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- PDB-3khd: Crystal Structure of PFF1300w. -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3khd
TitleCrystal Structure of PFF1300w.
ComponentsPyruvate kinase
KeywordsTRANSFERASE / malaria / pyruvate kinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Glycolysis / Neutrophil degranulation / pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / protein homotetramerization / phosphorylation / magnesium ion binding ...Glycolysis / Neutrophil degranulation / pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / protein homotetramerization / phosphorylation / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsWernimont, A.K. / Hutchinson, A. / Hassanali, A. / Mackenzie, F. / Cossar, D. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. ...Wernimont, A.K. / Hutchinson, A. / Hassanali, A. / Mackenzie, F. / Cossar, D. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hui, R. / Pizarro, J.C. / Bakszt, R. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of PFF1300w.
Authors: Wernimont, A.K. / Hutchinson, A. / Hassanali, A. / Mackenzie, F. / Cossar, D. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hui, R. / Pizarro, J.C. / Hills, T.
History
DepositionOct 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Pyruvate kinase
B: Pyruvate kinase
C: Pyruvate kinase
D: Pyruvate kinase


Theoretical massNumber of molelcules
Total (without water)227,4244
Polymers227,4244
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11810 Å2
ΔGint-107 kcal/mol
Surface area66280 Å2
MethodPISA
2
A: Pyruvate kinase
C: Pyruvate kinase


Theoretical massNumber of molelcules
Total (without water)113,7122
Polymers113,7122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-44 kcal/mol
Surface area34100 Å2
MethodPISA
3
B: Pyruvate kinase
D: Pyruvate kinase


Theoretical massNumber of molelcules
Total (without water)113,7122
Polymers113,7122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-44 kcal/mol
Surface area34980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.749, 94.285, 125.164
Angle α, β, γ (deg.)90.000, 94.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVALAA354 - 366354 - 366
21METMETVALVALBB354 - 366354 - 366
31METMETVALVALCC354 - 366354 - 366
41METMETVALVALDD354 - 366354 - 366
12ASPASPGLYGLYAA495 - 502495 - 502
22ASPASPGLYGLYBB495 - 502495 - 502
32ASPASPGLYGLYCC495 - 502495 - 502
42ASPASPGLYGLYDD495 - 502495 - 502

NCS ensembles :
ID
1
2

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Components

#1: Protein
Pyruvate kinase /


Mass: 56855.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PFF1300w / Plasmid: p15mlh / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: C6KTA4, pyruvate kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10 % PEG8k, 0.2 M Tris HCl, 4 mM MgAcetate, 2 mM AMPPNP, 2 mM NaPyruvate, 2 mM TCEP, 25% glycerol cryoprotectant, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 69260 / Num. obs: 68983 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 69.3 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.075 / Χ2: 1.283 / Net I/σ(I): 8.3
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 1.57 / Num. unique all: 3393 / Rsym value: 0.638 / Χ2: 0.806 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→35 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.297 / WRfactor Rwork: 0.259 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.767 / SU B: 31.859 / SU ML: 0.297 / SU R Cruickshank DPI: 0.643 / SU Rfree: 0.357 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.643 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.297 3463 5 %RANDOM
Rwork0.262 ---
all0.264 69484 --
obs0.264 68588 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 37.41 Å2 / Biso mean: 29.798 Å2 / Biso min: 18.55 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å20 Å20.62 Å2
2--1.05 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.7→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12367 0 0 1 12368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02212492
X-RAY DIFFRACTIONr_angle_refined_deg0.8791.97516977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.20251734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.47125.899395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.812151988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3231537
X-RAY DIFFRACTIONr_chiral_restr0.0530.22152
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219041
X-RAY DIFFRACTIONr_mcbond_it0.1331.58719
X-RAY DIFFRACTIONr_mcangle_it0.258213791
X-RAY DIFFRACTIONr_scbond_it0.4233773
X-RAY DIFFRACTIONr_scangle_it0.7584.53186
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A81TIGHT POSITIONAL0.010.05
1B81TIGHT POSITIONAL0.010.05
1C81TIGHT POSITIONAL0.010.05
1D81TIGHT POSITIONAL0.010.05
1A81TIGHT THERMAL0.010.5
1B81TIGHT THERMAL0.040.5
1C81TIGHT THERMAL0.020.5
1D81TIGHT THERMAL0.020.5
2A56TIGHT POSITIONAL0.010.05
2B56TIGHT POSITIONAL0.030.05
2C56TIGHT POSITIONAL0.030.05
2D56TIGHT POSITIONAL0.020.05
2A56TIGHT THERMAL0.010.5
2B56TIGHT THERMAL0.020.5
2C56TIGHT THERMAL0.020.5
2D56TIGHT THERMAL0.010.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 200 -
Rwork0.34 4265 -
all-4465 -
obs-3393 87.67 %
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)
11.3582-0.28370.43241.05620.14351.52680.1110.4064-0.3082-0.5782-0.03040.22690.3199-0.0952-0.08060.5117-0.1109-0.0380.4971-0.00190.26119.28138.61460.0882
20.29170.24230.20454.27451.86140.85140.26690.2055-0.2611-0.2216-0.32580.39710.0258-0.12770.05890.7693-0.0763-0.20610.86380.00820.5655-4.567720.8778-7.0932
30.54640.6678-0.7892.4039-1.39091.33810.1150.10550.0745-0.0446-0.0502-0.2745-0.04290.0721-0.06470.44130.009-0.0110.56690.08620.482719.724641.9734-5.9133
44.2040.47830.35240.9221-0.39761.42080.19340.15980.0085-0.1078-0.1428-0.3486-0.17630.1238-0.05070.53680.0091-0.01590.48220.10580.535118.36540.7541-3.1291
55.20890.4630.74763.2793-0.27621.9168-0.06160.03430.2330.06050.07210.0898-0.2557-0.1658-0.01040.409-0.01440.00530.36620.09580.24329.150731.925910.0115
61.0479-0.1279-0.94431.3716-0.32041.6791-0.05790.31990.1674-0.5079-0.0722-0.2596-0.0560.06910.13010.4285-0.04460.01240.4140.06620.30619.901418.00862.756
71.6143-0.31440.08981.8889-0.65312.7302-0.0050.3716-0.023-0.29320.0220.01660.15850.2551-0.01690.275-0.08530.01890.27960.02570.294513.54839.64069.9674
82.80940.32440.64353.3362-0.28642.7704-0.10810.10110.1125-0.15040.11460.0218-0.0478-0.2979-0.00650.1809-0.04870.00330.25220.03740.1352.86049.408320.7097
91.70480.53071.77911.3149-0.3862.67550.2401-0.0885-0.0150.08980.14590.4580.2351-0.3961-0.3860.4517-0.06710.00290.55190.02450.4165-5.87479.063913.7944
105.03190.1314-0.33028.54230.83064.6879-0.10020.17440.3361-0.39260.1680.5746-0.4087-0.4551-0.06780.259-0.0367-0.02520.37940.08090.2446-3.29765.772425.092
111.71311.652-0.57962.9008-2.19752.3169-0.1465-0.22220.4510.2973-0.09790.0489-0.6261-0.02580.24430.3941-0.0421-0.02380.3734-0.07410.401520.707611.405556.1332
122.71990.5267-0.49951.12630.67371.22970.1657-0.15780.15190.3091-0.09980.2382-0.1331-0.2569-0.06590.30240.08060.12970.1994-0.00430.2565-4.1687-5.210266.9652
131.8595-0.97380.78261.7788-1.27661.23790.0129-0.16190.07050.0758-0.0661-0.2274-0.01260.30170.05320.20570.0079-0.03040.2706-0.01480.319716.1454-35.563874.8398
142.33720.60211.8551.1405-0.68213.14550.0598-0.00590.1540.1044-0.2584-0.26460.02860.40050.19860.21860.0452-0.01540.25950.02780.402720.2173-33.489770.2761
152.0909-0.0808-0.25192.0827-0.84021.0131-0.00580.169-0.1404-0.14890.00540.13810.1014-0.09270.00030.1168-0.0418-0.01930.0449-0.02040.1651.2944-23.284855.9141
161.8088-0.3772-0.00830.87220.01920.13960.0992-0.3248-0.00320.325-0.1198-0.24190.11890.13910.02060.259-0.0029-0.0390.26910.02480.23915.3283-9.694361.7896
171.9346-0.043-0.34231.2651-0.97753.23410.0341-0.02130.06750.076-0.0518-0.09-0.01930.24830.01760.102-0.02120.00380.0253-0.01510.23119.98870.647650.121
183.531.1681-0.46632.2181-0.33131.67640.0138-0.1047-0.08670.1524-0.00260.1507-0.0888-0.0189-0.01120.08050.03090.00310.0172-0.01180.131-1.6078-1.734346.0455
192.3361-1.6627-0.87232.29660.39360.61960.08930.15840.1245-0.16740.01020.2567-0.1083-0.2984-0.09950.17850.0260.01120.23160.00140.2065-7.2186.583346.3892
203.53480.01780.00930.0224-0.26796.55670.08030.0618-0.289-0.06840.0002-0.01050.2527-0.4134-0.08060.3283-0.01470.03070.36820.03870.269-5.06891.986335.1969
213.7108-0.8513-1.45931.6370.46121.0396-0.15530.18970.3038-0.3570.0554-0.3945-0.12990.22330.09990.3925-0.04490.0430.4950.09190.397637.453818.756610.2978
224.53653.005-0.39414.0049-1.3990.6781-0.24540.72180.3445-0.55010.085-0.14030.2450.17690.16040.7512-0.02650.29190.90880.0680.689452.216813.0492-4.0496
230.29720.9023-0.75864.1422-1.71892.9462-0.02570.1054-0.0765-0.6901-0.0148-0.4504-0.02090.36770.04050.59390.07850.2231.0728-0.00440.912555.79893.1402-6.0399
243.48620.81830.05013.8746-0.75960.35770.11390.2883-0.4057-0.2221-0.0707-0.11490.25340.1434-0.04320.75430.10020.15650.6939-0.0870.572542.6276-8.3430.5617
251.00360.22660.15882.5356-0.66280.8154-0.1430.43110.1498-0.5736-0.03-0.20620.16270.07350.17290.50650.00980.15180.560.03290.429535.16089.7120.1993
262.2161-0.5730.8540.8124-0.72132.42360.09720.1067-0.188-0.0726-0.0624-0.10250.09340.2282-0.03490.2671-0.01140.04860.34910.01520.443240.54085.832822.0293
270.58050.48621.31552.36311.23933.11830.10890.1602-0.0329-0.2551-0.1712-0.29590.09990.45150.06220.32130.02920.11590.49450.09070.586748.01533.480418.8891
2813.07371.7278-0.80291.9949-0.63750.2185-0.2693-0.2081-0.23650.07290.2319-0.17170.00630.00680.03740.530.03680.09530.78630.05710.622253.79284.713311.8964
290.23921.10181.72785.31078.36813.1987-0.2940.1736-0.022-0.42110.9105-0.2575-0.6961.7828-0.61650.863-0.3430.20761.11090.14891.249159.809614.007122.3355
305.22190.99470.653118.6446-3.20354.82630.1639-0.09020.1514-0.3106-0.3362-0.7583-0.09180.49550.17230.3363-0.09890.05570.6210.06850.545552.83819.314329.0081
311.53620.54820.07870.55470.23711.06740.0525-0.1702-0.06140.2857-0.0621-0.34770.19890.51730.00960.2892-0.0405-0.11270.46130.04490.514639.3403-10.925962.1538
320.5028-0.51970.017412.38746.701810.36850.1581-0.19260.51540.7835-0.0004-0.64120.15520.1876-0.15770.4297-0.0951-0.12720.87710.03560.887554.9608-3.459474.7951
331.8671-3.9364-4.729810.10559.753512.08550.170.2289-0.24640.2338-0.67670.2632-0.4299-0.43090.50670.4379-0.073-0.19570.64550.00530.665846.00494.946770.8236
344.412-2.1172-3.75529.0225-4.54298.8251-0.05430.01250.19781.3306-0.3081-0.1085-0.98960.23580.36240.6133-0.3076-0.22130.8289-0.26350.811250.261814.501176.2803
355.7589-2.2922-1.37662.63622.45922.7047-0.0451-0.08850.55750.1408-0.057-0.1325-0.24880.00430.10210.6398-0.2539-0.20610.6303-0.09290.636445.426215.888166.9796
362.341-0.95120.22161.24680.38790.34-0.1649-0.43340.43640.2270.06870.0082-0.0530.02840.09620.4852-0.2277-0.04570.5287-0.1310.531430.938113.415465.621
371.1506-0.206-0.22190.75480.34150.8498-0.0143-0.3724-0.0350.3609-0.0459-0.2248-0.07940.22540.06030.2777-0.1299-0.09350.4464-0.01020.407132.1917-3.254165.8719
382.22530.587-0.57270.35290.01932.00050.07530.02190.149-0.0917-0.0996-0.0853-0.16750.19580.02420.1774-0.0467-0.02240.30140.010.443240.79580.545745.3966
393.6891.5858-1.80020.6879-0.77550.89450.1259-0.2733-0.14940.0836-0.1075-0.0384-0.04580.1742-0.01840.2678-0.0758-0.10130.57120.00970.619653.54880.477855.1391
402.0799-1.03440.30682.36860.00615.14140.0169-0.2479-0.20990.51730.0709-0.6930.05380.5233-0.08780.2817-0.0327-0.07290.53250.02020.613953.7875-6.877341.7695
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 79
2X-RAY DIFFRACTION2A80 - 103
3X-RAY DIFFRACTION3A104 - 170
4X-RAY DIFFRACTION4A171 - 229
5X-RAY DIFFRACTION5A230 - 287
6X-RAY DIFFRACTION6A288 - 358
7X-RAY DIFFRACTION7A359 - 403
8X-RAY DIFFRACTION8A404 - 451
9X-RAY DIFFRACTION9A452 - 490
10X-RAY DIFFRACTION10A491 - 520
11X-RAY DIFFRACTION11B19 - 38
12X-RAY DIFFRACTION12B40 - 108
13X-RAY DIFFRACTION13B109 - 164
14X-RAY DIFFRACTION14B165 - 214
15X-RAY DIFFRACTION15B215 - 282
16X-RAY DIFFRACTION16B283 - 358
17X-RAY DIFFRACTION17B359 - 417
18X-RAY DIFFRACTION18B418 - 458
19X-RAY DIFFRACTION19B459 - 501
20X-RAY DIFFRACTION20B502 - 520
21X-RAY DIFFRACTION21C19 - 56
22X-RAY DIFFRACTION22C57 - 79
23X-RAY DIFFRACTION23C80 - 227
24X-RAY DIFFRACTION24C228 - 292
25X-RAY DIFFRACTION25C296 - 372
26X-RAY DIFFRACTION26C373 - 429
27X-RAY DIFFRACTION27C430 - 450
28X-RAY DIFFRACTION28C451 - 470
29X-RAY DIFFRACTION29C474 - 489
30X-RAY DIFFRACTION30C491 - 519
31X-RAY DIFFRACTION31D23 - 78
32X-RAY DIFFRACTION32D83 - 101
33X-RAY DIFFRACTION33D104 - 115
34X-RAY DIFFRACTION34D212 - 229
35X-RAY DIFFRACTION35D231 - 265
36X-RAY DIFFRACTION36D266 - 298
37X-RAY DIFFRACTION37D299 - 372
38X-RAY DIFFRACTION38D373 - 448
39X-RAY DIFFRACTION39D449 - 471
40X-RAY DIFFRACTION40D474 - 520

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