[English] 日本語
Yorodumi
- PDB-4els: Structure of E. Coli. 1,4-dihydroxy-2- naphthoyl coenzyme A synth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4els
TitleStructure of E. Coli. 1,4-dihydroxy-2- naphthoyl coenzyme A synthases (MENB) in complex with bicarbonate
Components1,4-Dihydroxy-2-naphthoyl-CoA synthase
KeywordsLYASE / dihydroxynaphthoic acid synthetase
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase activity / bicarbonate binding / menaquinone biosynthetic process / cytosol
Similarity search - Function
1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 ...1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / DI(HYDROXYETHYL)ETHER / 1,4-dihydroxy-2-naphthoyl-CoA synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsSun, Y.R. / Song, H.G. / Li, J. / Jiang, M. / Li, Y. / Zhou, J.H. / Guo, Z.H.
CitationJournal: Biochemistry / Year: 2012
Title: Active site binding and catalytic role of bicarbonate in 1,4-dihydroxy-2-naphthoyl coenzyme A synthases from vitamin K biosynthetic pathways
Authors: Sun, Y.R. / Song, H.G. / Li, J. / Jiang, M. / Li, Y. / Zhou, J.H. / Guo, Z.H.
History
DepositionApr 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 8, 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 / struct_ncs_dom_lim / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
B: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
C: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
D: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
E: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
F: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,41428
Polymers190,0276
Non-polymers1,38722
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36380 Å2
ΔGint-168 kcal/mol
Surface area47390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.367, 133.888, 153.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

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
11ASPASPASPASPchain A and (resseq 5:87 or resseq 106:269 or resseq 275:285 )AA5 - 875 - 87
12LEULEUALAALAchain A and (resseq 5:87 or resseq 106:269 or resseq 275:285 )AA106 - 269106 - 269
13GLNGLNPROPROchain A and (resseq 5:87 or resseq 106:269 or resseq 275:285 )AA275 - 285275 - 285
21ASPASPASPASPchain B and (resseq 5:87 or resseq 106:269 or resseq 275:285 )BB5 - 875 - 87
22LEULEUALAALAchain B and (resseq 5:87 or resseq 106:269 or resseq 275:285 )BB106 - 269106 - 269
23GLNGLNPROPROchain B and (resseq 5:87 or resseq 106:269 or resseq 275:285 )BB275 - 285275 - 285
31ASPASPGLYGLYchain C and (resseq 5:86 or resseq 106:262 )CC5 - 865 - 86
32LEULEUGLUGLUchain C and (resseq 5:86 or resseq 106:262 )CC106 - 262106 - 262
41ASPASPASPASPchain D and (resseq 5:87 or resseq 106:269 or resseq 275:285 )DD5 - 875 - 87
42LEULEUALAALAchain D and (resseq 5:87 or resseq 106:269 or resseq 275:285 )DD106 - 269106 - 269
43GLNGLNPROPROchain D and (resseq 5:87 or resseq 106:269 or resseq 275:285 )DD275 - 285275 - 285
51ASPASPASPASPchain E and (resseq 5:87 or resseq 106:269 or resseq 275:285 )EE5 - 875 - 87
52LEULEUALAALAchain E and (resseq 5:87 or resseq 106:269 or resseq 275:285 )EE106 - 269106 - 269
53GLNGLNPROPROchain E and (resseq 5:87 or resseq 106:269 or resseq 275:285 )EE275 - 285275 - 285
61ASPASPASPASPchain F and (resseq 5:87 or resseq 106:269 or resseq 275:285 )FF5 - 875 - 87
62LEULEUALAALAchain F and (resseq 5:87 or resseq 106:269 or resseq 275:285 )FF106 - 269106 - 269
63GLNGLNPROPROchain F and (resseq 5:87 or resseq 106:269 or resseq 275:285 )FF275 - 285275 - 285

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
1,4-Dihydroxy-2-naphthoyl-CoA synthase / DHNA-CoA synthase


Mass: 31671.105 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: menB / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABU0, 1,4-dihydroxy-2-naphthoyl-CoA synthase

-
Non-polymers , 6 types, 405 molecules

#2: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 2% Tacsimate, 100mM Tris, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→42.849 Å / Num. all: 69785 / Num. obs: 69785 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 33.57 Å2 / Rmerge(I) obs: 0.199
Reflection shellResolution: 2.3→2.33 Å / % possible all: 99.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HO2

3ho2


Resolution: 2.303→42.849 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8409 / SU ML: 0.29 / σ(F): 1.91 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 3517 5.04 %RANDOM
Rwork0.1825 ---
obs0.1845 69785 99.35 %-
all-69785 --
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.303 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 138.32 Å2 / Biso mean: 38.7451 Å2 / Biso min: 6.89 Å2
Baniso -1Baniso -2Baniso -3
1-14.0076 Å2-0 Å2-0 Å2
2---3.3155 Å20 Å2
3----10.692 Å2
Refinement stepCycle: LAST / Resolution: 2.303→42.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11893 0 84 383 12360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712208
X-RAY DIFFRACTIONf_angle_d1.03716480
X-RAY DIFFRACTIONf_chiral_restr0.071779
X-RAY DIFFRACTIONf_plane_restr0.0052183
X-RAY DIFFRACTIONf_dihedral_angle_d12.9914439
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1942X-RAY DIFFRACTIONPOSITIONAL0.052
12B1942X-RAY DIFFRACTIONPOSITIONAL0.052
13C1782X-RAY DIFFRACTIONPOSITIONAL0.047
14D1927X-RAY DIFFRACTIONPOSITIONAL0.055
15E1935X-RAY DIFFRACTIONPOSITIONAL0.061
16F1929X-RAY DIFFRACTIONPOSITIONAL0.058
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3031-2.33470.30511300.23362551268196
2.3347-2.3680.28931390.23382571271099
2.368-2.40340.30781330.22322621275499
2.4034-2.44090.27261250.22812618274399
2.4409-2.48090.30481200.21462651277199
2.4809-2.52370.27061340.21112608274299
2.5237-2.56960.2651370.19922616275399
2.5696-2.6190.26931450.19012610275599
2.619-2.67250.25441420.18632621276399
2.6725-2.73060.21881390.18812629276899
2.7306-2.79410.28851530.19932589274299
2.7941-2.86390.26481450.19962638278399
2.8639-2.94130.23531270.1826652792100
2.9413-3.02790.23551420.181826362778100
3.0279-3.12560.24631440.173326292773100
3.1256-3.23730.23941570.179126402797100
3.2373-3.36680.19691440.1826442788100
3.3668-3.520.23571200.189626892809100
3.52-3.70550.20991400.181926712811100
3.7055-3.93750.21911290.170826952824100
3.9375-4.24120.18621370.15327052842100
4.2412-4.66760.15061560.144426732829100
4.6676-5.34190.17721550.163627112866100
5.3419-6.7260.23631500.211227392889100
6.726-42.85670.20271740.18162848302299
Refinement TLS params.Method: refined / Origin x: 2.2013 Å / Origin y: 133.6787 Å / Origin z: 18.9093 Å
111213212223313233
T0.0695 Å20.0267 Å2-0.0027 Å2-0.0721 Å20.004 Å2--0.0773 Å2
L0.1752 °20.0245 °20.0501 °2-0.2877 °20.0791 °2--0.3498 °2
S0.0026 Å °-0.0186 Å °0.0081 Å °-0.0112 Å °-0.0064 Å °0.0071 Å °0.0224 Å °0.0051 Å °-0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )A4 - 285
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )A301 - 303
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )A305
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )A304
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )A401 - 478
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )C4 - 262
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )C301 - 302
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )C303
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )C304
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )C401 - 457
11X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )B4 - 285
12X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )B301 - 303
13X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )B304
14X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )B401 - 472
15X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )E5 - 285
16X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )E301 - 302
17X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )E401 - 461
18X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )D4 - 285
19X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )D301 - 302
20X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )D303
21X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )D401 - 459
22X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )F5 - 285
23X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )F301 - 303
24X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )F304
25X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:285 OR RESID 301:303 OR RESID 305:305 OR RESID 304:304 OR RESID 401:478 ) ) OR ( CHAIN C AND ( RESID 4:262 OR RESID 301:302 OR RESID 303:303 OR RESID 304:304 OR RESID 401:457 ) ) OR ( CHAIN B AND ( RESID 4:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:472 ) ) OR ( CHAIN E AND ( RESID 5:285 OR RESID 301:302 OR RESID 401:461 ) ) OR ( CHAIN D AND ( RESID 4:285 OR RESID 301:302 OR RESID 303:303 OR RESID 401:459 ) ) OR ( CHAIN F AND ( RESID 5:285 OR RESID 301:303 OR RESID 304:304 OR RESID 401:456 ) )F401 - 456

+
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