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- PDB-5pzu: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosph... -

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Basic information

Entry
Database: PDB / ID: 5pzu
TitleHuman liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor [5-[2-amino-5-(2-methylpropyl)-1,3-thiazol-4-yl]furan-2-yl]phosphonic acid
ComponentsFructose-1,6-bisphosphatase 1Fructose 1,6-bisphosphatase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / D3R docking / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process ...cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process / fructose metabolic process / Gluconeogenesis / monosaccharide binding / negative regulation of glycolytic process / cellular hyperosmotic salinity response / regulation of gluconeogenesis / AMP binding / dephosphorylation / cellular response to cAMP / response to nutrient levels / gluconeogenesis / negative regulation of cell growth / cellular response to insulin stimulus / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / metal ion binding / nucleus / 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
Chem-94D / Fructose-1,6-bisphosphatase 1 / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.901 Å
Model detailsFor D3R project
AuthorsRuf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G. / Yang, H. / Shao, C. / Burley, S.K.
CitationJournal: To be published
Title: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor [5-[2-amino-5-(2-methylpropyl)-1,3-thiazol-4-yl]furan-2-yl]phosphonic acid
Authors: Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.2Feb 6, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Feb 10, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Mar 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)148,6478
Polymers147,4384
Non-polymers1,2094
Water24,9691386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15550 Å2
ΔGint-81 kcal/mol
Surface area44410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.657, 83.267, 277.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 61 or resid 72...
21(chain B and (resid 9 through 139 or resid 141 through 156 or resid 158 through 335))
31(chain C and (resid 9 through 61 or resid 72...
41(chain D and (resid 9 through 139 or resid 141 through 156 or resid 158 through 335))

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
11ASPASPGLYGLY(chain A and (resid 9 through 61 or resid 72...AA9 - 6110 - 62
12LYSLYSTYRTYR(chain A and (resid 9 through 61 or resid 72...AA72 - 13973 - 140
13LYSLYSGLYGLY(chain A and (resid 9 through 61 or resid 72...AA141 - 156142 - 157
14ASNASNSERSER(chain A and (resid 9 through 61 or resid 72...AA158 - 335159 - 336
21ASPASPTYRTYR(chain B and (resid 9 through 139 or resid 141 through 156 or resid 158 through 335))BB9 - 13910 - 140
22LYSLYSGLYGLY(chain B and (resid 9 through 139 or resid 141 through 156 or resid 158 through 335))BB141 - 156142 - 157
23ASNASNSERSER(chain B and (resid 9 through 139 or resid 141 through 156 or resid 158 through 335))BB158 - 335159 - 336
31ASPASPGLYGLY(chain C and (resid 9 through 61 or resid 72...CC9 - 6110 - 62
32LYSLYSTYRTYR(chain C and (resid 9 through 61 or resid 72...CC72 - 13973 - 140
33LYSLYSGLYGLY(chain C and (resid 9 through 61 or resid 72...CC141 - 156142 - 157
34ASNASNSERSER(chain C and (resid 9 through 61 or resid 72...CC158 - 335159 - 336
41ASPASPTYRTYR(chain D and (resid 9 through 139 or resid 141 through 156 or resid 158 through 335))DD9 - 13910 - 140
42LYSLYSGLYGLY(chain D and (resid 9 through 139 or resid 141 through 156 or resid 158 through 335))DD141 - 156142 - 157
43ASNASNSERSER(chain D and (resid 9 through 139 or resid 141 through 156 or resid 158 through 335))DD158 - 335159 - 336

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Components

#1: Protein
Fructose-1,6-bisphosphatase 1 / Fructose 1,6-bisphosphatase / Growth-inhibiting protein 17 / cDNA FLJ75786 / highly similar to Homo sapiens fructose-1 / 6- ...Growth-inhibiting protein 17 / cDNA FLJ75786 / highly similar to Homo sapiens fructose-1 / 6-bisphosphatase 1 (FBP1) / mRNA


Mass: 36859.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, hCG_1640493 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2TU34, UniProt: P09467*PLUS, fructose-bisphosphatase
#2: Chemical
ChemComp-94D / {5-[2-amino-5-(2-methylpropyl)-1,3-thiazol-4-yl]furan-2-yl}phosphonic acid


Mass: 302.287 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N2O4PS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1386 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES pH 7.0, 0.1M AMMONIUM ACETATE, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.987 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.901→28.961 Å / Num. obs: 123340 / % possible obs: 99.23 %

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.23data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→28.961 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 6225 5.05 %
Rwork0.1881 117115 -
obs0.1904 123340 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.7 Å2 / Biso mean: 23.6265 Å2 / Biso min: 4.65 Å2
Refinement stepCycle: final / Resolution: 1.901→28.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9729 0 76 1386 11191
Biso mean--19 36.97 -
Num. residues----1271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710077
X-RAY DIFFRACTIONf_angle_d0.94813628
X-RAY DIFFRACTIONf_chiral_restr0.0571536
X-RAY DIFFRACTIONf_plane_restr0.0061743
X-RAY DIFFRACTIONf_dihedral_angle_d11.9536138
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5998X-RAY DIFFRACTION9.598TORSIONAL
12B5998X-RAY DIFFRACTION9.598TORSIONAL
13C5998X-RAY DIFFRACTION9.598TORSIONAL
14D5998X-RAY DIFFRACTION9.598TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9012-1.92280.36221650.33373100326580
1.9228-1.94540.31722100.29253869407999
1.9454-1.96920.32981990.270138324031100
1.9692-1.99410.32142070.255239234130100
1.9941-2.02030.32352240.25438634087100
2.0203-2.0480.30822130.246438734086100
2.048-2.07720.30542040.23638834087100
2.0772-2.10820.28982190.22939034122100
2.1082-2.14120.27552170.216138844101100
2.1412-2.17630.28011850.219839264111100
2.1763-2.21380.25972020.215438524054100
2.2138-2.2540.29271980.23239564154100
2.254-2.29730.26591980.200638714069100
2.2973-2.34420.23371940.192339454139100
2.3442-2.39520.23422190.183238774096100
2.3952-2.45090.23441910.185639384129100
2.4509-2.51210.25912210.183339024123100
2.5121-2.580.24552090.184739054114100
2.58-2.65590.24792030.182639114114100
2.6559-2.74150.23882210.17939414162100
2.7415-2.83940.25472100.171139204130100
2.8394-2.9530.22992030.172139384141100
2.953-3.08730.22352230.166439624185100
3.0873-3.24980.19762170.157139294146100
3.2498-3.45310.19012040.158739684172100
3.4531-3.71920.20752100.158139504160100
3.7192-4.09260.19222210.159639754196100
4.0926-4.68260.16342260.144340004226100
4.6826-5.89150.18691950.160740654260100
5.8915-28.96460.22862170.203842544471100
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)
10.0215-0.0011-0.00350.00430.00230.01390.00280.0363-0.00690.0058-0.0069-0.0072-0.0765-0.0281-0.01630.0887-0.00480.00920.0660.00080.053216.120142.429517.4257
20.0028-0.00040.0054-0.00070.00020.00410.00730.0278-0.0374-0.0020.0218-0.0353-0.02810.019900.0863-0.0260.0140.1395-0.00050.112219.505239.92210.4006
30.00770.0095-0.0090.017-0.00240.0118-0.00850.04320.0246-0.03680.0224-0.0118-0.077-0.0057-0.00640.1182-0.02440.01490.09330.0110.075727.664248.411513.9968
40.01420.00250.00670.00010.00070.0032-0.00450.02050.0185-0.0097-0.0127-0.0178-0.0047-0.0035-0.01440.0901-0.0680.04920.21680.01880.158249.931736.90112.9255
50.01590.00340.00460.06020.00940.01010.02240.0406-0.0039-0.0474-0.0008-0.0431-0.04730.03020.02570.094-0.09330.05940.14540.00830.031536.884445.55792.7022
60.0017-0-0.00320.00050.00140.0078-0.020.0091-0.0029-0.00740.0011-0.00370.0079-0.0014-0.0010.0641-0.0045-0.00540.0582-0.02230.142226.06465.140832.8162
70.0079-0.00260.00730.00290.00490.0089-0.0003-0.0353-0.0263-0.0080.0142-0.0107-0.02930.0227-0.00350.04910.0034-0.00990.0719-0.02260.066734.289726.688837.3328
80.0012-0.00070.00070.0012-0.00050.00090.0159-0.00450.0195-0.00220.0107-0.0131-0.0118-0.008700.0973-0.0296-0.03180.1451-0.00540.140647.809218.459740.8708
90.00440.00420.00680.00710.01460.02990.03380.00080.0042-0.01540.0318-0.0118-0.02440.02040.00270.08390.01460.01510.1468-0.02720.160442.319322.558833.5127
100.00540.0045-0.00980.01830.00780.02810.0302-0.0104-0.00750.00890.0018-0.0187-0.0147-0.01070.02720.04930.0069-0.00940.1192-0.02580.089945.373411.727532.1601
110.0216-0.011-0.01040.01620.00780.0092-0.00260.0333-0.01620.02070.035-0.00850.01940.03440.02820.04890.01040.0110.0621-0.05090.088231.697715.839219.6486
120.0383-0.00540.01330.01640.00890.01390.01850.0804-0.0182-0.02160-0.0249-0.00730.062-0.0071-0.00750.01530.05410.1466-0.07330.001547.682621.368711.6114
130.0037-0.01470.00070.05580.00210.0269-0.02490.0227-0.0189-0.0238-0.0289-0.00210.0069-0.011-0.04460.0540.04010.03920.1753-0.08570.113352.897413.05614.3192
140.0026-0.00440.0010.00770.0070.00380.00630.02250.0196-0.06470.03340.013-0.06140.000800.11130.010.01620.0611-0.00350.084716.426746.708737.2598
150.0371-0.0059-0.00460.0224-0.00240.0041-0.022-0.02430.00460.01940.0148-0.0072-0.00190.0133-0.01210.16450.0060.02480.0626-0.00320.07215.702752.728848.3303
160.0044-0.0034-0.00250.00590.00190.00290.0088-0.0090.0094-0.00020.0082-0.00760.00070.01390.00240.12370.02440.04580.0457-0.00930.05899.997161.409245.3307
170.0228-0.01260.01440.0274-0.00220.02050.03760.00050.0312-0.0046-0.00560.0406-0.0618-0.046600.08470.00920.01860.07490.00230.0908-3.486442.975646.9058
180.00380.0026-0.0040.01690.00280.00160.0217-0.03210.05340.03230.00630.0149-0.0279-0.03180.01560.08930.02280.01140.0752-0.00150.0772-4.788848.938853.4585
190.01020.0033-0.02050.0130.00180.02360.00090.0581-0.0594-0.0625-0.0103-0.0243-0.00030.027200.0663-0.00350.00820.06890.00240.098812.90413.953336.7456
200.00460.00410.00070.0028-0.00220.00730.00630.0181-0.01560.00280.01190.01930.0156-0.022500.0993-0.0010.01820.0513-0.00310.11595.95319.066541.1458
210.0041-0.0015-0.00590.00030.00050.00650.0197-0.002-0.05290.0034-0.0186-0.00860.0415-0.002800.07160.00140.01020.06960.01490.090912.298516.996851.5996
220.0090.00640.00180.01730.00060.01640.0267-0.0081-0.00570.0056-0.0231-0.01390.0133-0.047-0.00480.0793-0.00170.01210.08530.00380.072-2.64621.774659.4438
230.0039-0.00330.00080.0095-0.00210.0037-0.002-0.0355-0.01850.0249-0.01660.0306-0.01450.0032-0.00830.1097-0.01140.00720.06470.01580.0748-2.989211.950761.6818
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 106 )A9 - 106
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 131 )A107 - 131
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 212 )A132 - 212
4X-RAY DIFFRACTION4chain 'A' and (resid 213 through 247 )A213 - 247
5X-RAY DIFFRACTION5chain 'A' and (resid 248 through 335 )A248 - 335
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 28 )B9 - 28
7X-RAY DIFFRACTION7chain 'B' and (resid 29 through 88 )B29 - 88
8X-RAY DIFFRACTION8chain 'B' and (resid 89 through 106 )B89 - 106
9X-RAY DIFFRACTION9chain 'B' and (resid 107 through 131 )B107 - 131
10X-RAY DIFFRACTION10chain 'B' and (resid 132 through 170 )B132 - 170
11X-RAY DIFFRACTION11chain 'B' and (resid 171 through 212 )B171 - 212
12X-RAY DIFFRACTION12chain 'B' and (resid 213 through 291 )B213 - 291
13X-RAY DIFFRACTION13chain 'B' and (resid 292 through 335 )B292 - 335
14X-RAY DIFFRACTION14chain 'C' and (resid 9 through 88 )C9 - 88
15X-RAY DIFFRACTION15chain 'C' and (resid 89 through 131 )C89 - 131
16X-RAY DIFFRACTION16chain 'C' and (resid 132 through 148 )C132 - 148
17X-RAY DIFFRACTION17chain 'C' and (resid 149 through 247 )C149 - 247
18X-RAY DIFFRACTION18chain 'C' and (resid 248 through 335 )C248 - 335
19X-RAY DIFFRACTION19chain 'D' and (resid 9 through 106 )D9 - 106
20X-RAY DIFFRACTION20chain 'D' and (resid 107 through 148 )D107 - 148
21X-RAY DIFFRACTION21chain 'D' and (resid 149 through 212 )D149 - 212
22X-RAY DIFFRACTION22chain 'D' and (resid 213 through 291 )D213 - 291
23X-RAY DIFFRACTION23chain 'D' and (resid 292 through 335 )D292 - 335

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