[English] 日本語
Yorodumi
- PDB-4d1m: Tetramerization domain of zebrafish p53 (crystal form II) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d1m
TitleTetramerization domain of zebrafish p53 (crystal form II)
ComponentsCELLULAR TUMOR ANTIGEN P53P53
KeywordsTRANSCRIPTION / P53 FAMILY / TUMOR SUPPRESSOR / TRANSCRIPTION FACTOR / TETRAMER / PROTEIN EVOLUTION
Function / homology
Function and homology information


epithelium development / anatomical structure morphogenesis / protein tetramerization / transcription cis-regulatory region binding / cell cycle / DNA-binding transcription factor activity / apoptotic process / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
p53, subunit A / p53-like tetramerisation domain / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily ...p53, subunit A / p53-like tetramerisation domain / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Cellular tumor antigen p53
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJoerger, A.C.
CitationJournal: Structure / Year: 2014
Title: Tracing the Evolution of the P53 Tetramerization Domain
Authors: Joerger, A.C. / Wilcken, R. / Andreeva, A.
History
DepositionMay 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Structure summary
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CELLULAR TUMOR ANTIGEN P53
B: CELLULAR TUMOR ANTIGEN P53
C: CELLULAR TUMOR ANTIGEN P53
D: CELLULAR TUMOR ANTIGEN P53
E: CELLULAR TUMOR ANTIGEN P53
F: CELLULAR TUMOR ANTIGEN P53
G: CELLULAR TUMOR ANTIGEN P53
H: CELLULAR TUMOR ANTIGEN P53
I: CELLULAR TUMOR ANTIGEN P53
J: CELLULAR TUMOR ANTIGEN P53
K: CELLULAR TUMOR ANTIGEN P53
L: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,15514
Polymers67,02412
Non-polymers1312
Water1,06359
1
E: CELLULAR TUMOR ANTIGEN P53
F: CELLULAR TUMOR ANTIGEN P53
G: CELLULAR TUMOR ANTIGEN P53
H: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4075
Polymers22,3414
Non-polymers651
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-69.4 kcal/mol
Surface area10230 Å2
MethodPISA
2
A: CELLULAR TUMOR ANTIGEN P53
B: CELLULAR TUMOR ANTIGEN P53
C: CELLULAR TUMOR ANTIGEN P53
D: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4075
Polymers22,3414
Non-polymers651
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-40.7 kcal/mol
Surface area12200 Å2
MethodPISA
3
I: CELLULAR TUMOR ANTIGEN P53
J: CELLULAR TUMOR ANTIGEN P53
K: CELLULAR TUMOR ANTIGEN P53
L: CELLULAR TUMOR ANTIGEN P53


Theoretical massNumber of molelcules
Total (without water)22,3414
Polymers22,3414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-56.3 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.861, 74.507, 74.945
Angle α, β, γ (deg.)90.00, 117.79, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide
CELLULAR TUMOR ANTIGEN P53 / P53 / P53


Mass: 5585.328 Da / Num. of mol.: 12 / Fragment: TETRAMERIZATION DOMAIN, RESIDUES 302-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: G1K2L5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsADDITIONAL GGS SEQUENCE AT THE N TERMINUS AS A RESULT OF CLONING STRATEGY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: SITTING DROP VAPOR DIFFUSION AT 20 DEGREE C; PROTEIN SOLUTION: 12 MG/ML IN 20 MM TRIS PH 7.5, 50 MM NACL, 5 MM DTT; CRYSTALLIZATION BUFFER: 160 MM ZINC ACETATE, 80 MM SODIUM CACODYLATE, PH 6. ...Details: SITTING DROP VAPOR DIFFUSION AT 20 DEGREE C; PROTEIN SOLUTION: 12 MG/ML IN 20 MM TRIS PH 7.5, 50 MM NACL, 5 MM DTT; CRYSTALLIZATION BUFFER: 160 MM ZINC ACETATE, 80 MM SODIUM CACODYLATE, PH 6.5, 12% (W/V) POLYETHYLENE GLYCOL 8,000 AND 19% (W/V) GLYCEROL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→28.9 Å / Num. obs: 34925 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / % possible all: 99.5

-
Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.9 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.903 / SU B: 15.086 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27996 1744 5 %RANDOM
Rwork0.2259 ---
obs0.22845 33164 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.722 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å2-0.29 Å2
2---0.14 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 2 59 4025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194002
X-RAY DIFFRACTIONr_bond_other_d0.0010.023970
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9995356
X-RAY DIFFRACTIONr_angle_other_deg0.77739135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8245464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09723.881219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2215815
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3871548
X-RAY DIFFRACTIONr_chiral_restr0.0740.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024394
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02878
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_it1.6262.8481893
X-RAY DIFFRACTIONr_mcbond_other1.6252.8471892
X-RAY DIFFRACTIONr_mcangle_it2.3694.2512346
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0573.1672109
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 129 -
Rwork0.282 2398 -
obs--98.98 %
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)
13.89041.0746-8.56993.31030.798330.20750.0475-0.7133-0.0090.2988-0.2382-0.1372-0.53720.89150.19070.31450.0131-0.03070.1876-0.00850.269522.35944.78-12.335
211.825211.8748-18.124815.493-18.808827.90170.25970.3088-0.1044-0.5817-0.26220.6362-0.2959-0.41830.00250.28150.2281-0.1210.1982-0.05510.198214.85636.303-16.947
312.56316.46247.18917.4960.857720.03110.11520.0629-0.84910.02540.05610.58470.8598-0.3633-0.17130.054-0.0086-0.0020.16770.03580.32934.32621.595-8.007
44.56630.85750.500322.7648-22.649522.9445-0.5499-0.26250.22980.13550.53980.0722-0.31-0.66220.01010.36040.0605-0.02530.2315-0.13910.13718.81745.132-15.529
514.15270.6721-12.1833.93530.319413.95420.2168-0.46570.0710.1528-0.0560.0224-0.19090.4822-0.16080.128-0.0544-0.02480.0814-0.0030.072527.29736.744-14.003
68.21224.532-1.008724.1305-3.861316.34560.46740.0171-0.8608-1.6948-0.5749-1.28451.09011.3310.10750.4425-0.01620.14080.3528-0.09230.250642.82228.74-25.642
720.4226-7.177311.18474.7968-1.24719.53160.2989-0.4276-1.19960.18490.08360.45550.4079-0.1381-0.38250.2224-0.13480.01950.22680.11030.439123.29417.315-18.01
825.24536.18879.37022.92463.85786.30090.17720.7601-0.7885-0.215-0.0353-0.0663-0.08290.3457-0.14190.14190.05-0.02750.1609-0.03690.100326.62527.679-22.872
911.7451-4.849311.193811.6489-13.926726.0309-0.06440.20190.92080.3674-0.2162-0.4501-1.48210.63940.28060.2685-0.13970.08170.2329-0.10430.261441.97540.003-18.401
1030.41484.986523.01494.3684-0.274322.1480.01520.2001-0.7601-0.314-0.102-0.51380.36340.19180.08690.1586-0.02350.01580.1887-0.15870.48923.01118.429-22.993
1125.28410.0732-3.57685.58740.78582.5454-0.2049-1.0037-0.96910.2983-0.1022-0.15340.08980.07670.30710.1028-0.047-0.02180.13760.06950.154118.59124.562-13.641
1212.62382.06797.203519.98145.401227.0134-0.6704-0.13710.8811-0.54970.83771.7903-1.4566-0.57-0.16730.14860.12750.0350.33840.07680.63240.61133.751-11.018
1319.8263-1.248-21.14632.6449-1.18725.8760.03130.46010.1251-0.2206-0.4629-0.4967-0.3342-0.00070.43160.4087-0.1436-0.00070.419-0.05530.341828.66621.0486.58
144.0755-10.4949-7.203427.165818.977920.4129-0.2189-0.12710.09830.60990.1417-0.19050.15220.90770.07720.0591-0.1472-0.02310.5344-0.00860.144625.23610.09110.45
158.1149-2.1715-11.911119.2225-2.441230.2763-0.8539-0.2716-1.20990.7936-0.00150.5352.344-1.22990.85540.3696-0.1009-0.1170.4090.09620.446523.107-9.5484.428
163.871-3.2786-8.30216.632912.951731.0779-0.0885-0.46790.23690.12190.5009-0.89290.17580.5606-0.41240.0754-0.1336-0.07140.4399-0.0510.342629.83518.75110.348
1717.9225-12.6002-11.380912.96558.344112.00430.60640.39110.5832-0.926-0.1719-0.5985-0.7970.0492-0.43450.2644-0.14860.06010.1525-0.00210.122419.29619.4524.477
185.52031.06781.413513.26523.058327.13190.43850.73770.1485-0.4088-0.40150.9213-0.0709-0.9188-0.0370.18340.0650.07150.2234-0.00540.27560.2826.6357.315
1912.7977-4.43113.066811.7626.786713.02590.67150.3389-0.2622-0.837-1.26272.08671.2491-1.06080.59120.4878-0.0264-0.31810.2531-0.13330.75466.0673.7195.076
204.5621-8.31953.996825.0512-15.932611.3562-0.0428-0.3345-0.22760.85150.19870.5428-0.718-0.1853-0.15590.0729-0.03220.00750.2704-0.09640.163310.23513.42310.792
210.20760.9027-1.624213.74251.436320.40950.1286-0.07010.0110.4857-0.1064-0.1836-1.19440.7257-0.02220.2131-0.06260.01540.21940.00680.33611.67832.1593.677
226.0821-8.084610.63822.5535-20.98835.66450.0833-0.5499-0.1410.819-0.05891.2582-0.8804-0.5934-0.02430.1018-0.06170.00720.2426-0.04550.37285.464.7599.98
2324.9973-18.89227.581519.6576-8.50888.10570.53470.2687-0.7261-0.9434-0.4390.7256-0.1450.3499-0.09570.1540.0007-0.09360.187-0.02060.146115.984.6123.765
248.20251.8501-6.835814.0682-5.634731.2941-0.04530.42040.1085-0.18390.0405-0.26850.07961.50570.00490.05030.0598-0.06910.32110.00370.219535.073-2.486.545
2521.5967-4.3704-12.21517.30145.096412.73540.2570.17411.64540.1224-0.1571-0.1907-0.9292-0.1952-0.09990.3908-0.0346-0.10480.12480.05630.281612.7657.286-20.252
2624.48910.2642-8.42295.193-3.16275.0999-0.36060.21790.6369-0.28840.31940.24050.1690.00150.04120.30220.03380.01960.1010.03120.10018.57-3.163-24.438
2715.515-5.4775-3.993525.23456.47498.8748-0.00760.4702-0.849-0.22460.12520.3970.5147-0.2964-0.11750.2304-0.04260.02960.22410.0620.1704-6.28-16.556-19.937
2829.20276.6847-22.25696.1711-5.430422.1261-0.19870.34280.6852-0.02540.07220.13620.1091-0.16440.12640.26610.0049-0.07890.05350.03970.282111.4596.148-24.135
2924.3896-1.3967-1.07763.99450.51214.6149-0.0354-0.62470.24110.1998-0.0830.1831-0.32970.30610.11830.3184-0.0242-0.02090.08650.0070.116.6740.045-15.158
308.06281.40470.173921.6689-7.184716.7841-0.27220.2904-1.2603-0.53340.2177-0.92281.07630.45560.05450.24940.17540.11170.41360.01440.440834.753-8.647-13.023
312.5317-1.26276.99475.38650.23427.33270.1076-0.4398-0.01110.2741-0.08420.07940.3647-0.5383-0.02340.2644-0.01940.03730.27330.00730.249914.412-20.448-13.911
3216.997710.150116.328810.064913.869519.9931-0.08610.5459-0.4306-0.18370.7426-0.5412-0.03261.052-0.65650.51350.21180.13960.20.04390.089220.664-11.501-18.787
337.91125.3447-9.633312.7147-5.053615.96350.0967-0.11780.7678-0.54690.0264-1.1136-1.10210.1846-0.12310.24160.0031-0.11790.2148-0.00090.655530.9523.783-9.832
344.96036.279211.179513.720719.150742.8295-0.02070.0299-0.40540.0297-0.0981-0.35760.05830.80570.11890.21060.05220.0540.16170.08090.209417.265-20.395-17.671
3518.39080.982414.50452.31360.055818.28940.1769-0.5698-0.13230.3609-0.08480.05670.5791-0.5284-0.09210.3220.02160.07340.04870.03710.07748.253-12.716-15.91
3622.5735-6.242-9.9298.41995.609524.62830.4221.11731.2612-1.5611-0.64510.6739-2.0118-1.57510.22310.66780.1189-0.15810.36670.13450.336-7.345-5.451-27.594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A303 - 311
2X-RAY DIFFRACTION2A312 - 331
3X-RAY DIFFRACTION3A332 - 340
4X-RAY DIFFRACTION4B303 - 311
5X-RAY DIFFRACTION5B312 - 331
6X-RAY DIFFRACTION6B332 - 342
7X-RAY DIFFRACTION7C302 - 311
8X-RAY DIFFRACTION8C312 - 331
9X-RAY DIFFRACTION9C332 - 341
10X-RAY DIFFRACTION10D303 - 311
11X-RAY DIFFRACTION11D312 - 331
12X-RAY DIFFRACTION12D332 - 341
13X-RAY DIFFRACTION13E303 - 311
14X-RAY DIFFRACTION14E312 - 331
15X-RAY DIFFRACTION15E332 - 344
16X-RAY DIFFRACTION16F303 - 311
17X-RAY DIFFRACTION17F312 - 331
18X-RAY DIFFRACTION18F332 - 343
19X-RAY DIFFRACTION19G302 - 311
20X-RAY DIFFRACTION20G312 - 331
21X-RAY DIFFRACTION21G332 - 341
22X-RAY DIFFRACTION22H303 - 311
23X-RAY DIFFRACTION23H312 - 331
24X-RAY DIFFRACTION24H332 - 342
25X-RAY DIFFRACTION25I303 - 311
26X-RAY DIFFRACTION26I312 - 331
27X-RAY DIFFRACTION27I332 - 341
28X-RAY DIFFRACTION28J303 - 311
29X-RAY DIFFRACTION29J312 - 331
30X-RAY DIFFRACTION30J332 - 340
31X-RAY DIFFRACTION31K302 - 311
32X-RAY DIFFRACTION32K312 - 331
33X-RAY DIFFRACTION33K332 - 341
34X-RAY DIFFRACTION34L303 - 311
35X-RAY DIFFRACTION35L312 - 331
36X-RAY DIFFRACTION36L332 - 341

+
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