[English] 日本語
Yorodumi
- PDB-4pca: X-ray crystal structure of an O-methyltransferase from Anaplasma ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pca
TitleX-ray crystal structure of an O-methyltransferase from Anaplasma phagocytophilum bound to SAH and Manganese
ComponentsO-methyltransferase family protein
KeywordsTRANSFERASE / methyltransferase SAH / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyVaccinia Virus protein VP39 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : / S-ADENOSYL-L-HOMOCYSTEINE / :
Function and homology information
Biological speciesAnaplasma phagocytophilum str. HGE1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFairman, J.W. / Abendroth, J. / Lorimer, D. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Plos Pathog. / Year: 2015
Title: An O-Methyltransferase Is Required for Infection of Tick Cells by Anaplasma phagocytophilum.
Authors: Oliva Chavez, A.S. / Fairman, J.W. / Felsheim, R.F. / Nelson, C.M. / Herron, M.J. / Higgins, L. / Burkhardt, N.Y. / Oliver, J.D. / Markowski, T.W. / Kurtti, T.J. / Edwards, T.E. / Munderloh, U.G.
History
DepositionApr 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: O-methyltransferase family protein
B: O-methyltransferase family protein
C: O-methyltransferase family protein
D: O-methyltransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,97018
Polymers100,8404
Non-polymers2,13014
Water17,691982
1
A: O-methyltransferase family protein
B: O-methyltransferase family protein
hetero molecules

D: O-methyltransferase family protein
hetero molecules

C: O-methyltransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,97018
Polymers100,8404
Non-polymers2,13014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area13530 Å2
ΔGint-84 kcal/mol
Surface area31650 Å2
MethodPISA
2
A: O-methyltransferase family protein
B: O-methyltransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4238
Polymers50,4202
Non-polymers1,0036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-36 kcal/mol
Surface area18520 Å2
MethodPISA
3
C: O-methyltransferase family protein
hetero molecules

D: O-methyltransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,54710
Polymers50,4202
Non-polymers1,1278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y+1/2,-z-1/21
Buried area4570 Å2
ΔGint-30 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.210, 102.760, 103.320
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
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: THR / End label comp-ID: THR

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1chain AAA-2 - 2186 - 226
2chain BBB0 - 2188 - 226
3chain CCC0 - 2188 - 226
4chain DDD-2 - 2186 - 226

-
Components

#1: Protein
O-methyltransferase family protein


Mass: 25210.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma phagocytophilum str. HGE1 (bacteria)
Gene: HGE1_02637 / Production host: Escherichia coli (E. coli) / References: UniProt: S6G476
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 982 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 400 nl of protein solution plus 400 nl of precipitant. Precipitant was MCSG2 well H5 - 0.1 M succinic acid pH 7.0, 15% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 12, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 145193 / Num. obs: 144437 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.18 % / Biso Wilson estimate: 12.02 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.08 / Χ2: 0.976 / Net I/σ(I): 16.27 / Num. measured all: 892627
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.5-1.546.180.850.5733.146505810619105230.62699.1
1.54-1.580.8970.453.996372210379102910.49299.2
1.58-1.630.9330.3674.91617871005599780.40199.2
1.63-1.680.9520.3085.7860481981897570.33799.4
1.68-1.730.9670.2457.1858668952294700.26899.5
1.73-1.790.9740.2098.4656835920491650.22899.6
1.79-1.860.9820.16610.3754960890188710.18299.7
1.86-1.940.9890.12813.0452855858285580.14199.7
1.94-2.020.9920.10515.6450686821481880.11599.7
2.02-2.120.9940.08818.2648470786278520.09699.9
2.12-2.240.9950.07321.646299750074950.0899.9
2.24-2.370.9960.06623.3843933710370980.07299.9
2.37-2.540.9970.05825.7341304667166670.06399.9
2.54-2.740.9970.05428.0838763625362510.059100
2.74-30.9970.04830.8235680575857510.05399.9
3-3.350.9980.04334.4832239522052110.04799.8
3.35-3.870.9980.0437.7628517465946430.04499.7
3.87-4.740.9980.03839.824153396839570.04199.7
4.74-6.710.9980.03838.7518444309830470.04298.4
6.710.9980.03840.089773180716640.04292.1

-
Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9pre_1665)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OA5

4oa5


Resolution: 1.5→40.584 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1721 7142 4.95 %RANDOM
Rwork0.1469 137271 --
obs0.1482 144413 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.99 Å2 / Biso mean: 17.7413 Å2 / Biso min: 5.83 Å2
Refinement stepCycle: final / Resolution: 1.5→40.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6694 0 132 982 7808
Biso mean--15.82 30.37 -
Num. residues----878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157271
X-RAY DIFFRACTIONf_angle_d1.5869916
X-RAY DIFFRACTIONf_chiral_restr0.0751171
X-RAY DIFFRACTIONf_plane_restr0.0081253
X-RAY DIFFRACTIONf_dihedral_angle_d14.242744
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3720X-RAY DIFFRACTION9.692TORSIONAL
12B3720X-RAY DIFFRACTION9.692TORSIONAL
13C3720X-RAY DIFFRACTION9.692TORSIONAL
14D3720X-RAY DIFFRACTION9.692TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5001-1.51710.24252210.20074503472499
1.5171-1.53490.21532320.19714545477799
1.5349-1.55370.222400.18454474471499
1.5537-1.57330.22562420.17544502474499
1.5733-1.5940.21012340.16884512474699
1.594-1.61590.19782330.16464533476699
1.6159-1.6390.2032470.16044537478499
1.639-1.66340.18322110.1644536474799
1.6634-1.68940.18952220.156445624784100
1.6894-1.71710.18232340.15624529476399
1.7171-1.74670.18782250.1514562478799
1.7467-1.77850.18132440.147845594803100
1.7785-1.81270.19832510.14914525477699
1.8127-1.84970.1782440.149745324776100
1.8497-1.88990.17032540.144245444798100
1.8899-1.93390.18022370.148945834820100
1.9339-1.98220.18462280.154745704798100
1.9822-2.03580.192180.148345964814100
2.0358-2.09570.16362590.144745674826100
2.0957-2.16340.15412390.140645824821100
2.1634-2.24070.15742530.138845894842100
2.2407-2.33040.16812430.143645584801100
2.3304-2.43640.16872280.144646494877100
2.4364-2.56490.17232070.142346394846100
2.5649-2.72550.15592330.142546454878100
2.7255-2.93590.17252450.147446154860100
2.9359-3.23130.17882380.14646624900100
3.2313-3.69860.16212510.139246544905100
3.6986-4.65870.14242740.123646844958100
4.6587-40.59910.16852550.14974723497896
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.48740.39880.88020.45690.66621.0017-0.08340.33860.2709-0.06920.02520.0828-0.0893-0.01190.02210.1034-0.01380.00050.14470.04150.1428-12.9039-47.2872-9.9394
20.45230.0925-0.04671.41070.14780.5440.0041-0.00480.0318-0.019-0.0048-0.0367-0.03110.00670.0010.0561-0.0071-0.0020.06620.00890.06721.2434-29.8957-12.1414
31.6097-2.0287-1.02143.01560.88681.44180.11420.144-0.0782-0.3085-0.09950.07630.0242-0.0668-0.00150.1681-0.0018-0.02470.1184-0.01070.08141.9619-50.3177-29.9906
41.3702-0.18750.42042.86050.50531.63710.06680.0223-0.0144-0.1548-0.0077-0.03-0.0172-0.0131-0.04680.0628-0.0010.00920.06010.00980.05938.0251-53.153-23.499
51.50220.2270.90321.24810.39911.68750.05190.0687-0.0099-0.0703-0.0356-0.2659-0.01860.1131-0.05820.0562-0.00030.00740.0798-0.00550.131118.6062-56.1302-20.5417
62.17030.19050.07993.585-0.85233.77580.05910.1697-0.1089-0.3529-0.0062-0.20830.10820.2053-0.030.09780.03610.03060.1019-0.03660.137820.3806-63.2414-27.4577
71.3068-0.27610.29641.0424-0.07970.7585-0.0008-0.0785-0.10060.08510.0056-0.01840.026-0.01060.0020.0715-0.0082-0.01980.06670.0140.08037.2563-58.3964-8.0821
85.28520.8694-0.26622.8409-0.66193.9946-0.0760.38090.0155-0.34290.14480.1604-0.045-0.2129-0.05340.1113-0.0083-0.02830.1159-0.00190.094522.0111-6.0709-51.8386
92.15482.53310.30786.97712.35271.5746-0.2770.2461-0.2443-0.6730.2365-0.2113-0.07620.12370.05430.1477-0.01770.01790.1231-0.01590.100628.116-19.5318-55.2008
100.91450.4388-0.39122.31110.02331.6877-0.1122-0.0322-0.1301-0.0161-0.0049-0.01620.0820.07180.07540.06940.01660.03370.10070.01060.089729.9919-21.6627-43.6287
110.18940.00630.11451.58910.44643.2458-0.1689-0.0523-0.20320.09630.00540.02930.34490.13550.12890.15670.01820.07260.09360.00160.163629.1424-33.2539-46.7881
121.6657-0.08010.90261.5825-0.18481.26930.055-0.1418-0.33560.2568-0.0955-0.0560.3720.19290.00140.20720.0390.030.1660.06480.155629.9566-27.8948-31.3336
131.0297-0.31450.31981.31530.05470.678-0.0924-0.2048-0.21440.2963-0.01420.08140.0760.08280.02820.12880.01730.03140.15940.05710.101225.3803-19.3444-29.8793
144.5626-0.8261-1.70052.9778-1.90063.8213-0.0039-0.2482-0.30740.04360.00040.72740.2033-0.7465-0.08230.1403-0.04220.02330.2917-0.0110.24157.4476-13.2103-28.1112
151.4697-0.0180.43481.55770.03361.3624-0.0125-0.2271-0.07460.2686-0.05780.00820.01850.11890.04250.0961-0.00080.00930.1310.030.070525.2438-11.6386-28.9019
163.832-0.23140.89290.68-0.04770.41410.14750.044-0.011-0.1651-0.0446-0.1136-0.0876-0.1115-0.06450.14430.00830.01670.13210.02540.088163.8594-46.6483-21.5017
171.8898-0.1346-0.40573.4232-0.43041.43130.04710.13520.07520.0408-0.0548-0.0767-0.0263-0.00070.03910.12110.0254-0.00770.12810.00470.048453.0958-47.3221-18.7352
181.2005-0.3326-0.1151.4328-0.03230.82970.04540.1696-0.0226-0.1282-0.07680.1119-0.1105-0.14610.01740.09860.0301-0.0220.1436-0.01720.07841.6803-42.9681-14.9638
191.8642-0.7828-0.19252.39783.57675.9807-0.0344-0.41450.52030.42630.3213-0.4082-0.18060.41970.00890.20020.0191-0.03860.2277-0.10560.27460.1779-42.13012.6409
201.7253-0.2941-0.29511.7720.01551.1193-0.0369-0.09490.09290.24130.05750.0648-0.0728-0.06850.04940.08830.02370.00520.1122-0.00140.09449.43-51.7593-1.4642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 16 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 218 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 30 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 31 through 55 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 56 through 90 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 91 through 116 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 117 through 218 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 0 through 16 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 17 through 30 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 31 through 90 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 91 through 116 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 117 through 138 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 139 through 168 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 169 through 182 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 183 through 218 )C0
16X-RAY DIFFRACTION16chain 'D' and (resid -2 through 30 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 31 through 55 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 56 through 165 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 166 through 180 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 181 through 218 )D0

+
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