and (resid 3 through 75 or (resid 76...G3 - 298
781(chain G and (resid 3 through 75 or (resid 76...G3 - 298
811(chain H and (resid 3 through 75 or (resid 76...H3 - 75
821(chain H and (resid 3 through 75 or (resid 76...H76
831(chain H and (resid 3 through 75 or (resid 76...H3 - 298
841(chain H and (resid 3 through 75 or (resid 76...H3 - 298
851(chain H and (resid 3 through 75 or (resid 76...H3 - 298
861(chain H and (resid 3 through 75 or (resid 76...H3 - 298
871(chain H and (resid 3 through 75 or (resid 76...H3 - 298
911(chain I and (resid 3 through 75 or (resid 76...I3 - 75
921(chain I and (resid 3 through 75 or (resid 76...I76
931(chain I and (resid 3 through 75 or (resid 76...I3 - 298
941(chain I and (resid 3 through 75 or (resid 76...I3 - 298
951(chain I and (resid 3 through 75 or (resid 76...I3 - 298
961(chain I and (resid 3 through 75 or (resid 76...I3 - 298
971(chain I and (resid 3 through 75 or (resid 76...I3 - 298
1011(chain J and (resid 3 through 75 or (resid 76...J3 - 75
1021(chain J and (resid 3 through 75 or (resid 76...J76
1031(chain J and (resid 3 through 75 or (resid 76...J3 - 298
1041(chain J and (resid 3 through 75 or (resid 76...J3 - 298
1051(chain J and (resid 3 through 75 or (resid 76...J3 - 298
1061(chain J and (resid 3 through 75 or (resid 76...J3 - 298
1071(chain J and (resid 3 through 75 or (resid 76...J3 - 298
1111(chain K and (resid 3 through 75 or (resid 76...K3 - 75
1121(chain K and (resid 3 through 75 or (resid 76...K76
1131(chain K and (resid 3 through 75 or (resid 76...K3 - 298
1141(chain K and (resid 3 through 75 or (resid 76...K3 - 298
1151(chain K and (resid 3 through 75 or (resid 76...K3 - 298
1161(chain K and (resid 3 through 75 or (resid 76...K3 - 298
1171(chain K and (resid 3 through 75 or (resid 76...K3 - 298
1211(chain L and (resid 3 through 75 or (resid 76...L3 - 75
1221(chain L and (resid 3 through 75 or (resid 76...L76
1231(chain L and (resid 3 through 75 or (resid 76...L3 - 298
1241(chain L and (resid 3 through 75 or (resid 76...L3 - 298
1251(chain L and (resid 3 through 75 or (resid 76...L3 - 298
1261(chain L and (resid 3 through 75 or (resid 76...L3 - 298
1271(chain L and (resid 3 through 75 or (resid 76...L3 - 298

-
Components

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

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


Mass: 34185.258 Da / Num. of mol.: 12
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 , 5 types, 572 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 47.55 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.3 M Magnesium acetate, 10 % PEG 8000, 0.1 M Sodium acetate (pH 7.4)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 28, 2019
RadiationMonochromator: Double beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.42→49.15 Å / Num. obs: 141419 / % possible obs: 98.47 % / Redundancy: 17 % / CC1/2: 0.994 / Rmerge(I) obs: 0.06747 / Net I/σ(I): 8.81
Reflection shellResolution: 2.42→2.506 Å / Rmerge(I) obs: 0.4298 / Num. unique obs: 14082 / CC1/2: 0.836

-
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: 2.42→49.15 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2678 7065 5 %
Rwork0.225 134207 -
obs0.2271 141272 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.57 Å2 / Biso mean: 55.0677 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.42→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27256 0 163 547 27966
Biso mean--64.72 48.21 -
Num. residues----3550
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10716X-RAY DIFFRACTION4.262TORSIONAL
12B10716X-RAY DIFFRACTION4.262TORSIONAL
13C10716X-RAY DIFFRACTION4.262TORSIONAL
14D10716X-RAY DIFFRACTION4.262TORSIONAL
15E10716X-RAY DIFFRACTION4.262TORSIONAL
16F10716X-RAY DIFFRACTION4.262TORSIONAL
17G10716X-RAY DIFFRACTION4.262TORSIONAL
18H10716X-RAY DIFFRACTION4.262TORSIONAL
19I10716X-RAY DIFFRACTION4.262TORSIONAL
110J10716X-RAY DIFFRACTION4.262TORSIONAL
111K10716X-RAY DIFFRACTION4.262TORSIONAL
112L10716X-RAY DIFFRACTION4.262TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.42-2.450.39192380.3599450498
2.45-2.480.38032280.339434898
2.48-2.510.38832360.3435449798
2.51-2.540.37792330.3505443098
2.54-2.570.39282340.3391442398
2.57-2.610.41082380.3452451098
2.61-2.640.41982290.3307433998
2.64-2.680.39742360.3276447198
2.68-2.730.35512350.3082445898
2.73-2.770.36132350.2858446498
2.77-2.820.36412320.2864441598
2.82-2.870.29732370.279450998
2.87-2.920.31882360.2702446999
2.92-2.980.35922370.2756450098
2.98-3.050.30582330.2668443798
3.05-3.120.27042340.2512443499
3.12-3.20.32892360.2476450298
3.2-3.280.3012340.2415444999
3.28-3.380.27572370.2328449399
3.38-3.490.27622380.2221453099
3.49-3.610.2572370.2184450099
3.61-3.760.26642330.2031442599
3.76-3.930.24512380.1981452699
3.93-4.140.25032380.1847450599
4.14-4.40.21282380.1782453599
4.4-4.740.20942360.1666447899
4.74-5.210.22122390.1856453499
5.21-5.960.22522390.201454699
5.96-7.510.21032380.1958451799
7.51-100.19562330.1943445996
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)
11.83240.64411.06292.98181.2944.12440.252-0.1531-0.21020.2245-0.09480.1020.5417-0.7674-0.05010.3667-0.0388-0.02830.38880.10720.4331-14.148-4.75836.693
21.3732-0.0738-0.23821.5587-0.42763.1072-0.0188-0.0918-0.0682-0.13030.08070.31440.5165-0.6643-0.15490.4713-0.050.01230.48360.06280.3674-14.376-8.13236.676
31.3678-0.10190.02812.64960.50151.3054-0.2392-0.13460.08570.15860.39350.81720.0692-0.7323-0.08070.3308-0.0152-0.01450.52230.08390.4702-19.214.25137.748
40.9348-0.12650.89110.6124-0.57460.9289-0.2168-0.246-0.04140.12090.06520.0372-0.10960.00930.11650.40620.00270.05480.44820.04670.3695-4.3627.40444.95
53.29221.09981.75392.0876-0.85612.028-0.0541-0.384-0.5311-0.0383-0.2056-0.27790.9461-0.23030.56410.2973-0.0008-0.00260.42070.0290.55067.062-7.66241.148
60.3363-0.91660.45421.8645-0.82251.67320.0064-0.24540.0815-0.2380.0591-0.11780.4255-0.1111-0.08430.5735-0.07740.00940.46140.01160.4239-7.003-9.00124.598
73.79730.4802-1.31132.6557-0.2883.8758-0.02530.2452-0.5326-0.46910.0124-0.4170.45530.52030.16440.48690.0643-0.00150.3547-0.04770.5682.203-15.75329.392
82.11530.90341.68312.25631.98812.70730.09560.0166-0.299-0.0155-0.08810.0330.1449-0.2443-0.01660.339-0.02930.0230.41490.15530.3935-17.226-31.667-14.795
92.0895-1.1872-0.0811.492-0.46322.6796-0.0657-0.012-0.14040.05080.1262-0.02580.1971-0.2838-0.1260.488-0.03320.05790.52380.08710.5882-18.318-34.814-14.73
102.8551-1.90681.85352.65360.64184.41270.28520.4317-0.012-0.08440.10030.7491-0.1168-0.5329-0.19220.44140.00280.15410.62840.11290.6135-25.665-28.034-13.892
110.77771.4189-0.18263.5942-1.57891.4851-0.30340.12030.15470.28580.61370.4303-0.1087-0.8865-0.30110.45830.03310.11480.59910.11020.5219-20.015-20.669-10.669
121.80390.1971.00562.7881-1.03371.6311-0.07170.00290.33230.09360.14440.2132-0.1178-0.2557-0.00470.42520.04280.0560.44760.02750.3996-9.006-14.741-13.889
130.0425-0.05080.66832.1605-0.26980.8379-0.1094-0.2359-0.13730.168-0.00770.00620.0140.10590.11310.4528-0.01260.06520.50090.0390.3737-1.053-26.667-6.914
143.57020.17571.68232.3172-0.17037.6603-0.3508-0.2928-0.50890.2577-0.2415-0.02170.66070.17670.49020.42930.02280.13410.46950.07480.64982.706-40.587-13.601
150.0678-0.18910.05792.8156-0.03730.13950.05420.5860.1707-0.17210.33990.15730.01060.2474-0.04220.5649-0.09130.01040.5630.00940.5909-10.09-38.212-26.205
160.8454-0.83020.88452.7612-1.99132.7225-0.41050.379-0.3812-0.51990.8296-0.0560.7399-0.5843-0.44290.4939-0.0892-0.07750.5030.08680.4757-16.323-37.023-29.351
172.2387-0.4367-0.43912.588-1.21283.94910.13980.0617-0.8906-0.2914-0.2924-0.21450.61660.10280.10530.4963-0.0162-0.04690.3592-0.02190.8149-6.003-46.635-24.448
181.2186-2.1523-0.67893.456-0.22391.41620.09450.1075-0.17260.2109-0.40490.35060.16790.22260.35350.49730.09960.08520.54720.12050.482533.157-22.004-48.666
191.51080.73770.19161.5744-1.16830.8344-0.19640.1309-0.1965-0.43080.0267-0.2530.49470.35130.17530.61920.05620.16280.58040.07630.479533.279-23.843-51.461
200.64831.22880.43191.83860.96472.4775-0.0494-0.19420.0154-0.0308-0.3439-0.4868-0.00150.85310.3150.40980.08570.05120.64920.16720.544740.44-17.213-43.908
211.41170.28040.31570.90070.49391.0774-0.1090.19550.0364-0.09870.0537-0.14830.04820.17940.07020.38150.00280.06350.40750.08750.412724.531-9.845-40.831
222.2122-0.2882-0.60493.249-1.43672.8551-0.2060.43450.22250.05540.3643-0.0944-0.2325-0.66-0.03650.3871-0.02780.0480.5149-0.00790.429512.238-17.661-54.379
230.10040.06310.27750.7418-1.34693.1434-0.20990.1339-0.1311-0.5333-0.2654-0.05530.6450.11380.24880.69410.07940.0770.4983-0.03480.463922.203-34.562-49.483
242.2109-0.61470.88551.00790.08062.9007-0.129-0.01990.0590.08990.04040.297-0.454-0.4772-0.02690.40760.03620.01660.36440.08420.3847-14.6171.068-36.709
250.4616-0.4893-0.75752.58470.10481.7697-0.29050.1046-0.10260.05280.2148-0.00190.0328-0.69180.08610.3901-0.0159-0.00280.55910.08660.5347-19.453-10.013-37.597
260.94960.3127-0.19460.0162-0.60121.1006-0.13110.1994-0.0406-0.23760.1483-0.0390.11860.0238-0.01750.4098-0.02390.00370.42180.06560.3938-4.858-13.574-44.52
270.7657-0.7592-0.14392.2978-0.29172.2328-0.14870.0027-0.02150.25060.1335-0.2931-0.26540.11420.03510.4302-0.0018-0.00460.37220.02350.4788-0.3284.603-32.001
281.3195-0.5046-0.20130.92970.69151.60410.05460.202-0.177-0.10020.0348-0.4829-0.08760.34930.01740.49190.02140.00170.46340.02580.6129-12.21936.541-17.201
292.4853-1.1243-0.18890.8034-1.83413.751-0.08410.14170.0331-0.2667-0.2385-0.8136-0.12270.74070.16090.5019-0.00430.01950.55320.07370.7067-7.23540.649-26.546
301.02740.55410.11261.9834-0.55471.269-0.09760.121-0.1943-0.34920.1176-0.23280.16880.05960.0350.47680.03990.0440.5006-0.04160.5286-23.70537.195-35.076
312.26281.69411.29742.1052-0.25712.70520.11180.0288-0.72040.03090.1047-0.66070.20530.2753-0.15630.45360.01450.01170.48740.02350.5971-26.70325.099-18.012
321.6882-0.37941.2012.7307-0.18371.7529-0.0335-0.3785-0.02860.40910.15220.1802-0.1284-0.4143-0.09160.46790.0364-0.02590.52560.06940.4582-23.30540.058-6.235
331.37751.0979-0.53462.94350.0911.33430.21-0.00080.08460.1733-0.3679-0.7419-0.29540.22190.08440.4018-0.041-0.10530.48930.10830.405833.43916.33748.591
340.95-0.60940.28631.3819-0.73920.5785-0.0318-0.12760.02580.3652-0.1371-0.463-0.28010.28810.14720.4786-0.1099-0.11320.39940.08640.399533.63618.05251.386
350.85860.4712-1.35991.7495-0.7062.74770.34680.53130.52090.049-0.59370.4362-0.37490.85490.06720.3814-0.1629-0.17840.83460.20060.672942.77316.74746.624
360.6799-0.67211.02771.60320.24743.7470.05150.3339-0.18830.0594-0.1176-0.2827-0.39620.8860.14840.3798-0.0254-0.02970.55740.1520.555139.4988.33442.139
370.75340.7940.29311.0609-0.60842.3744-0.07550.22-0.1586-0.06480.1018-0.1275-0.21410.36490.07790.4428-0.04570.00530.51060.05610.407432.2455.47932.086
383.1937-0.60480.95731.1842-1.00352.94880.34730.0690.4131-0.2458-0.3867-0.35760.2541-0.0260.10430.3511-0.01350.04070.37190.03340.518228.7325.78736.044
390.50490.8680.79311.54270.15091.255-0.1163-0.1221-0.0767-0.01850.0160.03230.01480.04540.07420.3654-0.0153-0.01230.36010.10420.340920.8933.10245.242
401.35491.4503-0.8721.1537-0.91712.5491-0.1421-0.1237-0.12110.2685-0.1622-0.015-0.3501-0.15870.21550.51040.0026-0.05680.42180.04290.426420.18721.60649.706
412.22190.9023-0.43842.4689-0.93553.5828-0.2674-0.0957-0.01180.3132-0.0932-0.0207-0.8868-1.09370.29520.66890.0449-0.0460.4142-0.18880.537117.04328.49754.482
422.6437-1.1576-1.59562.60861.48573.91870.13090.05160.17480.0717-0.15640.4423-0.3823-0.64970.12920.32850.009-0.01650.44770.14090.5282-17.06725.94614.775
432.49971.25760.02240.849-0.17252.8907-0.0740.32760.0019-0.38380.05560.16-0.1994-0.4438-0.10680.47510.0266-0.02350.48260.11880.5375-18.17729.11114.813
440.4731-1.17920.05932.2799-0.40950.2366-0.1183-0.1344-0.01040.01240.1627-0.0020.0282-0.3587-0.020.3568-0.0269-0.00890.50630.05390.4508-19.09415.85713.226
450.2721-0.33340.13031.6076-1.09123.03360.02960.11370.0332-0.1270.0032-0.03260.14660.0668-0.05150.3715-0.0108-0.01040.4420.06070.3817-2.83912.7019.089
461.1261-0.8671-0.28920.3267-0.89272.3425-0.06250.04640.340.11050.0843-0.1121-0.36740.0802-0.07850.4526-0.03520.01460.34260.05210.4968-5.5834.33418.426
472.6682-2.014-0.29551.59330.40642.2767-0.07660.4366-0.10250.0287-0.19490.0948-0.02620.40210.31340.3405-0.04650.03030.60680.09810.46135.76419.71210.716
481.5670.42681.23191.7745-0.461.13010.07850.06530.0459-0.1663-0.0919-0.1845-0.1330.36010.04560.4786-0.00330.09560.6070.11120.552636.79918.2197.793
493.3530.43230.70384.2263-0.13222.5936-0.04610.90690.76280.3879-0.3897-0.6428-0.94830.74420.29040.4146-0.1261-0.02330.68830.18880.663944.22422.34113.101
501.31980.4121-1.63321.55661.01052.7377-0.19540.12190.15810.1795-0.697-0.3367-0.9480.19010.54970.4953-0.0404-0.00360.57940.17250.608538.52828.79518.012
510.8397-0.2610.69030.63420.62461.6362-0.00260.2730.1782-0.08790.0086-0.1343-0.27520.07890.0370.4316-0.0777-0.00040.41110.13380.459922.56328.94116.448
523.6071-1.1170.63123.9131-1.24413.94350.17660.4136-0.088-0.6110.10280.23610.4529-0.4373-0.21030.5099-0.05930.06510.66930.00050.523615.65715.8622.665
530.40210.20790.56310.7688-0.95472.7081-0.01260.1483-0.1164-0.1388-0.130.00780.50660.06150.17420.50420.07270.0560.60120.01350.487529.1454.7278.54
541.87091.36340.20711.2438-0.19532.19820.1889-0.29960.1105-0.0803-0.4855-0.128-0.10660.41330.23930.37440.01770.01440.5040.14710.468135.685-25.453-10.743
551.8406-0.528-0.89881.2109-0.97331.9442-0.042-0.2887-0.24170.083-0.31-0.52520.40870.32340.39260.4374-0.009-0.02340.52150.10810.544736.682-23.989-7.938
562.65860.7726-2.07253.9474-0.71433.2015-0.0816-0.5345-0.97710.02-0.8392-0.74870.13360.5410.46520.46740.1664-0.04250.69390.12360.603744.019-27.955-13.187
570.9890.19910.29761.0857-0.09182.5965-0.0721-0.092-0.3957-0.0787-0.0623-0.50550.11390.25850.14930.50290.04380.0490.48170.13750.597133.244-35.272-22.916
581.0050.78840.30331.03180.00171.66720.0198-0.0794-0.13390.0034-0.0324-0.15820.1780.03120.01420.44790.05220.02960.44230.11130.50120.684-34.204-13.89
590.47290.27450.30192.6054-1.50642.4081-0.0276-0.12730.2637-0.09240.25360.64210.0662-0.30840.0790.51210.01460.05170.66680.02210.510515.546-23.69-1.75
600.735-0.1143-0.74111.6991-0.73892.77980.0414-0.1754-0.15590.3574-0.2754-0.1226-0.18650.10510.21690.4209-0.0464-0.04090.52030.05690.392731.992-11.281-12.478
611.9135-0.39020.55982.5253-1.30082.4341-0.2246-0.65190.22090.20980.18740.0361-0.5308-0.71350.17660.50750.0078-0.00710.6645-0.07320.578324.706-9.482-2.891
621.139-0.94650.3121.9721-0.77452.60680.24850.43-0.1357-0.0421-0.09420.4088-0.33010.465-0.16320.5139-0.0258-0.10170.3999-0.07690.624-61.64523.901-34.96
631.2343-0.8193-0.6991.9861-0.56911.31480.09420.01680.0493-0.4718-0.09730.36350.2068-0.2852-0.0340.607-0.0566-0.130.5505-0.10720.5815-61.89722.198-37.848
643.4151-3.03-1.27173.8789-0.06972.39930.3346-0.810.5131-0.35180.20190.36220.1268-0.2155-0.27560.5715-0.1127-0.12970.5979-0.03290.7835-70.4822.735-32.772
650.32810.4196-0.27623.4281.62352.55270.1838-0.31630.2276-0.6673-0.41060.964-0.5016-0.5558-0.0030.4374-0.0226-0.0750.51810.04430.7764-66.50924.764-23.856
661.971-0.42630.48960.96090.09830.6422-0.0761-0.1374-0.28730.0497-0.002-0.0380.17710.02570.06220.51-0.03650.00920.4508-0.00550.5228-51.89729.42-19.151
672.3501-0.6220.52631.4294-0.87921.30150.32220.1265-0.557-0.13820.0907-0.05330.17170.16-0.38990.54330.01830.04260.3998-0.04760.6191-47.10918.897-34.474
682.6616-1.3731.0313.4289-0.14472.70090.04690.3151-0.4231-0.45330.0426-0.18420.1840.2678-0.00420.5548-0.08320.09510.5538-0.04810.518-39.8122.159-37.728
692.7801-0.5413-0.1392.6579-0.19473.2392-0.58660.6614-0.5054-1.15610.58610.5549-0.77291.070.22150.8112-0.1089-0.13480.6596-0.1190.5778-54.91232.587-44.949
701.2517-0.4677-0.93792.6040.38171.19180.18090.73790.2253-0.6786-0.1398-0.3552-0.21440.11010.0350.6829-0.044-0.12770.6417-0.08750.3653-54.22531.105-49.019
712.5297-0.35470.04711.2923-1.12812.9092-0.0957-0.0680.17340.03350.01980.41620.0288-0.24550.07620.43260.03850.00660.4354-0.03690.5665-72.99856.744-18.01
723.078-1.69940.70881.31130.71362.833-0.1837-0.088-0.1673-0.06620.0570.8990.0009-0.63850.01230.4383-0.0041-0.05910.5248-0.01120.7081-74.53353.908-30.173
731.08430.66040.31091.79810.43851.2934-0.09960.07440.3164-0.26560.0940.2394-0.0729-0.05910.02870.48980.0293-0.04990.46410.06430.5503-60.19359.38-32.015
741.33031.0017-0.53062.7996-0.45931.2059-0.004-0.19130.10930.1299-0.0641-0.04490.10380.10740.07510.42880.04140.0310.5046-0.0740.502-57.76359.316-9.562
751.5404-1.4052-1.04220.92621.0062.606-0.04650.41840.1680.03650.0264-0.27720.58370.0375-0.07020.6377-0.05530.10520.52910.05810.7317-21.89870.422-34.95
761.7336-0.33860.76011.3578-0.67141.5365-0.10820.3760.3528-0.34450.0867-0.4144-0.17430.0589-0.01650.5797-0.08010.10240.42960.09730.4946-21.64572.193-37.806
772.4063-1.0397-0.7765.71310.28532.62060.18-0.03780.3505-0.05980.435-0.2616-0.20240.558-0.24190.5913-0.08260.08470.66160.00510.8185-13.05771.625-32.793
781.0572-0.20540.66294.1973-2.21413.25150.1997-0.13450.6763-0.3987-0.0702-0.75670.26540.48880.03310.4956-0.0220.03780.477-0.00950.7233-17.05869.771-24.003
790.65490.69630.15142.013-0.5890.7919-0.22160.04910.21820.09320.0491-0.2968-0.15390.17840.19280.5133-0.0457-0.01890.4623-0.0110.5804-25.59561.505-18.852
800.9473-0.62740.2071.2244-0.35083.7638-0.1289-0.28870.10980.30770.1338-0.0853-0.09230.06650.02310.512900.0020.4083-0.05120.6142-32.40766.816-15.864
812.94290.7471-0.15260.7446-0.57261.0052-0.0708-0.06630.0877-0.0403-0.05590.1209-0.12970.1450.11810.48550.0091-0.02960.30020.05460.5275-38.81372.036-27.83
821.4948-0.68760.13323.26140.25851.9401-0.33350.33790.142-0.22970.18910.5479-0.2224-0.04530.04740.5257-0.106-0.09880.62250.12570.4992-43.74372.309-37.672
832.51990.10520.10563.10150.06632.020.05170.5934-0.1107-0.5826-0.21580.0392-0.0007-0.28750.1550.74530.01310.0820.58290.04290.457-25.09560.963-45.861
841.3226-0.49470.30723.4830.94760.4480.00820.31070.0317-0.78820.4607-0.22790.17580.0351-0.27310.8656-0.05020.00860.85190.13850.5019-35.14265.925-50.914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:23 )A3 - 23
2X-RAY DIFFRACTION2( CHAIN A AND RESID 24:55 )A24 - 55
3X-RAY DIFFRACTION3( CHAIN A AND RESID 56:115 )A56 - 115
4X-RAY DIFFRACTION4( CHAIN A AND RESID 116:229 )A116 - 229
5X-RAY DIFFRACTION5( CHAIN A AND RESID 230:248 )A230 - 248
6X-RAY DIFFRACTION6( CHAIN A AND RESID 249:279 )A249 - 279
7X-RAY DIFFRACTION7( CHAIN A AND RESID 280:298 )A280 - 298
8X-RAY DIFFRACTION8( CHAIN B AND RESID 3:23 )B3 - 23
9X-RAY DIFFRACTION9( CHAIN B AND RESID 24:55 )B24 - 55
10X-RAY DIFFRACTION10( CHAIN B AND RESID 56:70 )B56 - 70
11X-RAY DIFFRACTION11( CHAIN B AND RESID 71:99 )B71 - 99
12X-RAY DIFFRACTION12( CHAIN B AND RESID 100:148 )B100 - 148
13X-RAY DIFFRACTION13( CHAIN B AND RESID 149:229 )B149 - 229
14X-RAY DIFFRACTION14( CHAIN B AND RESID 230:248 )B230 - 248
15X-RAY DIFFRACTION15( CHAIN B AND RESID 249:262 )B249 - 262
16X-RAY DIFFRACTION16( CHAIN B AND RESID 263:279 )B263 - 279
17X-RAY DIFFRACTION17( CHAIN B AND RESID 280:298 )B280 - 298
18X-RAY DIFFRACTION18( CHAIN C AND RESID 3:23 )C3 - 23
19X-RAY DIFFRACTION19( CHAIN C AND RESID 24:55 )C24 - 55
20X-RAY DIFFRACTION20( CHAIN C AND RESID 56:98 )C56 - 98
21X-RAY DIFFRACTION21( CHAIN C AND RESID 99:226 )C99 - 226
22X-RAY DIFFRACTION22( CHAIN C AND RESID 227:248 )C227 - 248
23X-RAY DIFFRACTION23( CHAIN C AND RESID 249:298 )C249 - 298
24X-RAY DIFFRACTION24( CHAIN D AND RESID 3:55 )D3 - 55
25X-RAY DIFFRACTION25( CHAIN D AND RESID 56:115 )D56 - 115
26X-RAY DIFFRACTION26( CHAIN D AND RESID 116:226 )D116 - 226
27X-RAY DIFFRACTION27( CHAIN D AND RESID 227:298 )D227 - 298
28X-RAY DIFFRACTION28( CHAIN E AND RESID 5:55 )E5 - 55
29X-RAY DIFFRACTION29( CHAIN E AND RESID 56:99 )E56 - 99
30X-RAY DIFFRACTION30( CHAIN E AND RESID 100:200 )E100 - 200
31X-RAY DIFFRACTION31( CHAIN E AND RESID 201:248 )E201 - 248
32X-RAY DIFFRACTION32( CHAIN E AND RESID 249:298 )E249 - 298
33X-RAY DIFFRACTION33( CHAIN F AND RESID 3:23 )F3 - 23
34X-RAY DIFFRACTION34( CHAIN F AND RESID 24:55 )F24 - 55
35X-RAY DIFFRACTION35( CHAIN F AND RESID 56:69 )F56 - 69
36X-RAY DIFFRACTION36( CHAIN F AND RESID 70:98 )F70 - 98
37X-RAY DIFFRACTION37( CHAIN F AND RESID 99:127 )F99 - 127
38X-RAY DIFFRACTION38( CHAIN F AND RESID 128:148 )F128 - 148
39X-RAY DIFFRACTION39( CHAIN F AND RESID 149:226 )F149 - 226
40X-RAY DIFFRACTION40( CHAIN F AND RESID 227:279 )F227 - 279
41X-RAY DIFFRACTION41( CHAIN F AND RESID 280:298 )F280 - 298
42X-RAY DIFFRACTION42( CHAIN G AND RESID 3:23 )G3 - 23
43X-RAY DIFFRACTION43( CHAIN G AND RESID 24:55 )G24 - 55
44X-RAY DIFFRACTION44( CHAIN G AND RESID 56:115 )G56 - 115
45X-RAY DIFFRACTION45( CHAIN G AND RESID 116:200 )G116 - 200
46X-RAY DIFFRACTION46( CHAIN G AND RESID 201:298 )G201 - 298
47X-RAY DIFFRACTION47( CHAIN H AND RESID 3:23 )H3 - 23
48X-RAY DIFFRACTION48( CHAIN H AND RESID 24:55 )H24 - 55
49X-RAY DIFFRACTION49( CHAIN H AND RESID 56:70 )H56 - 70
50X-RAY DIFFRACTION50( CHAIN H AND RESID 71:99 )H71 - 99
51X-RAY DIFFRACTION51( CHAIN H AND RESID 100:229 )H100 - 229
52X-RAY DIFFRACTION52( CHAIN H AND RESID 230:248 )H230 - 248
53X-RAY DIFFRACTION53( CHAIN H AND RESID 249:298 )H249 - 298
54X-RAY DIFFRACTION54( CHAIN I AND RESID 3:23 )I3 - 23
55X-RAY DIFFRACTION55( CHAIN I AND RESID 24:55 )I24 - 55
56X-RAY DIFFRACTION56( CHAIN I AND RESID 56:70 )I56 - 70
57X-RAY DIFFRACTION57( CHAIN I AND RESID 71:129 )I71 - 129
58X-RAY DIFFRACTION58( CHAIN I AND RESID 130:226 )I130 - 226
59X-RAY DIFFRACTION59( CHAIN I AND RESID 227:248 )I227 - 248
60X-RAY DIFFRACTION60( CHAIN I AND RESID 249:279 )I249 - 279
61X-RAY DIFFRACTION61( CHAIN I AND RESID 280:298 )I280 - 298
62X-RAY DIFFRACTION62( CHAIN J AND RESID 3:23 )J3 - 23
63X-RAY DIFFRACTION63( CHAIN J AND RESID 24:55 )J24 - 55
64X-RAY DIFFRACTION64( CHAIN J AND RESID 56:70 )J56 - 70
65X-RAY DIFFRACTION65( CHAIN J AND RESID 71:99 )J71 - 99
66X-RAY DIFFRACTION66( CHAIN J AND RESID 100:200 )J100 - 200
67X-RAY DIFFRACTION67( CHAIN J AND RESID 201:226 )J201 - 226
68X-RAY DIFFRACTION68( CHAIN J AND RESID 227:248 )J227 - 248
69X-RAY DIFFRACTION69( CHAIN J AND RESID 249:262 )J249 - 262
70X-RAY DIFFRACTION70( CHAIN J AND RESID 263:298 )J263 - 298
71X-RAY DIFFRACTION71( CHAIN K AND RESID 3:70 )K3 - 70
72X-RAY DIFFRACTION72( CHAIN K AND RESID 71:98 )K71 - 98
73X-RAY DIFFRACTION73( CHAIN K AND RESID 99:226 )K99 - 226
74X-RAY DIFFRACTION74( CHAIN K AND RESID 227:298 )K227 - 298
75X-RAY DIFFRACTION75( CHAIN L AND RESID 3:23 )L3 - 23
76X-RAY DIFFRACTION76( CHAIN L AND RESID 24:55 )L24 - 55
77X-RAY DIFFRACTION77( CHAIN L AND RESID 56:70 )L56 - 70
78X-RAY DIFFRACTION78( CHAIN L AND RESID 71:99 )L71 - 99
79X-RAY DIFFRACTION79( CHAIN L AND RESID 100:148 )L100 - 148
80X-RAY DIFFRACTION80( CHAIN L AND RESID 149:171 )L149 - 171
81X-RAY DIFFRACTION81( CHAIN L AND RESID 172:226 )L172 - 226
82X-RAY DIFFRACTION82( CHAIN L AND RESID 227:248 )L227 - 248
83X-RAY DIFFRACTION83( CHAIN L AND RESID 249:279 )L249 - 279
84X-RAY DIFFRACTION84( CHAIN L AND RESID 280:298 )L280 - 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://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