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- PDB-2p0w: Human histone acetyltransferase 1 (HAT1) -

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Basic information

Entry
Database: PDB / ID: 2p0w
TitleHuman histone acetyltransferase 1 (HAT1)
Components
  • Histone acetyltransferase type B catalytic subunit
  • Histone peptide H4
KeywordsTRANSFERASE / hat1 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H4K12 acetyltransferase activity / histone H4 acetyltransferase activity / internal protein amino acid acetylation / subtelomeric heterochromatin formation / chromosome organization / histone acetyltransferase activity / histone acetyltransferase / nuclear matrix / nucleosome assembly / HATs acetylate histones ...histone H4K12 acetyltransferase activity / histone H4 acetyltransferase activity / internal protein amino acid acetylation / subtelomeric heterochromatin formation / chromosome organization / histone acetyltransferase activity / histone acetyltransferase / nuclear matrix / nucleosome assembly / HATs acetylate histones / histone binding / chromosome, telomeric region / chromatin / protein-containing complex / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
: / Histone acetyltransferase type B catalytic subunit, C-terminal / Arc Repressor Mutant, subunit A - #390 / Histone Acetyltransferase; domain 1 / Histone acetyl transferase 1 (HAT1), N-terminal domain / Histone acetyltransferase HAT1, C-terminal / Histone acetyltransferase type B, catalytic subunit / Histone acetyl transferase HAT1 N-terminal / Histone acetyl transferase 1, N-terminal domain superfamily / Histone acetyl transferase HAT1 N-terminus ...: / Histone acetyltransferase type B catalytic subunit, C-terminal / Arc Repressor Mutant, subunit A - #390 / Histone Acetyltransferase; domain 1 / Histone acetyl transferase 1 (HAT1), N-terminal domain / Histone acetyltransferase HAT1, C-terminal / Histone acetyltransferase type B, catalytic subunit / Histone acetyl transferase HAT1 N-terminal / Histone acetyl transferase 1, N-terminal domain superfamily / Histone acetyl transferase HAT1 N-terminus / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETAMIDE / ACETYL COENZYME *A / ACETATE ION / Histone acetyltransferase type B catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWu, H. / Min, J. / Zeng, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human histone acetyltransferase 1 (HAT1) in complex with acetylcoenzyme A and histone peptide H4
Authors: Wu, H. / Min, J. / Zeng, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionMar 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase type B catalytic subunit
B: Histone acetyltransferase type B catalytic subunit
P: Histone peptide H4
Q: Histone peptide H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,91412
Polymers78,9644
Non-polymers1,9508
Water14,088782
1
A: Histone acetyltransferase type B catalytic subunit
P: Histone peptide H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5047
Polymers39,4822
Non-polymers1,0225
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-14 kcal/mol
Surface area16930 Å2
MethodPISA
2
B: Histone acetyltransferase type B catalytic subunit
Q: Histone peptide H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4105
Polymers39,4822
Non-polymers9283
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-1 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.557, 155.425, 53.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABPQ

#1: Protein Histone acetyltransferase type B catalytic subunit


Mass: 37968.121 Da / Num. of mol.: 2 / Fragment: Residues 20-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAT1 / Plasmid: pET28a-MHL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14929, histone acetyltransferase
#2: Protein/peptide Histone peptide H4


Mass: 1513.815 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide

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Non-polymers , 5 types, 790 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#6: Chemical
ChemComp-ACM / ACETAMIDE


Mass: 59.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 782 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 20000, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→47.35 Å / Num. all: 76880 / Num. obs: 76880 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BOB
Resolution: 1.9→47.35 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.633 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.14 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22834 3584 5 %RANDOM
Rwork0.18224 ---
all0.1846 68545 --
obs0.1846 68545 92.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.911 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5477 0 123 782 6382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225769
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9797797
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2985670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77823.633289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21115984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4251536
X-RAY DIFFRACTIONr_chiral_restr0.1020.2823
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024406
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.22737
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23936
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2592
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7941.53484
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2325404
X-RAY DIFFRACTIONr_scbond_it2.09232668
X-RAY DIFFRACTIONr_scangle_it3.0684.52392
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 277 -
Rwork0.267 5127 -
obs--95.68 %
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)
13.74940.3862.02550.40050.49791.3264-0.12670.33860.1392-0.11580.1208-0.012-0.14390.19360.00590.0053-0.02960.02790.10540.02660.0275106.7438-18.23162.6328
25.83686.77243.81338.26254.89385.3518-0.01240.5705-0.0496-0.33090.2917-0.1961-0.4740.1946-0.27930.0358-0.01410.0280.06510.04860.008396.1506-17.8212-7.7669
30.21690.1619-0.46650.9604-0.00291.14510.061-0.04310.09180.07780.0207-0.1011-0.15310.2401-0.0817-0.0278-0.0375-0.01480.0770.01170.0317109.2238-18.72328.6773
44.28650.0442-0.33460.2580.47450.9131-0.01950.11690.0112-0.00250.0043-0.0466-0.14690.01270.01520.01870.00570.00390.0540.01120.0273101.1631-26.25210.3226
535.2231-11.052513.02946.4509-5.41375.40850.24821.438-0.167-0.0111-0.2248-0.2060.05660.369-0.0234-0.1107-0.0080.03680.093-0.08610.0444126.3602-25.9185-0.415
628.72869.7673-6.70096.2965-3.23372.24730.04-0.0145-0.8350.2597-0.2218-0.51390.07570.11250.1818-0.02650.0485-0.04480.04370.00450.0416113.7313-30.2567.5831
70.451-0.09590.10270.2234-0.14380.58710.0180.0683-0.0099-0.0023-0.01710.01610.0357-0.0356-0.00090.03280.01810.00110.02370.00040.005585.573-24.99382.6616
82.491.8027-0.17682.9475-0.0670.0148-0.0370.0171-0.08170.0461-0.06890.05990.05250.07330.10590.04150.02570.0170.0218-0.00440.023691.4875-32.836211.8527
90.1271-0.0804-0.08490.11230.03760.9271-0.0132-0.0121-0.00620.03130.00530.0121-0.024-0.01740.00790.03570.00860.00150.02340.00570.019988.5284-26.783513.6347
100.49180.6564-0.17692.7527-2.17082.058-0.1119-0.00470.0765-0.0440.0484-0.03960.155-0.07230.06350.07580.00330.00820.01580.00820.008283.2151-30.476937.2417
110.19990.071-0.21430.4378-0.16521.2332-0.00750.01580.00120.0449-0.0029-0.0158-0.0784-0.04760.01040.03330.0215-0.00850.02120.00380.021784.1793-20.088621.8197
122.7042-1.3193-2.14112.96920.56261.89080.04510.0656-0.0862-0.0097-0.0982-0.1596-0.4409-0.05450.0530.06960.0106-0.0024-0.0044-0.00640.010984.8806-10.543724.7472
132.53240.89051.50618.7318.702514.5140.30560.57180.18870.04480.14730.341-0.7365-0.9729-0.45290.0320.13320.10460.06180.09460.027271.3855-4.776732.4396
140.68941.4496-0.70517.24032.04823.69510.2767-0.13060.02120.1657-0.21430.548-0.3474-0.2792-0.06240.10520.05430.08810.0113-0.00740.015274.3375-7.922839.0413
150.66790.8219-0.10633.99070.38380.65470.0646-0.09290.02790.25850.02730.1101-0.1252-0.0525-0.09190.09170.030.03560.0032-0.0088-0.005880.6322-6.628733.2872
162.2310.0773-0.20360.0027-0.00710.01860.17330.15-0.1944-0.0139-0.08750.0161-0.05790.0363-0.08580.0326-0.0117-0.02550.0443-0.01880.04564.739613.0722-0.9207
173.86111.0858-3.88962.00960.13886.211-0.17850.1408-0.2013-0.08060.0953-0.16790.2177-0.10560.08320.0175-0.0026-0.0138-0.0014-0.01710.03977.570311.7816-4.1257
180.9834-0.13390.37530.31490.20220.35950.01540.0283-0.0407-0.0153-0.05030.0507-0.0041-0.0480.03490.0009-0.0175-0.00730.0303-0.01550.037867.433218.08263.8124
195.7891-1.11110.09050.3674-0.10010.04580.06130.37090.14420.00710.0073-0.0839-0.0723-0.0071-0.0686-0.00080.0030.01230.0698-0.02780.058753.404719.6691-5.9401
2018.21696.14567.69232.16612.38923.7047-0.0413-0.10120.62840.034-0.20930.2325-0.008-0.06510.2505-0.01790.0153-0.0087-0.0009-0.06530.108158.763824.4083.7
213.2754-0.7427-1.04350.36730.55420.83950.09840.37080.2491-0.1316-0.00040.0358-0.1814-0.1831-0.09810.06360.0091-0.0230.0370.04350.001276.716427.7673-6.8071
220.3229-0.17320.43231.0463-0.17631.20610.01070.10060.0554-0.0527-0.0561-0.11820.08140.21960.04540.01270.00430.01520.0530.00940.021994.734922.2676.6513
232.36282.1070.30642.271.06591.646-0.0710.08910.0126-0.0404-0.00150.0617-0.2845-0.11430.07260.05710.0161-0.01390.00970.01110.031682.864732.38137.942
240.05820.01620.22330.18240.25951.0762-0.0197-0.00060.01780.0159-0.02180.0176-0.01430.06820.04150.0314-0.00330.0010.02290.00190.029384.300224.606714.1597
250.28320.34430.1721.33211.12971.4878-0.0101-0.0176-0.04660.0953-0.07630.04510.13840.01090.08630.03170.01390.00180.00320.00880.033387.474917.362118.1977
261.70291.23510.1191.93780.36381.0176-0.01350.00330.00630.1620.00610.01230.13890.08080.00730.04360.0091-0.0004-0.00970.00850.021789.874419.688126.3203
273.67690.21634.13692.147-0.30136.25020.12580.3892-0.21440.15320.0059-0.21780.50680.376-0.13160.12670.0755-0.0217-0.0309-0.00370.029395.91715.94329.0816
282.9458-1.68766.07931.0667-3.150513.6507-0.5134-1.90951.12381.17790.053-0.39981.0149-0.49340.46040.23180.05110.02230.2092-0.19610.176496.01773.53641.8013
290.67421.04510.00396.7169-1.10245.4479-0.0320.1250.0620.7111-0.0191-0.46040.10060.09390.05110.11010.0471-0.0726-0.0471-0.02590.002394.983414.507535.0634
306.9828-0.8184-0.02577.29880.18090.00450.2153-0.2492-0.2580.3889-0.1545-0.1551-0.1086-0.1452-0.06080.1240.005-0.013-0.04470.0085-0.014991.12461.465534.053
316.26046.9524-5.55058.1993-5.47995.89960.1173-0.2889-0.21910.3385-0.1358-0.228-0.16690.3590.0185-0.0077-0.0184-0.04580.069-0.00930.0108103.5279-23.586124.8235
326.93628.1763.918911.25245.8514.47640.564-0.61640.21010.7238-0.60390.16690.3292-0.51830.040.0448-0.06380.04450.04120.0113-0.013369.716319.55222.1299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA23 - 406 - 23
2X-RAY DIFFRACTION2AA41 - 4724 - 30
3X-RAY DIFFRACTION3AA48 - 7231 - 55
4X-RAY DIFFRACTION4AA73 - 9056 - 73
5X-RAY DIFFRACTION5AA91 - 10274 - 85
6X-RAY DIFFRACTION6AA103 - 11386 - 96
7X-RAY DIFFRACTION7AA114 - 16497 - 147
8X-RAY DIFFRACTION8AA165 - 183148 - 166
9X-RAY DIFFRACTION9AA184 - 226167 - 209
10X-RAY DIFFRACTION10AA227 - 236210 - 219
11X-RAY DIFFRACTION11AA237 - 279220 - 262
12X-RAY DIFFRACTION12AA280 - 294263 - 277
13X-RAY DIFFRACTION13AA295 - 302278 - 285
14X-RAY DIFFRACTION14AA303 - 319286 - 302
15X-RAY DIFFRACTION15AA320 - 341303 - 324
16X-RAY DIFFRACTION16BB18 - 411 - 24
17X-RAY DIFFRACTION17BB42 - 5325 - 36
18X-RAY DIFFRACTION18BB54 - 8737 - 70
19X-RAY DIFFRACTION19BB88 - 10071 - 83
20X-RAY DIFFRACTION20BB101 - 11484 - 97
21X-RAY DIFFRACTION21BB115 - 13298 - 115
22X-RAY DIFFRACTION22BB133 - 167116 - 150
23X-RAY DIFFRACTION23BB168 - 177151 - 160
24X-RAY DIFFRACTION24BB178 - 231161 - 214
25X-RAY DIFFRACTION25BB232 - 259215 - 242
26X-RAY DIFFRACTION26BB260 - 283243 - 266
27X-RAY DIFFRACTION27BB284 - 303267 - 286
28X-RAY DIFFRACTION28BB304 - 311287 - 294
29X-RAY DIFFRACTION29BB312 - 328295 - 311
30X-RAY DIFFRACTION30BB329 - 339312 - 322
31X-RAY DIFFRACTION31PC5 - 191 - 15
32X-RAY DIFFRACTION32QD6 - 192 - 15

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  • 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

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