[English] 日本語
Yorodumi
- PDB-8oiw: Crystal structure of the cysteine-rich Gallus gallus urate oxidas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8oiw
TitleCrystal structure of the cysteine-rich Gallus gallus urate oxidase in complex with the 8-azaxanthine inhibitor under oxidising conditions (space group P 21 21 21)
Components(UricaseUrate oxidase) x 2
KeywordsOXIDOREDUCTASE / COFACTOR-FREE OXIDASE / INHIBITOR / DIOXYGEN BINDING / CYSTEINE
Function / homologyfactor-independent urate hydroxylase / Uricase / Uricase / purine nucleobase metabolic process / peroxisome / oxidoreductase activity / 8-AZAXANTHINE / OXYGEN MOLECULE / Uricase
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsDi Palma, M. / Chegkazi, M. / Bui, S. / Mori, G. / Percudani, R. / Steiner, R.A.
Funding support United Kingdom, Italy, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P000169/1 United Kingdom
Italian Ministry of Education2017483NH8 Italy
CitationJournal: Mol.Biol.Evol. / Year: 2023
Title: Cysteine Enrichment Mediates Co-Option of Uricase in Reptilian Skin and Transition to Uricotelism.
Authors: Mori, G. / Liuzzi, A. / Ronda, L. / Di Palma, M. / Chegkazi, M.S. / Bui, S. / Garcia-Maya, M. / Ragazzini, J. / Malatesta, M. / Della Monica, E. / Rivetti, C. / Antin, P.B. / Bettati, S. / ...Authors: Mori, G. / Liuzzi, A. / Ronda, L. / Di Palma, M. / Chegkazi, M.S. / Bui, S. / Garcia-Maya, M. / Ragazzini, J. / Malatesta, M. / Della Monica, E. / Rivetti, C. / Antin, P.B. / Bettati, S. / Steiner, R.A. / Percudani, R.
History
DepositionMar 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Uricase
BBB: Uricase
CCC: Uricase
DDD: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,77136
Polymers156,8084
Non-polymers1,96432
Water10,755597
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31100 Å2
ΔGint-207 kcal/mol
Surface area43600 Å2
Unit cell
Length a, b, c (Å)101.775, 124.859, 128.265
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
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74BBB
84CCC
95BBB
105DDD
116CCC
126DDD

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALALAALAAAAA4 - 29927 - 322
211VALVALALAALABBBB4 - 29927 - 322
322VALVALALAALAAAAA4 - 29927 - 322
422VALVALALAALACCCC4 - 29927 - 322
533VALVALGLNGLNAAAA4 - 30027 - 323
633VALVALGLNGLNDDDD4 - 30027 - 323
744GLNGLNALAALABBBB3 - 29926 - 322
844GLNGLNALAALACCCC3 - 29926 - 322
955VALVALALAALABBBB4 - 29927 - 322
1055VALVALALAALADDDD4 - 29927 - 322
1166VALVALALAALACCCC4 - 29927 - 322
1266VALVALALAALADDDD4 - 29927 - 322

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

-
Components

-
Protein , 2 types, 4 molecules AAABBBCCCDDD

#1: Protein Uricase / Urate oxidase / Urate oxidase


Mass: 39189.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LOC101747367 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A8V0ZED1, factor-independent urate hydroxylase
#2: Protein Uricase / Urate oxidase / Urate oxidase


Mass: 39205.883 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LOC101747367 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A8V0ZED1, factor-independent urate hydroxylase

-
Non-polymers , 5 types, 629 molecules

#3: Chemical
ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H3N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: His6-tagged GgUOX at approx. 22 mg/ml in 50 mM Tris-HCl pH 8.0, 10 mM NaCl, 1 mM TCEP-HCl was incubated with a 20-fold molar excess of AZA. Crystals were obtained by mixing the protein with ...Details: His6-tagged GgUOX at approx. 22 mg/ml in 50 mM Tris-HCl pH 8.0, 10 mM NaCl, 1 mM TCEP-HCl was incubated with a 20-fold molar excess of AZA. Crystals were obtained by mixing the protein with 0.8M K/Na tartrate tetrahydrate, 0.1 M HEPES pH 7.5 using a 1:1 ratio. Crystals were transferred into cryoprotective solutions supplemented with 100 mM H2O2 and devoid of the TCEP-HCl reducing agent for approximately 15 minutes prior to cryocooling in liquid nitrogen.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97948 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.89→78.89 Å / Num. obs: 131041 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.048 / Net I/σ(I): 7.6
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 6365 / CC1/2: 0.253 / Rpim(I) all: 0.123 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→78.888 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 10.963 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.122
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2145 6233 4.868 %
Rwork0.1881 121801 -
all0.189 --
obs-128034 97.677 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.869 Å2
Baniso -1Baniso -2Baniso -3
1--0.517 Å20 Å2-0 Å2
2---0.129 Å20 Å2
3---0.646 Å2
Refinement stepCycle: LAST / Resolution: 1.89→78.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9620 0 118 597 10335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310111
X-RAY DIFFRACTIONr_bond_other_d0.0010.0159467
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.65313678
X-RAY DIFFRACTIONr_angle_other_deg1.251.57921840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23851232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12322.593540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.352151762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3661561
X-RAY DIFFRACTIONr_chiral_restr0.0670.21312
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022383
X-RAY DIFFRACTIONr_nbd_refined0.1940.21554
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.28491
X-RAY DIFFRACTIONr_nbtor_refined0.1630.24717
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.25148
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2542
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.10.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.225
X-RAY DIFFRACTIONr_nbd_other0.2190.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2990.213
X-RAY DIFFRACTIONr_mcbond_it1.2592.9344874
X-RAY DIFFRACTIONr_mcbond_other1.2592.9344873
X-RAY DIFFRACTIONr_mcangle_it24.3956118
X-RAY DIFFRACTIONr_mcangle_other24.3956119
X-RAY DIFFRACTIONr_scbond_it1.7183.1525237
X-RAY DIFFRACTIONr_scbond_other1.7183.1535238
X-RAY DIFFRACTIONr_scangle_it2.7224.6237558
X-RAY DIFFRACTIONr_scangle_other2.7224.6247559
X-RAY DIFFRACTIONr_lrange_it4.77433.87710667
X-RAY DIFFRACTIONr_lrange_other4.77333.88210668
X-RAY DIFFRACTIONr_ncsr_local_group_10.0550.059414
X-RAY DIFFRACTIONr_ncsr_local_group_20.0510.059454
X-RAY DIFFRACTIONr_ncsr_local_group_30.0520.059451
X-RAY DIFFRACTIONr_ncsr_local_group_40.0590.059393
X-RAY DIFFRACTIONr_ncsr_local_group_50.0550.059386
X-RAY DIFFRACTIONr_ncsr_local_group_60.0470.059410
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.055430.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.055430.05009
23AAAX-RAY DIFFRACTIONLocal ncs0.0510.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.0510.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.05190.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.05190.05009
47BBBX-RAY DIFFRACTIONLocal ncs0.059140.05009
48CCCX-RAY DIFFRACTIONLocal ncs0.059140.05009
59BBBX-RAY DIFFRACTIONLocal ncs0.05450.05009
510DDDX-RAY DIFFRACTIONLocal ncs0.05450.05009
611CCCX-RAY DIFFRACTIONLocal ncs0.046960.05009
612DDDX-RAY DIFFRACTIONLocal ncs0.046960.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.9380.3683450.3886400X-RAY DIFFRACTION70.3263
1.938-1.9910.3724280.3568748X-RAY DIFFRACTION97.8982
1.991-2.0490.3144180.3218643X-RAY DIFFRACTION100
2.049-2.1120.2984240.2988404X-RAY DIFFRACTION100
2.112-2.1810.2814440.2768160X-RAY DIFFRACTION100
2.181-2.2580.2644310.2527882X-RAY DIFFRACTION100
2.258-2.3430.2533830.2397628X-RAY DIFFRACTION100
2.343-2.4390.2653750.2277358X-RAY DIFFRACTION100
2.439-2.5470.2373570.217074X-RAY DIFFRACTION100
2.547-2.6710.2343460.1976751X-RAY DIFFRACTION100
2.671-2.8150.2283680.1896395X-RAY DIFFRACTION100
2.815-2.9860.1983000.1846139X-RAY DIFFRACTION100
2.986-3.1920.2172850.1665723X-RAY DIFFRACTION100
3.192-3.4470.2082670.1735363X-RAY DIFFRACTION100
3.447-3.7750.1982540.1664958X-RAY DIFFRACTION100
3.775-4.220.1842230.1484502X-RAY DIFFRACTION100
4.22-4.870.1442200.1183982X-RAY DIFFRACTION100
4.87-5.9590.1921740.163412X-RAY DIFFRACTION100
5.959-8.4040.2271030.1762708X-RAY DIFFRACTION100
8.404-78.8880.172880.1741571X-RAY DIFFRACTION100
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)
12.8028-0.0741-4.59240.93722.081611.81020.3179-0.08190.24950.1462-0.05530.128-0.1923-0.1498-0.26260.22020.01940.00020.21860.03690.23246.264842.689554.0953
21.9858-0.14730.40113.41675.209410.61610.07070.0555-0.0104-0.05230.1864-0.1483-0.18360.1954-0.2570.06820.00890.02160.02620.01890.08176.430124.829925.7234
33.12971.02862.63714.09993.69399.9248-0.0060.2575-0.0398-0.14330.09010.0345-0.1641-0.2194-0.08410.12310.03020.01660.12170.00760.13036.180117.77174.989
40.3057-0.7197-1.64311.70233.89399.0581-0.0163-0.05120.04570.04570.1226-0.0755-0.01190.2021-0.10630.10370.0662-0.01460.048-0.02330.14474.413933.184835.1331
51.4833-0.3761-1.80191.00761.36339.8888-0.01190.0904-0.0198-0.0643-0.00460.07240.0431-0.26210.01650.0570.0316-0.00670.0368-0.00920.1198-2.119627.939629.0674
69.7464-3.5943-9.43812.98413.673711.0640.10820.05290.1828-0.1916-0.03410.0061-0.2134-0.0948-0.07410.08530.0218-0.04210.01660.01450.08871.924635.140221.5869
78.215-7.8507-6.66559.17557.42776.1026-0.0147-0.11780.20960.00910.2161-0.3231-0.02220.1593-0.20150.09030.0193-0.03990.0163-0.00330.08598.901432.331526.0292
83.1087-0.6828-2.83160.57432.19678.57180.1414-0.08620.1031-0.03660.0351-0.082-0.1460.1242-0.17650.108-0.00330.00050.0398-0.00730.143718.096115.21024.8113
90.02030.06430.15884.54915.21996.61450.00330.02220.0286-0.09720.0847-0.1603-0.09490.2869-0.0880.0597-0.00250.02890.06060.01560.06317.519619.279110.1665
107.5532-4.5217-7.710310.73087.22968.72650.1929-0.10190.33560.19210.2747-0.6939-0.08440.1793-0.46750.09710.02240.01480.02380.0340.20725.810543.280325.7559
117.2338-0.46430.45631.66480.29820.2894-0.0235-0.0135-0.44720.0194-0.02430.0209-0.05470.0240.04780.1191-0.02610.02430.00950.00720.08131.487531.287517.1506
121.49320.18111.60850.9464-0.87257.39650.1276-0.00070.0490.03970.0254-0.366-0.05611.0076-0.1530.0946-0.04050.00460.2771-0.09160.36550.502539.314429.3811
138.8465-2.07951.40180.66180.01531.0939-0.0246-0.12950.08530.01710.02790.0141-0.0516-0.0748-0.00330.0942-0.01120.01340.02640.0210.140329.222234.815319.8624
144.3881-0.5481-5.24882.2333-3.386714.0809-0.2428-0.20780.0952-0.25970.1609-0.06260.87510.27640.08190.2488-0.00420.0090.34380.05970.24858.224844.964713.9243
1511.0719-3.06614.94225.2884-1.77862.72440.19050.7575-0.0701-0.5279-0.21810.21-0.0864-0.05020.02760.20370.157-0.05730.3907-0.0410.121717.493935.97539.3741
1613.2279-1.2667-5.43253.77331.16755.4640.17320.76440.5101-0.6419-0.12820.0441-0.067-0.1822-0.04510.1889-0.0080.01740.08120.06640.140834.799535.3588.3813
176.8095-1.25041.70181.46630.01561.8135-0.03550.28580.2726-0.238-0.0262-0.0382-0.0726-0.05280.06170.1148-0.01340.0190.02650.01210.174930.645741.093517.4164
1811.0703-4.22525.55583.0365-3.33894.54450.0907-0.23550.5060.0864-0.1502-0.4769-0.17660.42450.05950.1744-0.08020.04470.2337-0.14120.375552.415521.463222.8349
197.9558-7.5616.01479.2737-7.91298.2689-0.17560.08360.4596-0.0149-0.0458-0.3766-0.14350.00760.22140.1269-0.023-0.00420.0137-0.01780.121230.740739.793925.2155
203.5123-1.68273.61888.1705-0.46583.9505-0.12570.03060.4385-0.009-0.41040.232-0.1371-0.00520.53610.2408-0.0120.02360.30960.01090.267517.378354.923819.7891
211.82391.0333-3.99551.9957-2.22518.8090.0733-0.1348-0.1630.0798-0.32990.0994-0.14060.2250.25660.22350.0174-0.01980.24660.04010.27740.7366-15.308254.9402
220.3186-1.08591.23916.4204-5.99359.504-0.1314-0.02140.0040.1157-0.1172-0.3763-0.0165-0.01850.24860.16630.01610.02340.1488-0.01790.152641.8931-13.693342.8177
232.2743-0.1492-0.70319.9135-9.11699.6062-0.08480.12230.06930.0810.35610.0452-0.1098-0.33-0.27120.03940.0024-0.01580.0245-0.01280.077944.57612.040625.1091
242.53331.3709-2.46776.1108-2.77255.86340.04130.13650.2181-0.28330.06250.06130.1080.4099-0.10380.13420.011-0.01440.16660.00790.149146.756822.79237.4071
251.8308-2.9992.09738.3542-5.59614.3594-0.0655-0.07650.00640.16590.0906-0.00540.0172-0.0693-0.02510.08350.01230.00650.0703-0.03440.097944.79952.649327.512
261.07380.13290.24761.2072-0.75515.2656-0.07350.04810.1397-0.0707-0.0883-0.27470.00980.31630.16170.0320.01740.01880.03770.0190.161550.64234.717426.8292
271.0597-1.06540.24914.6762-1.7521.5350.09590.0951-0.0677-0.35450.00080.17650.12710.0132-0.09670.074-0.00060.03120.0275-0.02510.074742.723312.064216.0703
281.0079-0.61850.56288.2911-2.15210.730.0128-0.01680.0067-0.18360.0810.48890.0502-0.033-0.09380.1120.01230.01870.0976-0.00150.116331.649214.497315.0118
293.3882-3.18674.87611.9361-4.35227.02530.2239-0.0251-0.1294-0.2288-0.04140.2430.3248-0.0259-0.18260.08980.02010.01830.0683-0.00390.161745.8009-7.108620.1359
305.5989-0.0136-0.23961.48610.43780.22830.0427-0.19550.3386-0.0283-0.0141-0.10630.0177-0.0382-0.02860.0674-0.02350.00120.03-0.01220.041619.3186.301813.6072
314.86690.2373-3.21450.32470.36493.11210.19090.45790.42150.033-0.06010.1886-0.0387-0.6299-0.13080.119-0.0422-0.04520.30190.190.31540.0287-4.004221.2514
327.314-1.7504-1.30150.78130.18240.28260.0474-0.06610.09850.0279-0.0137-0.0309-0.0190.0297-0.03370.1075-0.0002-0.00680.08550.00590.087120.37373.736515.726
330.2385-0.102-0.12250.77260.20440.0957-0.11740.0682-0.1332-0.08150.1122-0.20290.04420.00010.00510.1989-0.00310.02050.2697-0.01570.307742.1723-4.9938.8835
349.6981-0.14330.08890.0461-0.08370.682-0.06140.39580.0848-0.081-0.0052-0.03150.03810.13290.06660.1904-0.01940.02640.08260.00080.108130.1694.75955.8828
357.9302-1.4973-4.41965.6271-6.084311.4318-0.00730.3389-0.4408-0.4822-0.22170.12040.6020.02160.2290.16410.0122-0.04270.021-0.0070.129712.82676.17870.2807
367.0996-1.3565-1.49212.2662-0.40331.75230.00880.3966-0.1318-0.3214-0.0242-0.11790.20850.06160.01540.10070-0.00690.0463-0.01580.036422.0015-3.5939.1255
378.5632-5.2164-1.11563.26660.71870.3391-0.077-0.0126-0.24710.1146-0.00070.23780.014-0.15190.07770.1502-0.01160.01360.13630.00420.13765.77569.789420.7028
3811.4487-0.8425-6.823.23151.79924.64790.03240.31230.0024-0.2419-0.12880.2973-0.0974-0.3620.09640.1433-0.0278-0.02820.33020.04410.1191-1.25316.666619.0101
396.4024-1.4588-6.11611.813.989510.48070.20130.6114-0.3637-0.1776-0.41680.0111-0.3459-0.97550.21550.16020.0936-0.02980.17530.00750.055220.5206-3.499718.7201
400.54530.5742-1.17159.6073-0.96062.5354-0.0427-0.0292-0.11110.1741-0.1911-0.10.1360.0240.23390.223-0.02830.00010.24170.0010.264835.0356-17.246211.4082
410.9351-0.8898-2.25791.06592.5788.85750.08730.1897-0.0033-0.1923-0.0090.04110.0962-0.0422-0.07830.2322-0.00980.01040.210.030.242824.3509-14.34146.83
423.6471-1.936-4.37914.21874.628610.89150.1445-0.06710.21090.00350.1357-0.1218-0.06190.1866-0.28020.0389-0.0188-0.03610.01660.02310.075611.33540.908835.235
439.4678-0.6379-8.48243.9414.342512.4745-0.0349-0.383-0.15520.3127-0.17660.25990.3262-0.29110.21150.18290.0064-0.02970.18540.0420.10535.38976.389454.3712
441.1313-1.3603-2.20011.882.01197.02710.1139-0.03670.148-0.22830.0392-0.30860.06440.2427-0.15310.1161-0.03630.00610.0470.00160.166914.6782-8.185424.1455
451.0189-0.5254-0.92781.72692.40979.41-0.0539-0.0338-0.01050.0676-0.04950.1170.0743-0.19710.10350.0574-0.0342-0.00240.03050.00680.13155.481-5.30631.4055
467.07395.11167.54686.38116.775710.7921-0.0984-0.0552-0.13910.24460.0973-0.05850.23060.09310.00110.07410.01470.02430.02330.02920.084311.9168-9.866140.2001
471.48751.55371.99948.89055.62494.6593-0.06790.07580.03560.16230.1449-0.11540.14010.1151-0.0770.088-0.0040.00050.02030.02410.061115.6616-6.078434.6491
480.81970.62840.82072.23814.15318.34920.0625-0.13970.05920.08190.0987-0.1075-0.10260.1627-0.16120.16490.0287-0.00920.13920.00150.146314.007513.977757.2848
492.6951-3.349-2.82844.17243.51194.8302-0.2502-0.32270.28780.33860.3933-0.37840.06280.1751-0.14310.12020.0162-0.05510.0699-0.03040.106816.245910.202652.1115
504.6171-0.19082.85036.65178.204812.19340.34250.208-0.09330.14170.0984-0.32950.42140.2509-0.44090.1537-0.0047-0.00540.01720.00650.135719.0673-16.0235.565
512.37971.5817-1.09711.5258-0.68280.58440.0090.03590.14960.02440.01120.0513-0.02440.0378-0.02020.08250.0126-0.06260.05510.02470.078939.13785.930246.3795
521.03521.18341.7252.09010.23757.55160.22470.4569-0.23740.33720.4214-0.349-0.12521.2759-0.64610.1777-0.04810.01920.3366-0.20020.503457.888.912137.4518
537.13516.44610.78796.32860.20240.7349-0.21730.18510.1839-0.16550.25220.1197-0.00450.002-0.03490.07680.0318-0.01420.0556-0.05030.103735.12032.046844.4052
540.1269-0.5555-1.00822.68184.90398.9763-0.01040.0276-0.0814-0.0144-0.13820.107-0.008-0.26370.14860.21520.00640.00150.1883-00.32220.6853-15.737248.7788
5511.97278.0179-1.66198.2381-1.49670.3620.0382-0.7359-0.11540.34760.0087-0.0107-0.0486-0.0491-0.04690.11350.0518-0.00610.22230.06930.038725.9616-3.131353.2087
565.9962.61670.40645.31453.9038.9421-0.0035-0.4432-0.08360.66490.0291-0.03650.34350.0163-0.02560.17390.0304-0.02750.07050.02070.07540.23534.721457.5214
574.17442.9216-1.46682.6557-0.88761.78-0.0356-0.07340.00240.08260.08-0.17170.00140.0075-0.04440.07230.0422-0.02780.0369-0.03250.063338.9077-3.048147.2064
588.51215.0442-1.85467.5147-1.53334.06150.0934-0.2060.07490.0664-0.1207-0.6082-0.15360.51320.02730.10.0265-0.0230.12790.00910.220249.81924.589544.568
592.41633.8538-1.946512.1097-8.88677.3565-0.0484-0.0606-0.20190.2864-0.1674-0.5787-0.20960.06840.21580.1190.0161-0.08610.02780.04590.203939.5707-1.485239.413
607.6969-0.7718-4.32593.7829-0.15332.5256-0.07550.0473-0.2438-0.0076-0.04490.10770.057-0.00810.12050.20630.0117-0.00020.2486-0.01540.204933.4073-21.024943.1177
612.98541.3111-0.39855.6991-5.857611.8051-0.14060.21690.4479-0.4806-0.1393-0.0853-0.00320.3630.27990.2402-0.0135-0.00310.2096-0.02280.310528.655952.263519.4498
623.2826-2.35293.54897.5593-8.829810.70070.0852-0.1954-0.03030.08160.13190.1533-0.0244-0.173-0.21720.0513-0.01160.03280.0291-0.04130.117339.353529.147341.9155
633.6012-0.63454.87749.53060.41587.3506-0.0639-0.1833-0.1290.2240.163-0.2364-0.24160.1595-0.09920.2049-0.0802-0.02680.29230.06130.135644.783618.646660.8294
640.456-0.4260.35037.8087-4.85163.6582-0.0057-0.0690.0609-0.15810.06740.08460.0941-0.0947-0.06170.0721-0.01830.01110.0696-0.04720.130635.188832.236342.5346
651.3395-0.4303-0.24272.2501-1.80274.9669-0.1463-0.0870.12280.1137-0.0941-0.3615-0.08490.22540.24040.0886-0.0319-0.02190.0418-0.02530.215741.167439.578838.9047
669.43553.5605-3.947711.3479-9.02119.15110.12820.03110.2280.39180.00880.1559-0.3067-0.1745-0.1370.1508-0.0373-0.03040.0308-0.02010.16140.203243.891944.8698
670.47161.3037-0.74447.3183-2.46651.22660.0206-0.0160.0276-0.00060.02290.129-0.00360.0176-0.04350.102-0.0214-0.02030.079-0.01530.113933.244336.83841.9283
687.07930.7103-0.96013.1857-4.94737.85070.1672-0.6404-0.15380.23550.0450.2216-0.1628-0.1202-0.21230.3336-0.02370.10820.0977-0.05130.180735.829311.896258.7115
693.381-6.49011.307612.5307-2.33040.95380.0481-0.0898-0.3116-0.05820.09280.58150.0845-0.2398-0.14090.0968-0.0294-0.01610.09640.01550.150327.302621.027348.8976
706.4282-0.0264-4.110712.2408-7.12126.79320.1160.13060.16480.52680.26690.5007-0.392-0.2366-0.38290.1570.00620.01290.0631-0.05740.202630.575146.956245.2019
718.16287.4578-0.10749.2157-0.14670.5386-0.03860.2945-0.1371-0.05380.1411-0.2194-0.0766-0.0382-0.10250.07130.0145-0.02060.02960.00390.055116.912523.650948.3081
727.0536-5.07246.844510.3321-8.60710.47080.0293-0.1808-0.0507-0.38870.33690.30260.3722-0.7146-0.36620.0951-0.02040.03060.15720.02850.1317-5.503324.164143.5878
733.24380.61181.6311.20060.58832.072-0.00890.122-0.13260.09050.0130.09260.0436-0.0473-0.00410.09420.02610.02380.0288-0.02480.11284.534824.70942.6901
741.11981.52480.71882.09310.97790.46660.1772-0.16060.00090.2467-0.1314-0.00260.0928-0.111-0.04580.37770.01210.00690.4780.0150.533127.54442.839857.4208
758.27174.05981.09492.1910.72820.36870.064-0.31480.03760.1795-0.0701-0.00140.10010.07650.00620.1780.0175-0.02550.1292-0.010.118619.916928.08157.4809
764.5916-4.77474.40924.9824-4.65639.7313-0.4618-0.38930.0120.51240.37370.0146-0.4723-0.32860.08810.1498-0.00190.06140.1065-0.01530.122.394321.349356.9279
776.47091.96132.90054.03642.38965.4716-0.1993-0.3690.22730.27760.09370.00290.0170.0510.10560.09130.05510.00520.0504-0.0120.103911.285832.192751.3325
787.70073.60873.21834.22463.98954.56310.03150.08340.1119-0.0017-0.17760.61490.071-0.42220.14610.12040.0246-0.03950.15110.08770.3835-0.45775.980739.5463
793.64843.29653.11729.15939.669312.1657-0.1213-0.21890.24070.3204-0.28690.28580.1084-0.26910.40820.12020.04020.02320.04920.02260.06449.998132.232643.3965
8015.5286-7.15674.976814.01121.87343.22580.0294-0.13940.3785-0.1293-0.2431-0.0533-0.042-0.21010.21370.3687-0.00410.02220.4193-0.02860.406115.249149.907953.3461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionSelection details
1X-RAY DIFFRACTION1ALL{ AAA|4-12 }
2X-RAY DIFFRACTION2ALL{ AAA|13-27 }
3X-RAY DIFFRACTION3ALL{ AAA|28-36 }
4X-RAY DIFFRACTION4ALL{ AAA|37-53 }
5X-RAY DIFFRACTION5ALL{ AAA|54-79 }
6X-RAY DIFFRACTION6ALL{ AAA|80-98 }
7X-RAY DIFFRACTION7ALL{ AAA|99-111 }
8X-RAY DIFFRACTION8ALL{ AAA|112-118 }
9X-RAY DIFFRACTION9ALL{ AAA|119-136 }
10X-RAY DIFFRACTION10ALL{ AAA|137-147 }
11X-RAY DIFFRACTION11ALL{ AAA|148-164 }
12X-RAY DIFFRACTION12ALL{ AAA|165-181 }
13X-RAY DIFFRACTION13ALL{ AAA|182-195 }
14X-RAY DIFFRACTION14ALL{ AAA|196-199 }
15X-RAY DIFFRACTION15ALL{ AAA|200-210 }
16X-RAY DIFFRACTION16ALL{ AAA|211-225 }
17X-RAY DIFFRACTION17ALL{ AAA|226-258 }
18X-RAY DIFFRACTION18ALL{ AAA|259-280 }
19X-RAY DIFFRACTION19ALL{ AAA|281-294 }
20X-RAY DIFFRACTION20ALL{ AAA|295-300 }
21X-RAY DIFFRACTION21ALL{ BBB|-1-6 }
22X-RAY DIFFRACTION22ALL{ BBB|7-14 }
23X-RAY DIFFRACTION23ALL{ BBB|15-26 }
24X-RAY DIFFRACTION24ALL{ BBB|27-36 }
25X-RAY DIFFRACTION25ALL{ BBB|37-48 }
26X-RAY DIFFRACTION26ALL{ BBB|49-89 }
27X-RAY DIFFRACTION27ALL{ BBB|90-126 }
28X-RAY DIFFRACTION28ALL{ BBB|127-136 }
29X-RAY DIFFRACTION29ALL{ BBB|137-147 }
30X-RAY DIFFRACTION30ALL{ BBB|148-165 }
31X-RAY DIFFRACTION31ALL{ BBB|166-181 }
32X-RAY DIFFRACTION32ALL{ BBB|182-193 }
33X-RAY DIFFRACTION33ALL{ BBB|194-199 }
34X-RAY DIFFRACTION34ALL{ BBB|200-217 }
35X-RAY DIFFRACTION35ALL{ BBB|218-225 }
36X-RAY DIFFRACTION36ALL{ BBB|226-253 }
37X-RAY DIFFRACTION37ALL{ BBB|254-266 }
38X-RAY DIFFRACTION38ALL{ BBB|267-280 }
39X-RAY DIFFRACTION39ALL{ BBB|281-294 }
40X-RAY DIFFRACTION40ALL{ BBB|295-301 }
41X-RAY DIFFRACTION41ALL{ CCC|3-12 }
42X-RAY DIFFRACTION42ALL{ CCC|13-27 }
43X-RAY DIFFRACTION43ALL{ CCC|28-37 }
44X-RAY DIFFRACTION44ALL{ CCC|38-54 }
45X-RAY DIFFRACTION45ALL{ CCC|55-79 }
46X-RAY DIFFRACTION46ALL{ CCC|80-96 }
47X-RAY DIFFRACTION47ALL{ CCC|97-111 }
48X-RAY DIFFRACTION48ALL{ CCC|112-118 }
49X-RAY DIFFRACTION49ALL{ CCC|119-136 }
50X-RAY DIFFRACTION50ALL{ CCC|137-147 }
51X-RAY DIFFRACTION51ALL{ CCC|148-168 }
52X-RAY DIFFRACTION52ALL{ CCC|169-181 }
53X-RAY DIFFRACTION53ALL{ CCC|182-195 }
54X-RAY DIFFRACTION54ALL{ CCC|196-200 }
55X-RAY DIFFRACTION55ALL{ CCC|201-213 }
56X-RAY DIFFRACTION56ALL{ CCC|214-225 }
57X-RAY DIFFRACTION57ALL{ CCC|226-258 }
58X-RAY DIFFRACTION58ALL{ CCC|259-280 }
59X-RAY DIFFRACTION59ALL{ CCC|281-294 }
60X-RAY DIFFRACTION60ALL{ CCC|295-300 }
61X-RAY DIFFRACTION61ALL{ DDD|4-14 }
62X-RAY DIFFRACTION62ALL{ DDD|15-27 }
63X-RAY DIFFRACTION63ALL{ DDD|28-34 }
64X-RAY DIFFRACTION64ALL{ DDD|35-45 }
65X-RAY DIFFRACTION65ALL{ DDD|4-14 }
66X-RAY DIFFRACTION66ALL{ DDD|88-97 }
67X-RAY DIFFRACTION67ALL{ DDD|98-111 }
68X-RAY DIFFRACTION68ALL{ DDD|112-126 }
69X-RAY DIFFRACTION69ALL{ DDD|127-136 }
70X-RAY DIFFRACTION70ALL{ DDD|137-147 }
71X-RAY DIFFRACTION71ALL{ DDD|148-160 }
72X-RAY DIFFRACTION72ALL{ DDD|161-170 }
73X-RAY DIFFRACTION73ALL{ DDD|171-194 }
74X-RAY DIFFRACTION74ALL{ DDD|195-200 }
75X-RAY DIFFRACTION75ALL{ DDD|201-217 }
76X-RAY DIFFRACTION76ALL{ DDD|218-229 }
77X-RAY DIFFRACTION77ALL{ DDD|230-258 }
78X-RAY DIFFRACTION78ALL{ DDD|259-280 }
79X-RAY DIFFRACTION79ALL{ DDD|281-294 }
80X-RAY DIFFRACTION80ALL{ DDD|295-300 }

+
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