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- PDB-2qp2: Structure of a MACPF/perforin-like protein -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2qp2
TitleStructure of a MACPF/perforin-like protein
ComponentsUnknown protein
KeywordsUNKNOWN FUNCTION / Toxin
Function / homology
Function and homology information


Vitelline Membrane Outer Layer Protein I, subunit A - #50 / MABP domain / MABP domain profile. / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesPhotorhabdus luminescens subsp. laumondii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsRosado, C.J. / Buckle, A.M. / Law, R.H.P. / Butcher, R.E. / Kan, W.T. / Bird, C.H. / Ung, K. / Browne, K.A. / Baran, K. / Bashtannyk-Puhalovich, T.A. ...Rosado, C.J. / Buckle, A.M. / Law, R.H.P. / Butcher, R.E. / Kan, W.T. / Bird, C.H. / Ung, K. / Browne, K.A. / Baran, K. / Bashtannyk-Puhalovich, T.A. / Faux, N.G. / Wong, W. / Porter, C.J. / Pike, R.N. / Ellisdon, A.M. / Pearce, M.C. / Bottomley, S.P. / Emsley, J. / Smith, A.I. / Rossjohn, J. / Hartland, E.L. / Voskoboinik, I. / Trapani, J.A. / Bird, P.I. / Dunstone, M.A. / Whisstock, J.C.
CitationJournal: Science / Year: 2007
Title: A common fold mediates vertebrate defense and bacterial attack
Authors: Rosado, C.J. / Buckle, A.M. / Law, R.H. / Butcher, R.E. / Kan, W.T. / Bird, C.H. / Ung, K. / Browne, K.A. / Baran, K. / Bashtannyk-Puhalovich, T.A. / Faux, N.G. / Wong, W. / Porter, C.J. / ...Authors: Rosado, C.J. / Buckle, A.M. / Law, R.H. / Butcher, R.E. / Kan, W.T. / Bird, C.H. / Ung, K. / Browne, K.A. / Baran, K. / Bashtannyk-Puhalovich, T.A. / Faux, N.G. / Wong, W. / Porter, C.J. / Pike, R.N. / Ellisdon, A.M. / Pearce, M.C. / Bottomley, S.P. / Emsley, J. / Smith, A.I. / Rossjohn, J. / Hartland, E.L. / Voskoboinik, I. / Trapani, J.A. / Bird, P.I. / Dunstone, M.A. / Whisstock, J.C.
History
DepositionJul 22, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _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_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_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_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_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Unknown protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2453
Polymers57,1651
Non-polymers802
Water6,413356
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.439, 154.507, 43.917
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Unknown protein


Mass: 57164.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (bacteria)
Species: Photorhabdus luminescens / Strain: subsp. laumondii / Gene: Photorhabdus luminescens / Plasmid: pDEST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami (DE3) pLysS / References: UniProt: Q7N6X0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG8000, 0.1M MES pH6.0, 0.2M Calcium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODEELLIOTT GX-1811.5418
SYNCHROTRONAPS 17-ID21
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEFeb 4, 2007
ADSC QUANTUM 42CCDApr 10, 2007
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
211
ReflectionRedundancy: 7.5 % / Av σ(I) over netI: 7.2 / Number: 172665 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Χ2: 1.14 / D res high: 2.457 Å / D res low: 155.012 Å / Num. obs: 23066 / % possible obs: 91
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsRsym valueChi squaredRedundancy
7.7246.3799.70.030.031.4147.7
5.467.721000.0360.0361.3398.5
4.465.461000.0490.0491.2778.6
3.864.461000.0640.0641.1588.6
3.453.861000.090.091.1038.4
3.153.451000.1330.1331.0258
2.923.1599.70.2070.2070.9847.6
2.732.9298.30.3120.3120.9877.5
2.572.7390.80.4440.4440.9885.9
2.442.5749.30.5850.5850.8724.2
ReflectionResolution: 2→100 Å / Num. obs: 44074 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.047 / Χ2: 1.144 / Net I/σ(I): 15.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3518 / Χ2: 0.872 / % possible all: 79.1

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Phasing

PhasingMethod: MIRAS
Phasing set
ID
1
2
3
4
Phasing MIR der

Native set-ID: 1 / Resolution: 2.51→48.67 Å

IDDer set-IDPower acentricPower centricReflection acentricReflection centric
ISO_1100192882902
ISO_220.6020.55572371550
ISO_330.9140.723114491931
ISO_440.3460.359101761684
Phasing MIR der shell
Highest resolution (Å)Lowest resolution (Å)Der-IDPower acentricPower centricReflection acentricReflection centric
10.9548.67ISO_100184151
7.8410.95ISO_100385163
6.437.84ISO_100509158
5.586.43ISO_100611159
55.58ISO_100710161
4.575ISO_100794167
4.234.57ISO_100866160
3.964.23ISO_100925162
3.743.96ISO_1001008156
3.553.74ISO_1001066168
3.383.55ISO_1001101152
3.243.38ISO_1001184161
3.113.24ISO_1001224159
33.11ISO_1001272148
2.93ISO_1001291146
2.812.9ISO_1001356132
2.722.81ISO_1001282124
2.652.72ISO_1001298116
2.582.65ISO_100120190
2.512.58ISO_100102169
10.9548.67ISO_20.9530.802183140
7.8410.95ISO_21.1480.966385163
6.437.84ISO_21.1280.995509158
5.586.43ISO_20.9750.81611153
55.58ISO_20.780.668710156
4.575ISO_20.5140.39788155
4.234.57ISO_20.4880.353859149
3.964.23ISO_20.440.337924149
3.743.96ISO_20.380.2711008145
3.553.74ISO_20.350.2481065156
3.383.55ISO_20.3790.25119526
3.243.38ISO_20000
3.113.24ISO_20000
33.11ISO_20000
2.93ISO_20000
2.812.9ISO_20000
2.722.81ISO_20000
2.652.72ISO_20000
2.582.65ISO_20000
2.512.58ISO_20000
10.9548.67ISO_31.0040.772182137
7.8410.95ISO_31.5471.073384151
6.437.84ISO_31.4881.276505141
5.586.43ISO_31.3941.039604145
55.58ISO_31.1910.931700142
4.575ISO_31.0360.697779147
4.234.57ISO_30.950.712847140
3.964.23ISO_30.8390.593906142
3.743.96ISO_30.8340.533984135
3.553.74ISO_30.7420.5321038146
3.383.55ISO_30.750.5271071127
3.243.38ISO_30.7330.5191149135
3.113.24ISO_30.7120.5121184134
33.11ISO_30.70.461109109
2.93ISO_30.647070
2.812.9ISO_30000
2.722.81ISO_30000
2.652.72ISO_30000
2.582.65ISO_30000
2.512.58ISO_30000
10.9548.67ISO_41.1971.041184140
7.8410.95ISO_40.9780.831384154
6.437.84ISO_40.9130.672507150
5.586.43ISO_40.7950.55607149
55.58ISO_40.5410.489703148
4.575ISO_40.3960.28780152
4.234.57ISO_40.2930.219844137
3.964.23ISO_40.2450.22887136
3.743.96ISO_40.2290.217950120
3.553.74ISO_40.2140.185943114
3.383.55ISO_40.2430.208948111
3.243.38ISO_40.2490.182976106
3.113.24ISO_40.2550.21591847
33.11ISO_40.2980.26154520
2.93ISO_40000
2.812.9ISO_40000
2.722.81ISO_40000
2.652.72ISO_40000
2.582.65ISO_40000
2.512.58ISO_40000

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
RefinementMethod to determine structure: MIRAS / Resolution: 2→41.21 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.983 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.154 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2245 5.1 %RANDOM
Rwork0.18 ---
obs0.182 44064 96.67 %-
all-44064 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.57 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2→41.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 2 356 4173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223969
X-RAY DIFFRACTIONr_angle_refined_deg0.9611.955406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9615525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39325.14179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92315645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2411513
X-RAY DIFFRACTIONr_chiral_restr0.0720.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023054
X-RAY DIFFRACTIONr_nbd_refined0.1720.21735
X-RAY DIFFRACTIONr_nbtor_refined0.2960.22765
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2349
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.213
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0750.21
X-RAY DIFFRACTIONr_mcbond_it0.58222585
X-RAY DIFFRACTIONr_mcangle_it1.2354047
X-RAY DIFFRACTIONr_scbond_it2.44471581
X-RAY DIFFRACTIONr_scangle_it3.703101345
LS refinement shellResolution: 2.004→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 138 -
Rwork0.218 2357 -
all-2495 -
obs--75.58 %
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)
17.3881-3.11373.39074.8721-1.94177.44030.0237-0.1223-0.1355-0.0148-0.0093-0.29940.17040.7748-0.01440.0687-0.00860.03870.1664-0.02280.05570.38749.73311.691
21.5330.17910.073.3796-0.9041.2864-0.07450.06060.0674-0.06430.07980.1108-0.1206-0.0634-0.00530.070.01180.00130.1167-0.02980.027956.95852.1769.646
31.42650.3877-0.9396.7913.529.42290.0158-0.12580.42490.00410.3649-0.0325-0.648-0.0551-0.38070.06130.1032-0.0647-0.0024-0.00170.106452.14467.99210.465
43.2925-0.24913.30691.7614-2.22577.6576-0.1166-0.28480.20390.20580.24060.234-0.5652-0.7751-0.1240.06120.116-0.00910.0383-0.0880.050652.5961.94419.693
51.6911-0.41060.35262.57381.46642.46690.0125-0.151-0.24140.1930.01250.14480.1638-0.113-0.02490.0686-0.0197-0.00160.11580.01410.062558.73735.69229.191
64.74550.2883.29432.7911-0.32484.2690.0187-0.254-0.31890.10130.04130.15220.189-0.3129-0.060.1309-0.0109-0.00010.07740.0020.03156.51236.94821.07
71.6254-1.21990.41758.2337-0.06222.38210.0707-0.0011-0.16740.02780.0361-0.10510.24380.1285-0.10680.04990.0206-0.020.1081-0.00260.058867.39935.45328.636
89.72472.43189.8050.82143.121615.45290.0818-0.3958-0.10280.36140.03480.1773-0.0672-0.5949-0.11660.13090.0852-0.02320.0458-0.0470.058154.658.29221.444
92.82262.44310.97589.42893.80843.3404-0.26230.21860.1839-0.4250.03410.4703-0.1005-0.2370.22830.01990.006-0.05490.1750.00690.018143.89546.1921.713
100.7150.00430.49360.3370.16560.9281-0.03210.1149-0.0943-0.02680.03470.0338-0.0079-0.0322-0.00260.0640.0080.00780.1211-0.03090.060357.11642.21915.963
111.1571-0.3146-0.37362.06061.14.43570.0204-0.0802-0.09010.1297-0.07470.13490.1384-0.04550.05430.03530.0329-0.0020.1211-0.00810.045267.6540.2142.107
120.6343-0.44660.22352.8123-1.35854.5445-0.04220.02530.0364-0.0127-0.0485-0.16850.08250.31390.09070.00550.0161-0.01060.1544-0.02120.12727344.00334.12
132.89630.86891.89821.16270.38732.8275-0.0525-0.26680.12980.1511-0.0747-0.0483-0.184-0.06440.12730.09680.00370.00450.0922-0.04150.060864.51952.71526.457
1410.6264-4.80865.13082.9608-1.90383.43160.0795-0.1377-0.32840.10820.02880.15050.2457-0.2155-0.10840.0217-0.0512-0.00710.10630.0060.065845.13733.53310.578
157.2406-12.09754.802120.6755-8.60723.92090.12070.2322-0.4028-0.41760.00990.4620.01040.0042-0.13050.08890.0347-0.09430.0052-0.03980.137867.83113.92225.019
165.7101-4.18061.542711.5836-4.025211.3233-0.00310.48660.66420.3124-0.3107-1.4353-0.41270.83280.3138-0.0746-0.042-0.0041-0.05650.03930.20282.9038.64231.617
174.3223-4.54682.64668.8-3.22363.28120.24880.0724-0.7968-0.52620.05360.88990.1983-0.0467-0.30230.07120.0089-0.0517-0.0195-0.05720.223168.576.14328.278
187.0495-5.9083.01349.3728-3.12092.7696-0.0497-0.1097-0.74140.37330.32421.1285-0.0216-0.1737-0.27440.06040.01720.0357-0.02260.01730.197769.5483.04433.74
197.5353-1.94925.90887.4262.93727.51440.4963-1.0789-0.16232.8369-0.62770.1481-0.32490.58410.13140.30970.06080.02550.3240.11070.32268.22811.31244.004
200.9427-1.31971.98358.8896-2.33044.8824-0.6657-0.4997-0.331.88760.78470.3194-0.4715-0.3823-0.1190.26520.1540.0833-0.0290.01130.017573.1785.72243.114
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 309 - 31
2X-RAY DIFFRACTION2AA31 - 6932 - 70
3X-RAY DIFFRACTION3AA70 - 8571 - 86
4X-RAY DIFFRACTION4AA86 - 10287 - 103
5X-RAY DIFFRACTION5AA103 - 120104 - 121
6X-RAY DIFFRACTION6AA121 - 138122 - 139
7X-RAY DIFFRACTION7AA139 - 158140 - 159
8X-RAY DIFFRACTION8AA159 - 165160 - 166
9X-RAY DIFFRACTION9AA166 - 189167 - 190
10X-RAY DIFFRACTION10AA190 - 219191 - 220
11X-RAY DIFFRACTION11AA220 - 250221 - 251
12X-RAY DIFFRACTION12AA251 - 275252 - 276
13X-RAY DIFFRACTION13AA276 - 331277 - 332
14X-RAY DIFFRACTION14AA332 - 354333 - 355
15X-RAY DIFFRACTION15AA355 - 367356 - 368
16X-RAY DIFFRACTION16AA368 - 391369 - 392
17X-RAY DIFFRACTION17AA392 - 428393 - 429
18X-RAY DIFFRACTION18AA429 - 469430 - 470
19X-RAY DIFFRACTION19AA474 - 486475 - 487
20X-RAY DIFFRACTION20AA487 - 509488 - 510

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  • 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

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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

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