[English] 日本語
Yorodumi
- PDB-6qxh: Crystal structure of His-tag human thymidylate synthase (HT-hTS) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qxh
TitleCrystal structure of His-tag human thymidylate synthase (HT-hTS) in complex with dUMP
ComponentsThymidylate synthase
KeywordsTRANSFERASE / human thymidylate synthase / folate pathway / substrate / dUMP
Function / homology
Function and homology information


uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion ...uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion / thymidylate synthase activity / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / developmental growth / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to cytokine / response to progesterone / liver regeneration / response to toxic substance / circadian rhythm / response to ethanol / methylation / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / protein homodimerization activity / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsPozzi, C. / Mangani, M.
Funding support1items
OrganizationGrant numberCountry
European UnionLSH-2005-2.2.0-8
CitationJournal: Molecules / Year: 2019
Title: Structural Comparison ofEnterococcus faecalisand Human Thymidylate Synthase Complexes with the Substrate dUMP and Its Analogue FdUMP Provides Hints about Enzyme Conformational Variabilities.
Authors: Pozzi, C. / Ferrari, S. / Luciani, R. / Tassone, G. / Costi, M.P. / Mangani, S.
History
DepositionMar 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thymidylate synthase
B: Thymidylate synthase
C: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8069
Polymers111,6443
Non-polymers1,1626
Water3,693205
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1876
Polymers74,4292
Non-polymers7584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-35 kcal/mol
Surface area21660 Å2
MethodPISA
2
C: Thymidylate synthase
hetero molecules

C: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2386
Polymers74,4292
Non-polymers8084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area5860 Å2
ΔGint-51 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.110, 61.590, 101.100
Angle α, β, γ (deg.)90.00, 115.38, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Thymidylate synthase / TSase


Mass: 37214.547 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS, OK/SW-cl.29 / Plasmid: pQE80L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04818, thymidylate synthase

-
Non-polymers , 5 types, 211 molecules

#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 27-30 % wt/vol PEG4000, 30 mM ammonium sulfate and 0.1 M TRIS, pH 9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.04→34.19 Å / Num. obs: 62630 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 43.18 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Net I/σ(I): 12.8
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 9114 / CC1/2: 0.937 / Rpim(I) all: 0.206 / Rrim(I) all: 0.528 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HWY
Resolution: 2.04→34.19 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 16.95 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.175
RfactorNum. reflection% reflectionSelection details
Rfree0.23676 4434 7.1 %RANDOM
Rwork0.18665 ---
obs0.19031 58183 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.393 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å22.87 Å2
2---2.98 Å20 Å2
3----0.63 Å2
Refine analyzeLuzzati coordinate error obs: 0.356 Å
Refinement stepCycle: LAST / Resolution: 2.04→34.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6804 0 73 205 7082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0127060
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.941.6369580
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8945859
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94321.952374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.645151115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9811546
X-RAY DIFFRACTIONr_chiral_restr0.1370.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025461
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.6393.723445
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.6695.5694301
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2533.8753615
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.16750.44710578
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 310 -
Rwork0.357 4281 -
obs--96.57 %
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)
10.45220.25420.76121.9707-3.07828.0309-0.09710.0274-0.02090.04740.0586-0.065-0.4411-0.01970.03840.3580.0357-0.08190.38320.06520.3356-28.362314.446518.3248
25.7255-0.0555-4.51246.4281-1.13863.8977-0.3656-1.84740.4392-0.61490.4472-0.45290.26951.5267-0.08160.257-0.0315-0.18260.91610.0370.3208-25.72566.333634.4364
31.9251-0.75611.35830.943-1.78653.49330.10190.09240.1710.1164-0.16450.0239-0.30760.52060.06260.40060.042-0.22560.5290.0710.2456-33.61049.188224.9793
46.1382-1.22560.21190.89030.08120.0319-0.0330.563-0.04820.03380.0366-0.0969-0.0120.0534-0.00370.35630.0269-0.14340.58380.02450.1636-31.19314.05549.6204
54.07350.5985-3.20952.3154-0.6122.548-0.12440.3111-0.3763-0.3135-0.09090.09020.1084-0.18540.21530.35530.0151-0.23970.3549-0.19740.4115-41.6417-9.881314.2442
61.467-3.3503-1.11947.71172.5881.42720.00730.1768-0.4402-0.1479-0.45870.8517-0.35340.07490.45140.34060.0392-0.04310.2718-0.03330.7672-35.5352-14.188216.0305
79.2692-0.5767-0.77627.2557-2.61851.49050.1207-0.1883-0.370.3832-0.2831-0.293-0.24010.18090.16250.29110.0224-0.16120.17450.00620.5459-37.2099-20.751930.2598
84.3503-4.8682-1.35989.8598-0.5441.4069-0.31430.2399-0.4850.37360.16340.36820.0966-0.24410.15090.2881-0.0026-0.18790.2815-0.09570.5722-43.9589-13.841724.0512
92.64540.81721.41330.50610.44520.75760.10980.2306-0.65270.22650.18720.0350.03030.1274-0.2970.43390.0339-0.08060.1790.00840.6378-52.574-9.786223.9081
100.1021-0.4-0.09348.37542.96541.08290.22310.0450.01450.2787-0.0988-0.3130.2581-0.036-0.12430.78270.0016-0.0510.16210.01820.4367-50.3776-21.030421.6734
110.08470.59610.193612.2335-3.27443.5744-0.05060.0228-0.0143-0.3460.37510.9351-0.07290.0666-0.32450.2680.0163-0.17470.2459-0.00280.561-57.0303-10.408221.0341
122.8689-0.44380.80630.11480.16223.00290.1720.3436-0.4335-0.0296-0.02420.1028-0.0646-0.3295-0.14780.32480.0377-0.28620.50260.03320.4275-58.43966.17616.3036
130.92481.8192-0.56967.5141-1.9540.52950.161-0.1202-0.47620.0481-0.17010.3165-0.06440.03830.00910.320.0787-0.13650.2180.11420.6534-47.5526-6.682230.36
144.3981-5.05932.99937.7381-5.29223.9759-0.16530.2841-0.24130.1043-0.04540.0765-0.0566-0.04040.21070.35080.0412-0.13310.35290.0340.2978-47.56686.579620.7607
151.7865-0.0704-0.0140.0624-0.08521.1605-0.07020.1597-0.11870.004-0.06140.05030.12090.04690.13160.41660.0573-0.22390.47810.01240.2714-38.74435.280418.6799
162.1477-0.9915-2.42340.80240.80923.01640.1629-0.11730.2057-0.1329-0.1292-0.3078-0.19050.2913-0.03370.3172-0.0016-0.1640.52390.15020.3086-21.31548.862114.164
171.0853-2.14050.72425.6729-0.80660.75610.2870.413-0.3598-0.4113-0.12570.82520.21640.5702-0.16130.26660.1205-0.17810.6621-0.18010.2758-47.4923-2.20512.6842
1813.03660.3711-1.84720.6827-0.92471.4007-0.03450.0789-0.1419-0.0374-0.0701-0.03410.05890.06830.10460.4490.0496-0.12690.4569-0.11350.2242-39.1622-1.4471.1131
197.05281.98335.30651.1412.48525.7612-0.14610.00860.2202-0.22320.1057-0.0801-0.33010.10190.04040.3540.08120.07680.4720.05270.2812-23.96183.55096.6689
206.13083.1149-6.42151.801-3.64117.3949-0.07990.114-0.16950.06280.0025-0.0481-0.1111-0.08380.07750.34510.05220.05970.33050.01880.2558-22.5837-3.750921.4404
211.3428-2.03110.47173.183-0.59290.3101-0.1875-0.06690.28880.23850.136-0.5281-0.1406-0.02530.05150.40030.0355-0.27590.33270.00650.5515-41.284328.096135.5164
225.2653.53716.72532.51224.60798.6573-0.29210.219-0.0159-0.37180.3824-0.1207-0.54970.3846-0.09030.536-0.13160.00210.3647-0.04780.5322-46.731427.904823.6051
2311.956113.4061.996715.03572.20224.63730.09710.00960.02980.1276-0.01160.0071-0.0417-0.2402-0.08550.36870.0687-0.08610.29550.10750.3383-57.481221.745517.1349
241.2446-0.04030.03341.2566-0.20611.3612-0.149-0.01420.2014-0.11120.0444-0.1775-0.23280.18640.10460.42180.0706-0.26030.37080.02490.2551-47.388720.440332.2843
254.76263.387-0.32696.4728-2.02120.8157-0.0211-0.34260.5660.69890.03940.4283-0.3484-0.0638-0.01830.49620.0722-0.16230.412-0.01640.2589-53.75226.006743.829
260.1384-0.04690.19350.65561.38613.5679-0.3679-0.2344-0.1840.29710.30780.25480.11590.42070.06010.6760.53530.31670.57530.43020.3997-59.07389.838646.1737
272.0371.16711.20433.53322.39333.4782-0.2961-0.1718-0.17670.10080.1850.4697-0.4339-0.08490.11120.2920.22010.04210.35720.18340.4126-67.22513.502144.0943
281.532-1.4965-2.53014.8192-0.21046.330.08590.1259-0.02170.0758-0.02020.1314-0.2284-0.2576-0.06580.29180.04050.00550.30470.04710.3721-75.22878.035932.5727
291.82122.40883.69286.33118.044210.66650.0738-0.0215-0.05740.0123-0.04210.02620.0583-0.091-0.03170.2185-0.01070.03170.29140.07090.408-74.32223.408337.889
303.0358-0.0288-0.32870.00430.02691.9155-0.3354-0.2516-0.28190.02090.04210.03990.19470.19650.29330.35830.11010.04830.27050.21580.5128-60.1129-0.369439.7478
319.79651.07060.23242.09460.54680.8541-0.2052-0.2945-0.38510.5810.1850.06850.09620.19030.02020.42310.10180.08050.24210.20920.2716-59.1094-3.925844.7699
323.13440.84540.39610.2793-0.15821.6201-0.12190.0114-0.3453-0.1205-0.0981-0.11050.54620.40230.220.56660.2704-0.04390.44350.24090.376-41.8218-0.294340.8261
336.25791.0651-9.14113.9715-1.846613.3834-0.2143-0.0505-0.3104-0.6898-0.14240.32620.31440.06660.35660.30960.0173-0.00470.22990.04750.4371-61.3026-1.497230.2113
347.9684-0.14712.14770.69360.1560.8901-0.2101-0.1386-0.23540.27660.12310.1821-0.04910.07620.0870.35620.0803-0.10380.35020.09650.2552-45.31937.93837.3502
351.0072-0.90430.1151.348-0.67540.8284-0.0888-0.12250.16640.05290.0545-0.00360.03850.02180.03430.42220.0743-0.22150.47010.00780.3019-48.085715.727936.8889
360.1885-0.7219-1.16042.88164.78378.40170.0304-0.02970.0696-0.3180.0009-0.1599-0.6126-0.2647-0.03140.42290.1013-0.14330.2255-0.01860.4613-54.061734.344929.6537
371.3994-1.65182.45526.3979-1.81274.6752-0.2903-0.20040.29890.196-0.0455-0.5494-0.3024-0.29880.33570.49650.1462-0.30130.4877-0.12950.2173-44.770527.920346.7952
382.0262-3.1525-0.69757.85615.61688.0043-0.173-0.4388-0.05280.18820.55420.0409-0.01360.2497-0.38120.53180.21430.05180.55120.10040.2262-48.29456.032356.7948
391.2408-0.1272-1.05040.33380.64791.8135-0.1175-0.6290.41880.035-0.00650.24010.10340.35990.1240.36960.1177-0.06160.4663-0.2550.4045-50.753724.097550.5997
408.80848.2453-0.17737.73590.06183.0726-0.09030.1899-0.3409-0.10610.1828-0.3293-0.1337-0.1207-0.09240.25580.0547-0.08760.3249-0.02710.4948-61.927327.944233.5684
412.63161.0525-0.77731.73771.70393.3177-0.1896-0.125-0.3776-0.03570.1702-0.19460.12480.33260.01940.2423-0.0028-0.25250.44020.08280.5514-83.64354.548711.108
426.22111.85644.65358.72790.38293.60480.2450.0641-0.35170.02490.03160.05430.18050.0533-0.27660.2744-0.0056-0.16130.4068-0.03970.4093-79.44295.80721.615
431.35291.4699-0.02399.02-3.65575.76330.10730.2168-0.2424-0.4363-0.2048-0.08960.32380.26210.09750.23110.0657-0.10690.4392-0.13530.3367-74.282810.3617-6.853
440.1661-0.5057-0.46461.65051.50521.3744-0.02550.0465-0.05110.0543-0.00290.02310.0438-0.02660.02840.32890.0063-0.02920.3948-0.02110.3274-68.046321.9264-4.3359
451.3683-1.00080.65490.8519-0.51940.330.20150.099-0.627-0.06450.03510.25030.05830.0185-0.23650.1421-0.0021-0.24310.3728-0.14720.7021-85.780612.17514.0563
461.3329-0.64060.1290.8588-0.35280.1977-0.0756-0.3343-0.29860.24050.0820.0106-0.19090.0648-0.00640.4437-0.0307-0.19710.5589-0.01450.2583-79.325822.870818.0308
473.12722.23650.34152.3511.96544.40360.0244-0.37910.42080.1996-0.26940.22920.44830.0560.2450.3984-0.0467-0.19680.5164-0.02040.425-72.134931.510717.2254
4810.06522.9101-4.61938.2411-6.80046.1570.0395-0.44070.305-0.29810.08920.02360.21450.0211-0.12870.3666-0.0947-0.05970.4133-0.01540.235-66.47638.90555.1879
490.93931.60410.06432.77110.10280.1028-0.06960.0574-0.13710.00670.1075-0.3205-0.1407-0.1165-0.03790.47410.0355-0.20730.4815-0.04950.2646-80.065839.57068.2838
509.5234-0.8976-0.68681.45861.86063.8821-0.03910.02890.1371-0.04420.00980.0529-0.29310.01180.02920.3783-0.019-0.00910.2598-0.04880.2651-81.983846.386410.9226
511.93382.8874-0.44944.3197-0.67450.11380.0755-0.03770.21020.0542-0.0210.3377-0.0325-0.0573-0.05450.47460.0628-0.11740.4990.03710.1995-94.565936.767513.0057
521.7503-0.8006-0.65511.17180.52160.3115-0.2055-0.1431-0.0018-0.27640.22660.1556-0.06160.0715-0.02110.35540.0757-0.17830.59390.0650.2461-100.035227.66899.3414
534.16533.94911.98723.7651.59778.67510.19010.0661-0.20860.23170.0447-0.2388-0.3248-0.4722-0.23480.3873-0.008-0.06490.43280.04580.26-82.78538.4134-0.8679
543.02594.83790.41689.012-1.00162.33060.0395-0.3444-0.0164-0.237-0.4082-0.30260.135-0.19310.36870.4921-0.04720.02450.3359-0.08310.2897-81.442629.58923.1339
550.927-0.27540.08450.1350.08420.3870.1158-0.0877-0.27310.00190.0918-0.0265-0.0821-0.0085-0.20770.28670.0138-0.2070.53160.00730.3628-85.423317.44879.6207
561.9180.1151-2.14392.3524-1.89310.80920.07530.1752-0.27570.00760.0547-0.04260.1711-0.0008-0.12990.24310.0228-0.06740.2533-0.00980.4258-74.1881.942513.6293
575.2728-0.2683-0.8860.93020.07440.1958-0.0734-0.787-0.21330.4110.0499-0.1418-0.10370.06810.02340.5290.1454-0.13290.5790.11160.0756-88.187522.380626.0864
589.4181-4.36214.28517.51521.35553.99080.0439-0.56150.07170.4041-0.1023-0.11570.1744-0.53450.05850.46090.1409-0.18070.45880.12110.1888-83.307421.870828.2431
5910.6748-3.0226-6.41065.49371.84864.8040.0343-0.4964-0.62190.08870.1317-0.18260.04680.1069-0.16610.16090.0603-0.12490.2920.0960.4211-76.83328.461123.4017
602.02022.0466-2.9686.1994-8.917812.83760.2709-0.0777-0.24970.5345-0.05160.1884-0.76990.1353-0.21930.35060.0506-0.14010.38690.01380.3548-66.209815.44189.9419
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 39
2X-RAY DIFFRACTION2A40 - 50
3X-RAY DIFFRACTION3A51 - 68
4X-RAY DIFFRACTION4A69 - 81
5X-RAY DIFFRACTION5A82 - 99
6X-RAY DIFFRACTION6A100 - 111
7X-RAY DIFFRACTION7A112 - 127
8X-RAY DIFFRACTION8A128 - 137
9X-RAY DIFFRACTION9A138 - 146
10X-RAY DIFFRACTION10A147 - 152
11X-RAY DIFFRACTION11A153 - 160
12X-RAY DIFFRACTION12A161 - 177
13X-RAY DIFFRACTION13A178 - 192
14X-RAY DIFFRACTION14A193 - 205
15X-RAY DIFFRACTION15A206 - 262
16X-RAY DIFFRACTION16A263 - 277
17X-RAY DIFFRACTION17A278 - 293
18X-RAY DIFFRACTION18A294 - 299
19X-RAY DIFFRACTION19A300 - 306
20X-RAY DIFFRACTION20A307 - 313
21X-RAY DIFFRACTION21B26 - 34
22X-RAY DIFFRACTION22B35 - 43
23X-RAY DIFFRACTION23B44 - 49
24X-RAY DIFFRACTION24B50 - 73
25X-RAY DIFFRACTION25B74 - 82
26X-RAY DIFFRACTION26B83 - 98
27X-RAY DIFFRACTION27B99 - 114
28X-RAY DIFFRACTION28B115 - 122
29X-RAY DIFFRACTION29B123 - 130
30X-RAY DIFFRACTION30B131 - 148
31X-RAY DIFFRACTION31B149 - 161
32X-RAY DIFFRACTION32B162 - 182
33X-RAY DIFFRACTION33B183 - 189
34X-RAY DIFFRACTION34B190 - 208
35X-RAY DIFFRACTION35B209 - 260
36X-RAY DIFFRACTION36B261 - 270
37X-RAY DIFFRACTION37B271 - 282
38X-RAY DIFFRACTION38B283 - 290
39X-RAY DIFFRACTION39B291 - 306
40X-RAY DIFFRACTION40B307 - 313
41X-RAY DIFFRACTION41C26 - 34
42X-RAY DIFFRACTION42C35 - 39
43X-RAY DIFFRACTION43C40 - 48
44X-RAY DIFFRACTION44C49 - 54
45X-RAY DIFFRACTION45C55 - 68
46X-RAY DIFFRACTION46C69 - 99
47X-RAY DIFFRACTION47C100 - 110
48X-RAY DIFFRACTION48C111 - 121
49X-RAY DIFFRACTION49C122 - 144
50X-RAY DIFFRACTION50C145 - 153
51X-RAY DIFFRACTION51C154 - 165
52X-RAY DIFFRACTION52C166 - 182
53X-RAY DIFFRACTION53C183 - 189
54X-RAY DIFFRACTION54C190 - 198
55X-RAY DIFFRACTION55C199 - 267
56X-RAY DIFFRACTION56C268 - 274
57X-RAY DIFFRACTION57C275 - 293
58X-RAY DIFFRACTION58C294 - 298
59X-RAY DIFFRACTION59C299 - 304
60X-RAY DIFFRACTION60C305 - 313

+
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