[English] 日本語
Yorodumi
- PDB-3ifc: Human muscle fructose-1,6-bisphosphatase E69Q mutant in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ifc
TitleHuman muscle fructose-1,6-bisphosphatase E69Q mutant in complex with AMP and alpha fructose-6-phosphate
ComponentsFructose-1,6-bisphosphatase isozyme 2
KeywordsHYDROLASE / gluconeogenesis / glyconeogenesis / muscle fructose-1 / 6-bisphosphatase / protein engineering / calcium inhibition / Allosteric enzyme / Carbohydrate metabolism / Magnesium / Metal-binding / Phosphoprotein
Function / homology
Function and homology information


sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / Gluconeogenesis / fructose 6-phosphate metabolic process / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / anchoring junction / gluconeogenesis / Z disc ...sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / Gluconeogenesis / fructose 6-phosphate metabolic process / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / anchoring junction / gluconeogenesis / Z disc / extracellular exosome / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 6-O-phosphono-alpha-D-fructofuranose / Fructose-1,6-bisphosphatase isozyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsKolodziejczyk, R. / Zarzycki, M. / Jaskolski, M. / Dzugaj, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of E69Q mutant of human muscle fructose-1,6-bisphosphatase
Authors: Zarzycki, M. / Kolodziejczyk, R. / Maciaszczyk-Dziubinska, E. / Wysocki, R. / Jaskolski, M. / Dzugaj, A.
History
DepositionJul 24, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2013Group: Database references / Refinement description
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructose-1,6-bisphosphatase isozyme 2
B: Fructose-1,6-bisphosphatase isozyme 2
C: Fructose-1,6-bisphosphatase isozyme 2
D: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,51027
Polymers146,6644
Non-polymers3,84723
Water12,647702
1
A: Fructose-1,6-bisphosphatase isozyme 2
B: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules

A: Fructose-1,6-bisphosphatase isozyme 2
B: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,79030
Polymers146,6644
Non-polymers4,12726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area21570 Å2
ΔGint-227 kcal/mol
Surface area44390 Å2
MethodPISA
2
C: Fructose-1,6-bisphosphatase isozyme 2
D: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules

C: Fructose-1,6-bisphosphatase isozyme 2
D: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,23024
Polymers146,6644
Non-polymers3,56620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area20160 Å2
ΔGint-205 kcal/mol
Surface area44290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.14, 234.54, 71.75
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

-
Components

-
Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Fructose-1,6-bisphosphatase isozyme 2 / FBPase 2 / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase 2


Mass: 36665.910 Da / Num. of mol.: 4 / Mutation: E69Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 8789 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL2-blue / References: UniProt: O00757, fructose-bisphosphatase
#3: Sugar
ChemComp-P6P / 6-O-phosphono-alpha-D-fructofuranose / alpha fructose-6-phosphate / 6-O-phosphono-alpha-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 4 types, 721 molecules

#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE SEQUENCE OF THE PROTEIN BASED ON REFERENCE 1 AND 4 OF UNIPROTKB/SWISS-PROT O00757 (F16P2_HUMAN). ...THE SEQUENCE OF THE PROTEIN BASED ON REFERENCE 1 AND 4 OF UNIPROTKB/SWISS-PROT O00757 (F16P2_HUMAN). V85L IS NATURAL VARIANT OF F16P2_HUMAN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M ammonium sulfate, 0.1M MES pH 6.5, 10% 1,4-dioxane, crystal soaked with 5mM D-fructose-6-phosphate dipotassium salt, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2008
Details: two mirrors and double crystal monochromator between them
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. all: 130416 / Num. obs: 119283 / % possible obs: 91.5 % / Observed criterion σ(I): -2 / Redundancy: 4.3 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.1 / Num. unique all: 6314 / % possible all: 48.8

-
Processing

Software
NameVersionClassification
MAR345CCDdata collection
MOLREPphasing
REFMAC5.5.0089refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1fj6
Resolution: 1.97→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.071 / SU ML: 0.089 / Cross valid method: Rfree / σ(I): -2 / ESU R: 0.127 / ESU R Free: 0.12 / Stereochemistry target values: Engh & Huber / Details: Hydrogen atoms were added at riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.19711 1334 1.1 %RANDOM
Rwork0.16672 ---
all0.16706 130416 --
obs0.16706 117923 91.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.016 Å2
Baniso -1Baniso -2Baniso -3
1--2.92 Å20 Å20 Å2
2---0.11 Å20 Å2
3---3.03 Å2
Refinement stepCycle: LAST / Resolution: 1.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9776 0 237 702 10715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02210038
X-RAY DIFFRACTIONr_bond_other_d0.0010.026665
X-RAY DIFFRACTIONr_angle_refined_deg1.7392.00913654
X-RAY DIFFRACTIONr_angle_other_deg1.018316317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36951301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48724.919370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.961151654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.471538
X-RAY DIFFRACTIONr_chiral_restr0.1030.21595
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021869
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8541.56389
X-RAY DIFFRACTIONr_mcbond_other0.2451.52640
X-RAY DIFFRACTIONr_mcangle_it1.483210242
X-RAY DIFFRACTIONr_scbond_it2.45133649
X-RAY DIFFRACTIONr_scangle_it3.7964.53399
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.076 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.305 124 -
Rwork0.265 10417 -
obs-10417 56.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.43610.81830.56183.9232-0.16152.8965-0.08180.83660.0888-0.53320.11150.0925-0.04540.0538-0.02970.2991-0.0255-0.11330.19780.030.1632-18.3121-62.229117.3492
23.67790.29321.73431.60060.39071.6782-0.1354-0.11810.32370.1790.0460.0884-0.1826-0.06760.08930.14790.0002-0.02480.06030.00560.0727-10.5124-63.816537.2498
32.58841.08650.05311.56750.9141.6022-0.0405-0.37470.07150.285-0.01780.11510.0187-0.04760.05830.20210.0268-0.01080.14920.01640.1055-19.3054-69.573639.6662
49.68560.1535-4.45071.65961.0127.07130.11880.70960.482-0.1142-0.10190.9755-0.1147-1.3083-0.01690.1605-0.0133-0.08210.28570.04530.6437-35.5103-74.115529.7325
52.40510.7904-0.95921.95930.05481.837-0.0970.3249-0.0907-0.10590.08620.28480.0127-0.20560.01080.11960.0011-0.04110.0545-0.01220.0779-18.3127-75.881627.2121
63.82374.77043.0669.58955.71345.75250.01220.07180.126-0.1875-0.0122-0.1234-0.0934-0.056400.15360.0073-0.03050.120.03950.053-7.2031-66.876722.2876
71.9136-0.29890.31633.917-1.17242.5004-0.05930.0854-0.1558-0.156-0.0102-0.10220.22990.04940.06950.0787-0.0208-0.00050.0785-0.01370.0264-5.6203-96.098428.7282
81.7318-2.0892-0.24525.8721.40923.6343-0.1550.1417-0.0496-0.01670.02080.09670.05760.04850.13420.0454-0.0465-0.00140.06340.00890.0093-2.3003-89.634627.5872
93.2649-0.8571-0.39463.10930.08522.0794-0.1-0.14350.01490.17010.09430.20290.00870.03080.00570.0765-0.0219-0.01620.0736-0.0040.0319-15.4227-87.988432.2256
100.8828-0.7879-0.24223.34031.21511.3884-0.06250.087-0.16980.0423-0.02670.42280.1742-0.13530.08920.0775-0.0242-0.01930.1246-0.01070.0732-18.1768-93.443526.4131
113.69370.30271.66021.9848-0.61046.5451-0.1086-0.16980.2702-0.01610.06260.58280.0249-0.67030.0460.2458-0.024-0.12050.16090.05190.2772-22.2825-52.332123.1892
124.333-0.99011.35941.3753-0.70532.2522-0.04170.13520.0585-0.17220.056-0.17870.05210.0989-0.01430.1982-0.0259-0.05110.06840.01170.0819-0.6021-50.577126.463
139.1759-4.91085.59822.6506-3.01183.4434-0.02910.35720.3732-0.0307-0.2147-0.25610.02310.29540.24380.30130.0053-0.00090.28860.02090.23035.2879-48.767420.6105
142.3058-0.6023-0.07082.93640.06883.5989-0.05350.45320.157-0.49170.0808-0.0629-0.11010.1821-0.02730.2639-0.0297-0.05980.16480.08410.1186-7.3119-42.660713.0979
151.5123-0.04110.22871.9272-0.37342.57230.010.23420.1321-0.24060.09950.2551-0.0729-0.1616-0.10950.1323-0.0146-0.09880.09290.05920.1549-14.5489-39.307921.6307
169.4345-7.27631.3438.6931-2.28911.544-0.0726-0.0460.08750.1340.04970.07220.0724-0.09770.02290.1458-0.0174-0.01380.11450.01350.0981-14.2316-48.694334.4182
174.98922.0455-0.47063.822-0.93881.87160.00830.01040.43030.09070.0050.0397-0.2761-0.0255-0.01330.15020.0289-0.09970.0720.01870.2323-7.3259-17.665431.6136
183.86650.06890.50175.58210.75251.62330.0411-0.19410.4660.02590.00730.1005-0.2179-0.1485-0.04840.1249-0.0017-0.07760.08690.03180.1923-7.8449-22.024136.7748
192.87181.034-0.55813.07410.95062.6564-0.05020.07340.254-0.18710.06440.0463-0.00330.1246-0.01420.11570.0108-0.09470.1040.09330.2074-9.9313-27.444423.5585
201.8531-0.3807-0.83392.94790.88872.91880.03240.09430.4129-0.33240.0460.0905-0.3167-0.0717-0.07830.1333-0.0056-0.10830.12990.10990.2653-13.9613-20.082421.3511
212.92470.9247-0.25659.64073.20824.88260.0358-0.47290.09010.7712-0.0493-0.02060.05030.05080.01350.21090.00940.00940.2344-0.0690.2036-46.1301-102.663320.9927
221.05271.27280.26653.99394.74099.4753-0.02-0.09250.11750.0549-0.0920.2313-0.07820.02460.1120.10920.0101-0.01310.1337-0.02370.1836-44.8031-96.172811.2126
232.07812.20413.8564.55795.14387.7925-0.16240.21950.0978-0.68970.00610.1181-0.53610.10350.15640.14470.0155-0.02570.33390.02150.1455-44.3618-111.2129-9.4068
243.2908-0.5068-1.60649.29334.95689.2741-0.28960.5330.0135-0.6144-0.08980.3848-0.098-0.03360.37940.1557-0.0466-0.08730.1607-0.01320.12-41.9223-97.6299-3.0198
255.05010.2931-1.05034.26060.49414.17560.00340.25860.5999-0.2566-0.04780.1474-0.5414-0.08030.04440.1966-0.0381-0.10680.09790.01330.1692-38.2816-88.44952.4725
261.6432-1.3761-0.042710.29163.48731.30580.11030.42840.066-0.84390.089-0.5866-0.27970.1651-0.19940.2028-0.01630.01590.2411-0.01140.1396-31.8053-107.6623-2.8534
273.07361.2363-0.44265.098-2.40475.1404-0.2357-0.13571.02690.26720.19190.1288-1.04140.02240.04380.3175-0.0632-0.09510.1461-0.04940.3783-31.9968-84.05168.4919
282.39410.02290.13130.80420.42711.3456-0.0704-0.0589-0.08180.06150.0660.06550.04690.20420.00440.0884-0.00840.00420.1265-0.01920.0151-23.5083-111.41279.8105
292.7336-0.7858-0.5263.2011-0.59513.225-0.06420.17660.1998-0.20090.09130.1166-0.09890.1671-0.02720.064-0.0679-0.01780.16-0.0230.0521-20.8011-102.44726.3182
302.9051-0.71810.91071.6345-0.25082.4863-0.09150.17330.4249-0.010.0379-0.1376-0.18660.51950.05360.0856-0.0697-0.00410.204-0.02660.0789-14.4253-100.20510.9756
313.42980.8602-0.6034.28321.58565.1451-0.0482-0.06190.5696-0.0908-0.00820.2807-0.76670.03350.05630.1734-0.0083-0.01750.2032-0.12470.2608-55.9463-96.067414.2454
321.1915-0.8466-0.75181.82631.86973.2696-0.1079-0.1577-0.24160.2253-0.04550.170.37240.02690.15330.1283-0.00140.02430.1681-0.04280.162-58.2853-120.582612.1661
331.988-1.1912-0.71032.0385-1.75264.0981-0.2127-0.2833-0.1490.15850.20140.0950.2685-0.09980.01130.2823-0.06960.01560.3013-0.06220.1784-64.5782-113.3722.958
342.2535-0.3022-0.78092.02430.16643.8836-0.0499-0.42340.13730.3216-0.00050.1434-0.17950.00940.05040.08610.01180.01630.1591-0.11190.1735-68.5646-104.315617.993
356.1234-5.1367-2.164711.07340.15953.07860.0146-0.04810.01060.09020.0111-0.0720.01870.0729-0.02580.1273-0.0135-0.01040.1511-0.01420.1321-55.8093-106.61942.4202
364.00471.1498-0.17961.90180.12681.2018-0.08620.01990.0453-0.062-0.04040.1884-0.0228-0.09680.12660.11160.0330.00460.0931-0.11240.1802-85.6305-108.27444.6354
376.0684-0.38810.66463.19030.44881.814-0.10990.030.1144-0.16440.04570.3846-0.2093-0.23340.06420.11060.00430.00050.095-0.08440.1966-87.6621-109.20250.0893
382.93270.29820.60091.9219-0.29753.21910.0535-0.2209-0.03820.048-0.07520.14160.21890.06740.02170.1030.02550.04690.1172-0.1160.2146-81.06-109.30312.9777
392.6122-0.12080.82291.7431-0.61912.4939-0.0342-0.41480.13560.1293-0.02230.2825-0.0791-0.08770.05650.11290.0130.06550.1443-0.1210.2122-83.0539-104.209116.7565
409.53031.3868-0.63718.6102-1.03387.691-0.0495-0.0240.17480.03430.14690.5914-0.0226-0.6808-0.09730.16080.05250.0020.1641-0.09020.2248-96.8476-102.273410.7683
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 31
2X-RAY DIFFRACTION2A32 - 56
3X-RAY DIFFRACTION3A57 - 137
4X-RAY DIFFRACTION4A138 - 149
5X-RAY DIFFRACTION5A150 - 178
6X-RAY DIFFRACTION6A179 - 198
7X-RAY DIFFRACTION7A199 - 232
8X-RAY DIFFRACTION8A233 - 257
9X-RAY DIFFRACTION9A258 - 289
10X-RAY DIFFRACTION10A290 - 337
11X-RAY DIFFRACTION11B9 - 33
12X-RAY DIFFRACTION12B34 - 56
13X-RAY DIFFRACTION13B57 - 85
14X-RAY DIFFRACTION14B86 - 147
15X-RAY DIFFRACTION15B148 - 184
16X-RAY DIFFRACTION16B185 - 200
17X-RAY DIFFRACTION17B201 - 228
18X-RAY DIFFRACTION18B229 - 254
19X-RAY DIFFRACTION19B255 - 295
20X-RAY DIFFRACTION20B296 - 336
21X-RAY DIFFRACTION21C9 - 26
22X-RAY DIFFRACTION22C27 - 39
23X-RAY DIFFRACTION23C40 - 71
24X-RAY DIFFRACTION24C72 - 88
25X-RAY DIFFRACTION25C89 - 117
26X-RAY DIFFRACTION26C118 - 136
27X-RAY DIFFRACTION27C137 - 155
28X-RAY DIFFRACTION28C156 - 257
29X-RAY DIFFRACTION29C258 - 291
30X-RAY DIFFRACTION30C292 - 335
31X-RAY DIFFRACTION31D9 - 34
32X-RAY DIFFRACTION32D35 - 85
33X-RAY DIFFRACTION33D86 - 130
34X-RAY DIFFRACTION34D131 - 184
35X-RAY DIFFRACTION35D185 - 195
36X-RAY DIFFRACTION36D196 - 224
37X-RAY DIFFRACTION37D225 - 254
38X-RAY DIFFRACTION38D255 - 289
39X-RAY DIFFRACTION39D290 - 324
40X-RAY DIFFRACTION40D325 - 336

+
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