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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8oih
TitleCrystal structure of the cysteine-rich Gallus gallus urate oxidase in complex with the 8-azaxanthine inhibitor under oxidising conditions (space group C 2 2 21)
Components(Uricase) x 2
KeywordsOXIDOREDUCTASE / COFACTOR-FREE OXIDASE / INHIBITOR / DIOXYGEN BINDING / CYSTEINE
Function / homology
Function and homology information


factor-independent urate hydroxylase / purine nucleobase metabolic process / peroxisome / oxidoreductase activity
Similarity search - Function
8-AZAXANTHINE / BROMIDE ION / OXYGEN MOLECULE / Uricase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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
Citation
Journal: 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.
#1: Journal: tobedecided / Year: 2023
Title: Crystal structure of the cysteine-rich Gallus gallus urate oxidase in complex with the 8-azaxanthine inhibitor under reducing conditions (space group C 2 2 21)
Authors: Di Palma, M. / Chegkazi, M. / Mori, G. / Percudani, R. / Steiner, R.A.
History
DepositionMar 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
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)160,41960
Polymers156,9844
Non-polymers3,43656
Water13,457747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22570 Å2
ΔGint-73 kcal/mol
Surface area56650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.510, 125.990, 240.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 2 types, 4 molecules AAABBBCCCDDD

#1: Protein Uricase / Urate oxidase


Mass: 39237.879 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
#2: Protein Uricase / Urate oxidase


Mass: 39269.879 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

-
Non-polymers , 6 types, 803 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


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


Mass: 62.068 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 747 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
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 8% PGA-LM, 0.3M KBr, 0.1M Tris-HCl pH 7.8 using a 1:1 ratio. Crystals were then 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: 1.86→77.06 Å / Num. obs: 135367 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.033 / Net I/σ(I): 12.1
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 6674 / CC1/2: 0.3 / Rpim(I) all: 0.11 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→77.058 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 7.747 / SU ML: 0.108 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2064 6736 4.985 %
Rwork0.1719 128395 -
all0.174 --
obs-135131 99.858 %
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: 45.567 Å2
Baniso -1Baniso -2Baniso -3
1-0.812 Å2-0 Å2-0 Å2
2---1.637 Å20 Å2
3---0.825 Å2
Refinement stepCycle: LAST / Resolution: 1.86→77.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9641 0 202 747 10590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310296
X-RAY DIFFRACTIONr_bond_other_d0.0010.0159639
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.6613894
X-RAY DIFFRACTIONr_angle_other_deg1.281.57922241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23551249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1422.802546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.517151768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7761559
X-RAY DIFFRACTIONr_chiral_restr0.0750.21332
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211761
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022401
X-RAY DIFFRACTIONr_nbd_refined0.1950.21566
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.28445
X-RAY DIFFRACTIONr_nbtor_refined0.1630.24668
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.25010
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2605
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0180.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.267
X-RAY DIFFRACTIONr_nbd_other0.1770.2299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.249
X-RAY DIFFRACTIONr_mcbond_it1.3923.0544925
X-RAY DIFFRACTIONr_mcbond_other1.393.0534924
X-RAY DIFFRACTIONr_mcangle_it2.0264.5686196
X-RAY DIFFRACTIONr_mcangle_other2.0264.576197
X-RAY DIFFRACTIONr_scbond_it1.9933.3385371
X-RAY DIFFRACTIONr_scbond_other1.9913.3385371
X-RAY DIFFRACTIONr_scangle_it3.0074.8697697
X-RAY DIFFRACTIONr_scangle_other3.0074.8697698
X-RAY DIFFRACTIONr_lrange_it5.51835.92910774
X-RAY DIFFRACTIONr_lrange_other5.4135.31710618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.86-1.9080.4184890.40393020.40399590.440.45998.31310.403
1.908-1.9610.3434540.34891870.34896470.5420.52499.93780.343
1.961-2.0170.3034660.29489330.29594020.7560.76399.96810.281
2.017-2.0790.2914410.25586690.25791140.820.84699.95610.234
2.079-2.1480.2734040.23584540.23688600.8620.8899.97740.212
2.148-2.2230.2614340.21782090.21986430.8920.9091000.191
2.223-2.3070.2524350.19778210.282570.9070.92799.98790.171
2.307-2.4010.2073920.18475950.18579870.9410.9461000.157
2.401-2.5070.2223810.17672710.17976520.9430.9511000.151
2.507-2.630.2333630.17469690.17773330.9450.95499.98640.15
2.63-2.7720.2043570.16966290.17169860.9480.9571000.148
2.772-2.940.2043340.16462980.16666320.9510.9611000.148
2.94-3.1420.2183370.16259030.16462400.9450.961000.15
3.142-3.3940.2013080.16454990.16658070.9480.9631000.157
3.394-3.7170.1972440.16651060.16753510.9560.96399.98130.165
3.717-4.1540.1782490.15246360.15348850.9610.971000.156
4.154-4.7950.1682220.12540950.12743170.9720.9781000.138
4.795-5.8660.1712130.14734630.14836770.9730.97799.97280.161
5.866-8.2730.2121400.1727570.17228970.9570.9691000.186
8.273-77.0580.157730.14615990.14716750.9720.97599.82090.171
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)
12.46860.013-1.27083.77625.26288.71110.3611-0.50640.18960.2095-0.11730.0359-0.21-0.2202-0.24380.30730.06630.04440.26080.01010.307240.77729.460479.2314
21.03090.49811.47275.2626.56749.69450.0370.0974-0.0659-0.0807-0.0167-0.0383-0.0833-0.111-0.02030.02610.020.04050.0553-0.00360.103237.2027-11.185152.1353
34.06732.81793.466.43444.53259.5699-0.01170.2121-0.0129-0.285-0.0380.0722-0.209-0.32240.04970.11680.02530.00620.1367-0.01460.127535.8259-20.485732.2942
41.4915-0.753-1.76892.75834.09566.42180.0524-0.14240.16010.06280.1102-0.06850.02490.1986-0.16260.1220.07190.01270.0632-0.00460.123136.985-1.414860.3792
51.2056-0.1694-1.27542.87723.402510.4444-0.02450.1186-0.0625-0.0998-0.06420.1951-0.0389-0.3740.08860.04490.0497-0.00820.0873-0.00270.148629.5058-5.754654.7396
68.0739-4.2784-6.7984.29094.48516.99380.19630.11780.1568-0.419-0.06050.1188-0.5633-0.3103-0.13580.14030.0809-0.01330.08490.01810.081235.2964-0.732646.5783
74.2266-5.7559-3.787310.81466.8234.6321-0.02740.03110.13980.11480.1294-0.31850.0295-0.0743-0.1020.04780.03850.00810.0855-0.0340.06641.2614-4.502151.7263
83.8431-1.1673-3.03891.01393.295911.020.0837-0.10880.1083-0.02810.0574-0.0768-0.03580.1439-0.14110.0827-0.03440.03510.019-0.03550.148346.8439-25.911233.3957
90.31651.28030.87595.36393.87413.021-0.0380.0189-0.0176-0.14480.1118-0.0765-0.10410.1238-0.07380.0164-0.01140.02770.0174-0.02770.077247.0704-21.132538.0599
102.6156-2.4166-3.67398.52024.145.26960.1802-0.06670.0997-0.1548-0.0397-0.0854-0.27840.0329-0.14050.14850.04220.00110.12170.01440.16440.69316.903750.1935
116.5106-2.20250.61273.35280.00830.23140.0578-0.0225-0.4514-0.1072-0.02120.0779-0.1450.0526-0.03660.1367-0.0495-0.00980.02470.00850.036263.197-11.96244.3572
121.7574-0.30120.80440.70391.07776.930.0501-0.0663-0.09850.14980.194-0.32510.15941.0507-0.24410.1254-0.0319-0.02990.236-0.03520.313783.4454-7.23856.5127
139.3106-3.93041.83331.9103-0.7660.92970.0095-0.04260.0128-0.1072-0.0225-0.0555-0.1147-0.01310.0130.0988-0.00970.02940.028-0.0030.078261.8004-7.666746.53
145.3799-3.0597-5.92111.87772.81128.7945-0.05470.17140.111-0.0653-0.1238-0.12290.4006-0.03640.17850.28950.0011-0.00430.24720.0230.257843.69256.343438.4554
157.7232-3.52771.67862.0899-0.32722.71460.18460.27320.0169-0.3926-0.08360.0087-0.0892-0.1652-0.10110.2215-0.03250.00120.12170.01010.09851.018-5.061135.2955
167.4305-2.3348-1.23176.18221.64172.93920.06150.67780.1771-0.5866-0.079-0.1178-0.04690.04190.01750.1614-0.05420.05640.11350.02090.073467.5414-10.041735.3453
175.5325-2.06371.24852.4197-0.19152.2912-0.00610.3580.0954-0.2824-0.0373-0.0316-0.21320.1180.04350.1007-0.03440.03170.03720.00170.08564.7816-2.313843.3967
187.1511-2.53474.28374.5293-3.5934.5152-0.1989-0.03470.2020.2268-0.0581-0.699-0.07760.48850.2570.11570.0675-0.0160.3222-0.08970.274880.9745-25.643452.3921
195.6014-5.41444.2838.1823-6.87758.48790.00520.16630.2448-0.1599-0.2137-0.2428-0.0960.18590.20850.1103-0.03730.0220.0254-0.0030.035764.4212-2.593651.3492
203.24532.52361.55066.23530.51733.5558-0.0594-0.0510.1870.1438-0.08010.0852-0.1201-0.04950.13950.23950.0154-0.01120.23940.01380.24655.117614.406943.4148
2114.428-6.95014.86859.7769-4.163314.8439-0.0986-0.53660.4730.15940.385-0.15310.07070.4889-0.28640.213-0.0272-0.01890.2467-0.04770.236962.5689-54.31484.5424
221.77041.1816-3.66997.6219-6.899911.8946-0.3702-0.2646-0.38280.1402-0.1336-0.54880.33390.28610.50390.28110.04480.07350.19090.06590.351861.7028-54.604275.9118
230.60580.822-1.71216.57-7.108310.19540.04860.07490.01010.10810.06910.0707-0.07810.1315-0.11760.01390.0310.01430.0948-0.01420.143671.0468-32.676755.3458
244.73712.7073-3.51189.1227-5.937510.74570.06890.44680.0759-0.3284-0.1278-0.24070.19870.53120.05890.13780.03220.02340.1891-0.03130.166476.1268-25.154836.594
250.7131-1.43681.20447.1846-6.18375.3863-0.1111-0.0943-0.0289-0.01010.1299-0.03480.073-0.1032-0.01890.13030.04690.01070.0497-0.01360.163468.8665-41.465558.8752
261.50680.1521.02111.257-0.34115.5122-0.20680.1138-0.0244-0.1362-0.0492-0.29170.35090.51760.2560.12120.06670.06110.08740.02050.176675.1209-40.925158.2791
270.7926-0.0152-0.1764.5862-2.5472.71470.03180.1002-0.0842-0.47360.13860.16440.32720.1682-0.17050.09340.00460.02940.0743-0.0270.099869.4602-33.374746.2685
280.5132.2695-0.676910.5177-3.16070.9528-0.0650.07360.1042-0.08710.2150.50110.0109-0.0696-0.150.1089-0.01960.01950.09430.00280.127659.3576-28.535644.2771
295.6146-1.85815.053412.501-8.55868.54520.3907-0.1998-0.2127-0.1599-0.22750.07980.4045-0.0015-0.16320.26880.07830.05290.0676-0.03520.27667.775-52.098652.7938
304.3531-1.3730.05591.5602-0.23660.8596-0.0896-0.28750.2655-0.0110.0416-0.14750.1832-0.1630.04810.0543-0.03770.02890.0619-0.03850.069645.4633-33.594143.0934
314.077-0.4478-5.18460.07060.59317.48590.19020.27360.2657-0.0105-0.00060.0414-0.0669-0.8731-0.18960.0844-0.07580.02370.39030.05080.276123.9248-37.794750.7533
3210.2388-6.17810.52033.96140.0520.7802-0.0181-0.11240.12780.00030.0516-0.13230.1305-0.0449-0.03340.1203-0.01190.03990.0088-0.02120.109945.8231-36.069145.6355
330.5411-0.5067-0.16085.6630.41140.06110.05160.3265-0.3669-0.0037-0.1426-0.0562-0.0073-0.08640.0910.25310.0628-0.01390.3161-0.1350.365465.1513-50.615741.4253
348.4227-2.04160.18670.54750.05740.4697-0.02610.33030.0074-0.0434-0.0274-0.01410.09790.15110.05350.199-0.01650.04080.0867-0.01880.125955.9409-38.726836.3241
356.39750.9469-1.70331.7526-0.4437.5322-0.16140.0785-0.2496-0.36790.01170.20030.3486-0.0360.14970.1654-0.0094-0.01850.0881-0.03140.140239.7615-34.010729.5179
367.5386-2.7059-0.89211.9752-0.40012.07720.04410.3454-0.3629-0.2797-0.12070.07490.3639-0.04910.07660.1489-0.02830.0440.0346-0.05180.120645.8002-44.381540.0718
376.8563-6.3317-0.2487.1478-0.14230.2137-0.167-0.2122-0.0150.08870.19110.1424-0.0027-0.1261-0.02420.1422-0.01050.00670.2137-0.02660.132932.9449-26.244248.9967
388.4802-4.6128-2.18776.07182.27033.3220.06310.18150.0459-0.29590.05590.4312-0.4094-0.4264-0.11890.1158-0.02340.0380.1815-0.01160.173227.9332-18.163446.0231
395.354-6.4418-3.509610.53127.25967.48760.0290.1402-0.2559-0.1284-0.21570.2260.1063-0.18310.18660.1375-0.06840.05520.0521-0.01530.086844.0552-42.63549.4646
403.86911.6875-2.6075.86780.0352.0255-0.0751-0.2475-0.2920.0703-0.1-0.18080.07960.15790.1750.2290.0208-0.0110.2364-0.00370.259354.9037-60.145244.7247
410.30941.0866-1.0145.1172-4.72474.37170.15890.16250.04090.2423-0.1975-0.0387-0.3030.1860.03860.6987-0.00280.07830.68060.07450.519460.0005-36.4951-27.1805
422.13350.00991.89633.0024-3.410610.77320.032-0.1181-0.0458-0.04370.1834-0.1064-0.0238-0.219-0.21540.0104-0.02010.04260.0457-0.07760.199366.3554-50.3913.5661
431.8534-0.42663.55161.1747-1.88478.14890.0091-0.0394-0.0220.2036-0.0607-0.1203-0.18680.23670.05160.16280.0071-0.00060.2176-0.02930.205569.1497-54.861723.6039
440.5005-1.21151.6273.4701-4.03346.65030.0743-0.0229-0.0069-0.42050.27670.1621-0.2097-0.2926-0.3510.3114-0.06080.09140.15520.00910.310466.0988-41.9156-8.5952
450.4101-0.43690.36741.2869-1.01758.6857-0.0506-0.00620.1-0.01140.0129-0.1935-0.10830.26390.03770.0444-0.06140.02750.1176-0.04770.224273.7423-46.0948-0.2173
467.67633.1141-5.23783.1402-3.23546.17640.0653-0.03320.04790.1460.0349-0.3213-0.28760.204-0.10020.0475-0.0440.02150.0714-0.09740.210467.8864-39.38927.6627
473.98963.2387-4.25727.7114-5.75346.24730.20060.14430.13720.12410.12880.0522-0.340.0404-0.32940.0539-0.03590.03210.0803-0.08810.164463.829-42.74971.9664
484.43651.9227-4.50064.0941-1.602910.63470.139-0.37430.12720.56860.04130.14410.0538-0.3317-0.18030.19910.0155-0.06010.1526-0.05340.182958.8914-60.123726.2061
491.8124-1.99862.6055.4703-5.25156.4630.0287-0.3217-0.09620.41420.28120.12570.0069-0.337-0.30980.1470.0082-0.04920.0982-0.05980.153558.0385-56.543420.5346
5011.41872.5628-6.53397.5953-8.840811.74430.38350.29260.5411-0.00510.19430.4742-0.372-0.1146-0.57780.2857-0.18760.00350.15060.03260.309562.8097-32.18841.7842
511.61261.04781.14132.58520.92741.03530.1990.0942-0.2560.0922-0.16880.09760.0141-0.0954-0.03020.10920.0872-0.07310.1286-0.12940.167837.3565-47.776712.3113
520.630.2894-0.60042.45410.85656.75830.1636-0.03370.0999-0.1135-0.11350.65870.1304-0.7907-0.050.13160.0151-0.02930.2823-0.09110.352319.0976-46.981.8879
537.59814.50670.18693.39960.75670.60910.0201-0.0832-0.2154-0.0435-0.0667-0.0724-0.0853-0.03930.04650.05050.0210.00550.0355-0.03960.092142.327-45.164510.4276
541.38162.4309-4.28274.303-7.560213.34330.0401-0.0385-0.01020.1105-0.1026-0.0861-0.24040.10480.06250.2144-0.014-0.00430.22930.01210.313360.2092-30.843614.6694
559.04432.9737-0.52361.8631-0.58711.1035-0.0125-0.4163-0.02350.20380.0184-0.1112-0.10310.0787-0.00590.11450.0278-0.00960.0831-0.06610.107651.7539-41.280219.7813
565.94881.5019-1.32992.1396-3.19368.940.0163-0.3440.1860.3892-0.01140.2007-0.062-0.0755-0.00490.1820.03080.0340.0628-0.06910.151435.6975-45.222223.2009
574.6671.50360.92982.31111.19771.9890.0177-0.07130.15070.002-0.11440.2105-0.1566-0.09860.09660.04910.0219-0.00660.0231-0.03560.08939.6384-39.045212.4365
5810.24985.73191.315.14681.0052.3651-0.01660.09430.07190.0250.09480.59440.303-0.4647-0.07820.1701-0.02520.03370.2549-0.06490.320222.6915-63.664710.9221
593.90614.86612.30839.46495.6944.33820.006-0.03230.1264-0.229-0.15010.2598-0.1319-0.10950.1440.07870.0536-0.02110.0413-0.01320.061739.2404-41.22034.7038
6016.13254.24326.48597.8429-6.531612.8098-0.53530.7180.55440.23920.0774-0.2005-0.81880.35260.4580.5209-0.04120.02960.30870.03690.561450.2144-23.11856.6231
613.4154-0.6448-0.97832.32172.434812.2395-0.04340.3163-0.2796-0.0173-0.08380.20810.7448-0.46450.12720.2875-0.06050.02440.1501-0.02640.27439.4949-98.7565-11.9597
620.6238-0.684-1.01029.86867.88278.48070.0877-0.0976-0.05170.0724-0.20510.0934-0.1111-0.32610.11740.0491-0.03410.0330.0929-0.05160.131831.9599-70.75129.9504
631.8931-0.0173-2.56356.43740.95514.4084-0.021-0.2501-0.03640.25470.03070.35390.097-0.0725-0.00970.1862-0.03880.020.2836-0.00740.188427.7985-57.519927.215
640.36910.20120.28927.66743.51542.5933-0.0785-0.0227-0.02080.1480.1053-0.09660.09070.0604-0.02690.0951-0.03810.02320.12040.00130.13735.2936-74.655511.1507
651.3615-0.0761.02483.00432.20354.1687-0.0591-0.1456-0.05080.3641-0.3550.49940.2118-0.45480.41410.1398-0.11910.12470.139-0.09550.214528.0778-80.85767.4686
669.02021.89493.45287.96656.7448.92960.0828-0.1797-0.45060.5928-0.08960.11080.2203-0.0860.00670.2234-0.13650.12060.1568-0.03190.171227.4664-84.623813.9409
672.48363.67151.70139.31632.79441.28260.1747-0.1297-0.17970.3197-0.1521-0.26250.1773-0.1428-0.02260.1404-0.06240.06010.0983-0.03140.128336.0223-79.751711.1267
683.775-0.51560.99261.85222.86229.63950.032-0.32340.08790.6044-0.1116-0.12560.1913-0.10610.07960.3882-0.1122-0.04560.0653-0.01180.127338.1103-53.06825.4115
690.2537-1.3284-0.19847.58871.18450.19290.0331-0.04420.10360.02790.0148-0.45270.03130.0001-0.04790.1579-0.01590.01420.1423-0.02180.148345.0759-64.903317.2253
705.51894.54454.15349.18624.66774.91650.45970.2818-0.4780.8469-0.2687-0.26030.5664-0.1828-0.1910.3275-0.04420.02510.16510.02440.210736.1204-89.749915.4388
718.04074.60710.61054.20030.56740.9832-0.13590.17560.1456-0.02450.16340.02660.21050.0413-0.02760.14250.0416-0.01630.045-0.03510.092854.5983-69.876417.8161
724.1412-3.7924-3.1048.19273.60964.43570.0058-0.2403-0.0778-0.31520.2565-0.5438-0.33940.6859-0.26230.20190.0106-0.09830.2333-0.13280.325176.6756-75.690415.324
732.01260.0249-1.39340.89920.28972.2719-0.09550.0164-0.09420.33490.227-0.34020.25440.1969-0.13160.15060.0817-0.12690.0879-0.05790.284266.8542-74.128313.4791
740.94120.3647-0.39640.68790.26650.4943-0.2236-0.4787-0.37950.23970.1769-0.25140.37140.46740.04660.72720.04740.0470.65320.08040.56238.9316-85.118827.232
7511.57152.4436-1.71531.3499-1.03120.94540.0714-1.01090.15660.3117-0.05180.0449-0.0426-0.0113-0.01950.38270.00670.00610.1667-0.00310.128249.9812-72.583427.0335
763.8278-3.545-1.56537.47375.99595.5928-0.1684-0.4922-0.20120.69490.3001-0.01410.60790.0848-0.13170.3389-0.0159-0.15350.254-0.00380.206468.5437-69.956427.6186
774.20981.1596-2.04192.1574-0.45165.01950.0274-0.3483-0.16080.58590.0698-0.01850.28810.0803-0.09720.27020.0753-0.06940.06440.0110.186657.912-79.088622.0175
787.62642.4861-2.36922.9303-2.46964.3518-0.0052-0.1088-0.2215-0.145-0.053-0.5433-0.02090.57840.05820.090.0232-0.01620.1866-0.10260.31576.2439-57.50459.4516
795.56444.3624-5.42527.3944-7.997711.9979-0.094-0.2784-0.31380.3887-0.0737-0.2625-0.01050.07170.16770.20230.077-0.0640.0667-0.0450.15159.6842-80.248414.2107
805.5117-4.8915-1.03585.505-1.37738.0893-0.01860.2124-0.0990.0453-0.2446-0.01130.07730.27780.26320.2593-0.02640.00950.27510.00060.270649.6481-95.083624.9016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA3 - 12
2X-RAY DIFFRACTION2ALLAAA13 - 27
3X-RAY DIFFRACTION3ALLAAA28 - 36
4X-RAY DIFFRACTION4ALLAAA37 - 53
5X-RAY DIFFRACTION5ALLAAA54 - 79
6X-RAY DIFFRACTION6ALLAAA80 - 98
7X-RAY DIFFRACTION7ALLAAA99 - 111
8X-RAY DIFFRACTION8ALLAAA112 - 118
9X-RAY DIFFRACTION9ALLAAA119 - 136
10X-RAY DIFFRACTION10ALLAAA137 - 147
11X-RAY DIFFRACTION11ALLAAA148 - 164
12X-RAY DIFFRACTION12ALLAAA165 - 181
13X-RAY DIFFRACTION13ALLAAA182 - 195
14X-RAY DIFFRACTION14ALLAAA196 - 199
15X-RAY DIFFRACTION15ALLAAA200 - 210
16X-RAY DIFFRACTION16ALLAAA211 - 225
17X-RAY DIFFRACTION17ALLAAA226 - 258
18X-RAY DIFFRACTION18ALLAAA259 - 280
19X-RAY DIFFRACTION19ALLAAA281 - 294
20X-RAY DIFFRACTION20ALLAAA295 - 300
21X-RAY DIFFRACTION21ALLBBB4 - 6
22X-RAY DIFFRACTION22ALLBBB7 - 14
23X-RAY DIFFRACTION23ALLBBB15 - 26
24X-RAY DIFFRACTION24ALLBBB27 - 36
25X-RAY DIFFRACTION25ALLBBB37 - 48
26X-RAY DIFFRACTION26ALLBBB49 - 89
27X-RAY DIFFRACTION27ALLBBB90 - 126
28X-RAY DIFFRACTION28ALLBBB127 - 136
29X-RAY DIFFRACTION29ALLBBB137 - 147
30X-RAY DIFFRACTION30ALLBBB148 - 165
31X-RAY DIFFRACTION31ALLBBB166 - 181
32X-RAY DIFFRACTION32ALLBBB182 - 193
33X-RAY DIFFRACTION33ALLBBB194 - 199
34X-RAY DIFFRACTION34ALLBBB200 - 217
35X-RAY DIFFRACTION35ALLBBB218 - 225
36X-RAY DIFFRACTION36ALLBBB226 - 253
37X-RAY DIFFRACTION37ALLBBB254 - 266
38X-RAY DIFFRACTION38ALLBBB267 - 280
39X-RAY DIFFRACTION39ALLBBB281 - 294
40X-RAY DIFFRACTION40ALLBBB295 - 301
41X-RAY DIFFRACTION41ALLCCC3 - 12
42X-RAY DIFFRACTION42ALLCCC13 - 27
43X-RAY DIFFRACTION43ALLCCC28 - 37
44X-RAY DIFFRACTION44ALLCCC38 - 54
45X-RAY DIFFRACTION45ALLCCC55 - 79
46X-RAY DIFFRACTION46ALLCCC80 - 96
47X-RAY DIFFRACTION47ALLCCC97 - 111
48X-RAY DIFFRACTION48ALLCCC112 - 118
49X-RAY DIFFRACTION49ALLCCC119 - 136
50X-RAY DIFFRACTION50ALLCCC137 - 147
51X-RAY DIFFRACTION51ALLCCC148 - 168
52X-RAY DIFFRACTION52ALLCCC169 - 181
53X-RAY DIFFRACTION53ALLCCC182 - 195
54X-RAY DIFFRACTION54ALLCCC196 - 200
55X-RAY DIFFRACTION55ALLCCC201 - 213
56X-RAY DIFFRACTION56ALLCCC214 - 225
57X-RAY DIFFRACTION57ALLCCC226 - 258
58X-RAY DIFFRACTION58ALLCCC259 - 280
59X-RAY DIFFRACTION59ALLCCC281 - 294
60X-RAY DIFFRACTION60ALLCCC295 - 301
61X-RAY DIFFRACTION61ALLDDD0 - 14
62X-RAY DIFFRACTION62ALLDDD15 - 27
63X-RAY DIFFRACTION63ALLDDD28 - 34
64X-RAY DIFFRACTION64ALLDDD35 - 45
65X-RAY DIFFRACTION65ALLDDD46 - 87
66X-RAY DIFFRACTION66ALLDDD88 - 97
67X-RAY DIFFRACTION67ALLDDD98 - 111
68X-RAY DIFFRACTION68ALLDDD112 - 126
69X-RAY DIFFRACTION69ALLDDD127 - 136
70X-RAY DIFFRACTION70ALLDDD137 - 147
71X-RAY DIFFRACTION71ALLDDD148 - 160
72X-RAY DIFFRACTION72ALLDDD161 - 170
73X-RAY DIFFRACTION73ALLDDD171 - 194
74X-RAY DIFFRACTION74ALLDDD195 - 200
75X-RAY DIFFRACTION75ALLDDD201 - 217
76X-RAY DIFFRACTION76ALLDDD218 - 229
77X-RAY DIFFRACTION77ALLDDD230 - 258
78X-RAY DIFFRACTION78ALLDDD259 - 280
79X-RAY DIFFRACTION79ALLDDD281 - 294
80X-RAY DIFFRACTION80ALLDDD295 - 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