[English] 日本語
Yorodumi
- PDB-8oje: Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8oje
TitleArabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 in complex with L-malate
ComponentsPhosphoenolpyruvate carboxylase 1
KeywordsPLANT PROTEIN / Phosphoenolpyruvate carboxylase / Citric acid cycle / TCA cycle / photosynthesis
Function / homology
Function and homology information


phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / leaf development / apoplast / carbon fixation / cellular response to phosphate starvation / tricarboxylic acid cycle / photosynthesis / protein tetramerization / nucleus / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxylase, Lys active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase, bacterial/plant-type / Phosphoenolpyruvate carboxylase, His active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase active site 2. / Phosphoenolpyruvate carboxylase active site 1. / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / DI(HYDROXYETHYL)ETHER / Phosphoenolpyruvate carboxylase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14239899937 Å
AuthorsHaesaerts, S. / Loris, R. / Larsen, P.B.
Funding support United States, Belgium, 2items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)2021-67014-34888 United States
Research Foundation - Flanders (FWO)G011420N Belgium
CitationJournal: To Be Published
Title: Amino acid changes that deregulate PHOSPHOENOLPYRUVATE CARBOXYLASE in plants
Authors: Meyer, T.J. / Sheng, J. / Haesaerts, S. / Frausto, K. / O'Leary, S. / Loris, R. / Larsen, P.B.
History
DepositionMar 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_struct_assembly_gen / pdbx_struct_oper_list / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoenolpyruvate carboxylase 1
B: Phosphoenolpyruvate carboxylase 1
C: Phosphoenolpyruvate carboxylase 1
D: Phosphoenolpyruvate carboxylase 1
E: Phosphoenolpyruvate carboxylase 1
F: Phosphoenolpyruvate carboxylase 1
G: Phosphoenolpyruvate carboxylase 1
H: Phosphoenolpyruvate carboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)897,31879
Polymers891,1858
Non-polymers6,13371
Water2,396133
1
A: Phosphoenolpyruvate carboxylase 1
B: Phosphoenolpyruvate carboxylase 1
hetero molecules

E: Phosphoenolpyruvate carboxylase 1
F: Phosphoenolpyruvate carboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)448,64139
Polymers445,5934
Non-polymers3,04935
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
2
C: Phosphoenolpyruvate carboxylase 1
D: Phosphoenolpyruvate carboxylase 1
hetero molecules

G: Phosphoenolpyruvate carboxylase 1
H: Phosphoenolpyruvate carboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)448,67740
Polymers445,5934
Non-polymers3,08436
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Unit cell
Length a, b, c (Å)116.080, 352.200, 176.040
Angle α, β, γ (deg.)90.000, 101.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

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
11LEULEULEULEU(chain 'A' and ((resid 6 through 11 and (name N...AA6 - 13913 - 146
12GLUGLUPROPRO(chain 'A' and ((resid 6 through 11 and (name N...AA141 - 154148 - 161
13GLUGLUVALVAL(chain 'A' and ((resid 6 through 11 and (name N...AA156 - 178163 - 185
14ARGARGTHRTHR(chain 'A' and ((resid 6 through 11 and (name N...AA180 - 300187 - 307
15ASPASPGLUGLU(chain 'A' and ((resid 6 through 11 and (name N...AA302 - 320309 - 327
16LEULEUSERSER(chain 'A' and ((resid 6 through 11 and (name N...AA322 - 346329 - 353
17LYSLYSGLNGLN(chain 'A' and ((resid 6 through 11 and (name N...AA352 - 483359 - 490
18TRPTRPILEILE(chain 'A' and ((resid 6 through 11 and (name N...AA485 - 595492 - 602
19SERSERHISHIS(chain 'A' and ((resid 6 through 11 and (name N...AA598 - 635605 - 642
110GLYGLYPROPRO(chain 'A' and ((resid 6 through 11 and (name N...AA638 - 732645 - 739
111PHEPHEMETMET(chain 'A' and ((resid 6 through 11 and (name N...AA734 - 750741 - 757
112ARGARGLEULEU(chain 'A' and ((resid 6 through 11 and (name N...AA755 - 887762 - 894
113LEULEUSERSER(chain 'A' and ((resid 6 through 11 and (name N...AA889 - 922896 - 929
114GLYGLYGLYGLY(chain 'A' and ((resid 6 through 11 and (name N...AA947 - 967954 - 974
215LEULEULEULEU(chain 'B' and ((resid 6 through 11 and (name N...BB6 - 13913 - 146
216GLUGLUPROPRO(chain 'B' and ((resid 6 through 11 and (name N...BB141 - 154148 - 161
217GLUGLUVALVAL(chain 'B' and ((resid 6 through 11 and (name N...BB156 - 178163 - 185
218ARGARGTHRTHR(chain 'B' and ((resid 6 through 11 and (name N...BB180 - 300187 - 307
219ASPASPGLUGLU(chain 'B' and ((resid 6 through 11 and (name N...BB302 - 320309 - 327
220LEULEUSERSER(chain 'B' and ((resid 6 through 11 and (name N...BB322 - 346329 - 353
221LYSLYSGLNGLN(chain 'B' and ((resid 6 through 11 and (name N...BB352 - 483359 - 490
222TRPTRPILEILE(chain 'B' and ((resid 6 through 11 and (name N...BB485 - 595492 - 602
223SERSERHISHIS(chain 'B' and ((resid 6 through 11 and (name N...BB598 - 635605 - 642
224GLYGLYPROPRO(chain 'B' and ((resid 6 through 11 and (name N...BB638 - 732645 - 739
225PHEPHEMETMET(chain 'B' and ((resid 6 through 11 and (name N...BB734 - 750741 - 757
226ARGARGLEULEU(chain 'B' and ((resid 6 through 11 and (name N...BB755 - 887762 - 894
227LEULEUSERSER(chain 'B' and ((resid 6 through 11 and (name N...BB889 - 922896 - 929
228GLYGLYGLYGLY(chain 'B' and ((resid 6 through 11 and (name N...BB947 - 967954 - 974
329LEULEULEULEU(chain 'C' and ((resid 6 through 11 and (name N...CC6 - 13913 - 146
330GLUGLUPROPRO(chain 'C' and ((resid 6 through 11 and (name N...CC141 - 154148 - 161
331GLUGLUVALVAL(chain 'C' and ((resid 6 through 11 and (name N...CC156 - 178163 - 185
332ARGARGTHRTHR(chain 'C' and ((resid 6 through 11 and (name N...CC180 - 300187 - 307
333ASPASPGLUGLU(chain 'C' and ((resid 6 through 11 and (name N...CC302 - 320309 - 327
334LEULEUSERSER(chain 'C' and ((resid 6 through 11 and (name N...CC322 - 346329 - 353
335LYSLYSGLNGLN(chain 'C' and ((resid 6 through 11 and (name N...CC352 - 483359 - 490
336TRPTRPILEILE(chain 'C' and ((resid 6 through 11 and (name N...CC485 - 595492 - 602
337SERSERHISHIS(chain 'C' and ((resid 6 through 11 and (name N...CC598 - 635605 - 642
338GLYGLYPROPRO(chain 'C' and ((resid 6 through 11 and (name N...CC638 - 732645 - 739
339PHEPHEMETMET(chain 'C' and ((resid 6 through 11 and (name N...CC734 - 750741 - 757
340ARGARGLEULEU(chain 'C' and ((resid 6 through 11 and (name N...CC755 - 887762 - 894
341LEULEUSERSER(chain 'C' and ((resid 6 through 11 and (name N...CC889 - 922896 - 929
342GLYGLYGLYGLY(chain 'C' and ((resid 6 through 11 and (name N...CC947 - 967954 - 974
443LEULEULEULEU(chain 'D' and ((resid 6 through 11 and (name N...DD6 - 13913 - 146
444GLUGLUPROPRO(chain 'D' and ((resid 6 through 11 and (name N...DD141 - 154148 - 161
445GLUGLUVALVAL(chain 'D' and ((resid 6 through 11 and (name N...DD156 - 178163 - 185
446ARGARGTHRTHR(chain 'D' and ((resid 6 through 11 and (name N...DD180 - 300187 - 307
447ASPASPGLUGLU(chain 'D' and ((resid 6 through 11 and (name N...DD302 - 320309 - 327
448LEULEUSERSER(chain 'D' and ((resid 6 through 11 and (name N...DD322 - 346329 - 353
449LYSLYSGLNGLN(chain 'D' and ((resid 6 through 11 and (name N...DD352 - 483359 - 490
450TRPTRPILEILE(chain 'D' and ((resid 6 through 11 and (name N...DD485 - 595492 - 602
451SERSERHISHIS(chain 'D' and ((resid 6 through 11 and (name N...DD598 - 635605 - 642
452GLYGLYPROPRO(chain 'D' and ((resid 6 through 11 and (name N...DD638 - 732645 - 739
453PHEPHEMETMET(chain 'D' and ((resid 6 through 11 and (name N...DD734 - 750741 - 757
454ARGARGLEULEU(chain 'D' and ((resid 6 through 11 and (name N...DD755 - 887762 - 894
455LEULEUSERSER(chain 'D' and ((resid 6 through 11 and (name N...DD889 - 922896 - 929
456GLYGLYGLYGLY(chain 'D' and ((resid 6 through 11 and (name N...DD947 - 967954 - 974
557LEULEULEULEU(chain 'E' and ((resid 6 through 11 and (name N...EE6 - 13913 - 146
558GLUGLUPROPRO(chain 'E' and ((resid 6 through 11 and (name N...EE141 - 154148 - 161
559GLUGLUVALVAL(chain 'E' and ((resid 6 through 11 and (name N...EE156 - 178163 - 185
560ARGARGTHRTHR(chain 'E' and ((resid 6 through 11 and (name N...EE180 - 300187 - 307
561ASPASPGLUGLU(chain 'E' and ((resid 6 through 11 and (name N...EE302 - 320309 - 327
562LEULEUSERSER(chain 'E' and ((resid 6 through 11 and (name N...EE322 - 346329 - 353
563LYSLYSGLNGLN(chain 'E' and ((resid 6 through 11 and (name N...EE352 - 483359 - 490
564TRPTRPILEILE(chain 'E' and ((resid 6 through 11 and (name N...EE485 - 595492 - 602
565SERSERHISHIS(chain 'E' and ((resid 6 through 11 and (name N...EE598 - 635605 - 642
566GLYGLYPROPRO(chain 'E' and ((resid 6 through 11 and (name N...EE638 - 732645 - 739
567PHEPHEMETMET(chain 'E' and ((resid 6 through 11 and (name N...EE734 - 750741 - 757
568ARGARGLEULEU(chain 'E' and ((resid 6 through 11 and (name N...EE755 - 887762 - 894
569LEULEUSERSER(chain 'E' and ((resid 6 through 11 and (name N...EE889 - 922896 - 929
570GLYGLYGLYGLY(chain 'E' and ((resid 6 through 11 and (name N...EE947 - 967954 - 974
671LEULEULEULEU(chain 'F' and ((resid 6 through 11 and (name N...FF6 - 13913 - 146
672GLUGLUPROPRO(chain 'F' and ((resid 6 through 11 and (name N...FF141 - 154148 - 161
673GLUGLUVALVAL(chain 'F' and ((resid 6 through 11 and (name N...FF156 - 178163 - 185
674ARGARGTHRTHR(chain 'F' and ((resid 6 through 11 and (name N...FF180 - 300187 - 307
675ASPASPGLUGLU(chain 'F' and ((resid 6 through 11 and (name N...FF302 - 320309 - 327
676LEULEUSERSER(chain 'F' and ((resid 6 through 11 and (name N...FF322 - 346329 - 353
677LYSLYSGLNGLN(chain 'F' and ((resid 6 through 11 and (name N...FF352 - 483359 - 490
678TRPTRPILEILE(chain 'F' and ((resid 6 through 11 and (name N...FF485 - 595492 - 602
679SERSERHISHIS(chain 'F' and ((resid 6 through 11 and (name N...FF598 - 635605 - 642
680GLYGLYPROPRO(chain 'F' and ((resid 6 through 11 and (name N...FF638 - 732645 - 739
681PHEPHEMETMET(chain 'F' and ((resid 6 through 11 and (name N...FF734 - 750741 - 757
682ARGARGLEULEU(chain 'F' and ((resid 6 through 11 and (name N...FF755 - 887762 - 894
683LEULEUSERSER(chain 'F' and ((resid 6 through 11 and (name N...FF889 - 922896 - 929
684GLYGLYGLYGLY(chain 'F' and ((resid 6 through 11 and (name N...FF947 - 967954 - 974
785LEULEULEULEU(chain 'G' and ((resid 6 through 11 and (name N...GG6 - 13913 - 146
786GLUGLUPROPRO(chain 'G' and ((resid 6 through 11 and (name N...GG141 - 154148 - 161
787GLUGLUVALVAL(chain 'G' and ((resid 6 through 11 and (name N...GG156 - 178163 - 185
788ARGARGTHRTHR(chain 'G' and ((resid 6 through 11 and (name N...GG180 - 300187 - 307
789ASPASPGLUGLU(chain 'G' and ((resid 6 through 11 and (name N...GG302 - 320309 - 327
790LEULEUSERSER(chain 'G' and ((resid 6 through 11 and (name N...GG322 - 346329 - 353
791LYSLYSGLNGLN(chain 'G' and ((resid 6 through 11 and (name N...GG352 - 483359 - 490
792TRPTRPILEILE(chain 'G' and ((resid 6 through 11 and (name N...GG485 - 595492 - 602
793SERSERHISHIS(chain 'G' and ((resid 6 through 11 and (name N...GG598 - 635605 - 642
794GLYGLYPROPRO(chain 'G' and ((resid 6 through 11 and (name N...GG638 - 732645 - 739
795PHEPHEMETMET(chain 'G' and ((resid 6 through 11 and (name N...GG734 - 750741 - 757
796ARGARGLEULEU(chain 'G' and ((resid 6 through 11 and (name N...GG755 - 887762 - 894
797LEULEUSERSER(chain 'G' and ((resid 6 through 11 and (name N...GG889 - 922896 - 929
798GLYGLYGLYGLY(chain 'G' and ((resid 6 through 11 and (name N...GG947 - 967954 - 974
899LEULEULEULEU(chain 'H' and ((resid 6 through 11 and (name N...HH6 - 13913 - 146
8100GLUGLUPROPRO(chain 'H' and ((resid 6 through 11 and (name N...HH141 - 154148 - 161
8101GLUGLUVALVAL(chain 'H' and ((resid 6 through 11 and (name N...HH156 - 178163 - 185
8102ARGARGTHRTHR(chain 'H' and ((resid 6 through 11 and (name N...HH180 - 300187 - 307
8103ASPASPGLUGLU(chain 'H' and ((resid 6 through 11 and (name N...HH302 - 320309 - 327
8104LEULEUSERSER(chain 'H' and ((resid 6 through 11 and (name N...HH322 - 346329 - 353
8105LYSLYSGLNGLN(chain 'H' and ((resid 6 through 11 and (name N...HH352 - 483359 - 490
8106TRPTRPILEILE(chain 'H' and ((resid 6 through 11 and (name N...HH485 - 595492 - 602
8107SERSERHISHIS(chain 'H' and ((resid 6 through 11 and (name N...HH598 - 635605 - 642
8108GLYGLYPROPRO(chain 'H' and ((resid 6 through 11 and (name N...HH638 - 732645 - 739
8109PHEPHEMETMET(chain 'H' and ((resid 6 through 11 and (name N...HH734 - 750741 - 757
8110ARGARGLEULEU(chain 'H' and ((resid 6 through 11 and (name N...HH755 - 887762 - 894
8111LEULEUSERSER(chain 'H' and ((resid 6 through 11 and (name N...HH889 - 922896 - 929
8112GLYGLYGLYGLY(chain 'H' and ((resid 6 through 11 and (name N...HH947 - 967954 - 974

-
Components

#1: Protein
Phosphoenolpyruvate carboxylase 1 / AtPPC1 / PEPC 1 / PEPCase 1 / 107-kDa PEPC polypeptide


Mass: 111398.164 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PPC1, p107, At1g53310, F12M16.21 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9MAH0, phosphoenolpyruvate carboxylase
#2: Chemical
ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 70.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 30%PEG400, 0.1 M Hepes Sodium Salt pH 7.5, 200mM Magnesium Chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.981 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 3.142→50 Å / Num. obs: 237667 / % possible obs: 99.3 % / Redundancy: 7.11 % / Biso Wilson estimate: 82.2502477245 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.292 / Net I/σ(I): 6.94
Reflection shellResolution: 3.143→3.33 Å / Redundancy: 6.42 % / Rmerge(I) obs: 2.102 / Mean I/σ(I) obs: 0.89 / Num. unique obs: 36978 / CC1/2: 0.352 / % possible all: 96.1

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.14239899937→48.9254741206 Å / SU ML: 0.527092632809 / Cross valid method: FREE R-VALUE / σ(F): 1.3280661634 / Phase error: 25.6059321202
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239756715239 11875 4.99962108135 %
Rwork0.202062209888 225643 -
obs0.20393187438 237518 99.3022196022 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.9200195511 Å2
Refinement stepCycle: LAST / Resolution: 3.14239899937→48.9254741206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58490 0 295 133 58918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057783318625660198
X-RAY DIFFRACTIONf_angle_d0.83680890531681660
X-RAY DIFFRACTIONf_chiral_restr0.04700905103519163
X-RAY DIFFRACTIONf_plane_restr0.0059871953906210633
X-RAY DIFFRACTIONf_dihedral_angle_d12.676923545936274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1424-3.17810.4681740872363190.4442247365366051X-RAY DIFFRACTION81.0123362584
3.1781-3.21550.4181353951614010.3805801142097616X-RAY DIFFRACTION99.9875280619
3.2155-3.25470.3587862868093980.3453764594717560X-RAY DIFFRACTION99.9623162919
3.2547-3.29590.3616542176453960.3330038650787530X-RAY DIFFRACTION99.9621642073
3.2959-3.33920.3580534025264000.323667113177587X-RAY DIFFRACTION99.9249343175
3.3392-3.3850.348330149693960.3083832208487524X-RAY DIFFRACTION99.9495204442
3.385-3.43330.3403685143254000.3052509178197591X-RAY DIFFRACTION99.9499687305
3.4333-3.48450.324044903673950.2887578364227505X-RAY DIFFRACTION99.9493927126
3.4845-3.5390.300734746194010.2757956541457631X-RAY DIFFRACTION99.9626633479
3.539-3.5970.2827913874173960.2599474287017539X-RAY DIFFRACTION99.9496158206
3.597-3.6590.3190377854153960.2557814460637530X-RAY DIFFRACTION99.9621642073
3.659-3.72550.2825013007743990.2550385354417570X-RAY DIFFRACTION99.9372962127
3.7255-3.79710.2690590824143960.2325686196277539X-RAY DIFFRACTION99.9622071051
3.7971-3.87460.265948435654000.2174309154347595X-RAY DIFFRACTION99.9499937492
3.8746-3.95880.2360985676823980.198817481367555X-RAY DIFFRACTION99.9497297977
3.9588-4.05090.2197658402453980.1863535241827566X-RAY DIFFRACTION100
4.0509-4.15210.2426772434333980.1943894089157577X-RAY DIFFRACTION99.9749279178
4.1521-4.26430.2244148511483980.1791849688647563X-RAY DIFFRACTION99.9497802888
4.2643-4.38970.2096608009893980.1733819410067556X-RAY DIFFRACTION99.9748617396
4.3897-4.53130.1968243116223990.1566667621787576X-RAY DIFFRACTION99.912302681
4.5313-4.69320.1935033001693990.1461552271747574X-RAY DIFFRACTION99.9122807018
4.6932-4.88090.1821380417483990.1497969738697578X-RAY DIFFRACTION99.8998121478
4.8809-5.10280.2060481092463990.159688004087559X-RAY DIFFRACTION99.9372095944
5.1028-5.37150.206527724253980.1583991714527563X-RAY DIFFRACTION99.9497802888
5.3715-5.70760.2127468673593990.1664190492247591X-RAY DIFFRACTION99.974974975
5.7076-6.14750.2451579620754010.1893033639167612X-RAY DIFFRACTION99.9875218368
6.1475-6.76470.2253966433913990.1797913869957595X-RAY DIFFRACTION99.9499874969
6.7647-7.74030.2047479018733990.1604988619447597X-RAY DIFFRACTION99.9375078115
7.7403-9.73930.1537023571624000.1313437755767602X-RAY DIFFRACTION99.9001248439
9.7393-48.92547412060.215114366934000.1896789164127611X-RAY DIFFRACTION99.2197176121

+
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