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- PDB-3rst: Crystal structure of Bacillus subtilis signal peptide peptidase A -

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Basic information

Entry
Database: PDB / ID: 3rst
TitleCrystal structure of Bacillus subtilis signal peptide peptidase A
ComponentsSignal peptide peptidase sppA
KeywordsHYDROLASE / alpha/beta protein fold / signal peptide digestion / bacterial cell membrane
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / membrane raft / proteolysis / plasma membrane
Similarity search - Function
peptide peptidase (sppa) fold / peptide peptidase (sppa) fold - #10 / : / Peptidase S49 / Peptidase S49, SppA / Peptidase family S49 / Other non-globular / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...peptide peptidase (sppa) fold / peptide peptidase (sppa) fold - #10 / : / Peptidase S49 / Peptidase S49, SppA / Peptidase family S49 / Other non-globular / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Special / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Putative signal peptide peptidase SppA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsNam, S.E. / Paetzel, M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal Structure of Bacillus subtilis Signal Peptide Peptidase A.
Authors: Nam, S.E. / Kim, A.C. / Paetzel, M.
History
DepositionMay 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / Other
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Jun 6, 2012Group: Database references
Revision 1.4Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.5Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Signal peptide peptidase sppA
B: Signal peptide peptidase sppA
C: Signal peptide peptidase sppA
D: Signal peptide peptidase sppA
E: Signal peptide peptidase sppA
F: Signal peptide peptidase sppA
G: Signal peptide peptidase sppA
H: Signal peptide peptidase sppA


Theoretical massNumber of molelcules
Total (without water)209,2948
Polymers209,2948
Non-polymers00
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23180 Å2
ΔGint-103 kcal/mol
Surface area76510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.779, 131.066, 207.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Signal peptide peptidase sppA


Mass: 26161.713 Da / Num. of mol.: 8
Fragment: Protease domain lacking the N-terminal transmembrane segment, residues 56-295
Mutation: K199A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU29530 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): TUNER(DE3)
References: UniProt: O34525, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATES THE EXPRESSED PROTEIN(36000DA) IS COMPOSED OF AN N-TERMINAL HISTINE AFFINITY TAG WITH ...AUTHOR STATES THE EXPRESSED PROTEIN(36000DA) IS COMPOSED OF AN N-TERMINAL HISTINE AFFINITY TAG WITH LINKER REGION (MGSSHHHHHHSSGLVPAGSH-) PLUS RESIDUES 26-335 OF THE SPPA. THE PURIFIED PROTEIN WAS SUBJECTED TO LIMITED PROTEOLYSIS BEFORE CRYSTALLIZATION WHICH RESULTED IN A FINAL SIZE PROTEIN ABOUT 28000DA. SEQRES RECORD REPRESENTS SEQUENCE EXTRACTED FROM COORDINATES (RESIDUES FROM 56 TO 295).

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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: 2.67 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM Tris pH 8.5 23% Tert-butanol 5% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 25, 2011 / Details: vertical collimating mirror
RadiationMonochromator: double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. all: 96535 / Num. obs: 96535 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 52.7
Reflection shellResolution: 2.37→2.49 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 7.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERfor MR 2.1phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BFO , Chain A, C-terminal Domain (residues 326-549)
Resolution: 2.37→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 14.691 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24052 4806 5 %RANDOM
Rwork0.20571 ---
obs0.20748 91450 98.16 %-
all-95998 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.998 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2--1.1 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.37→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13685 0 0 257 13942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02213855
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.97718582
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3151787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54525.395532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.322152658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5731546
X-RAY DIFFRACTIONr_chiral_restr0.0740.22110
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029989
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4431.58884
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.888214224
X-RAY DIFFRACTIONr_scbond_it1.64834971
X-RAY DIFFRACTIONr_scangle_it2.7364.54357
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.37→2.428 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 263 -
Rwork0.238 5440 -
obs--79.43 %
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)
13.52571.67640.973916.63623.6885.5837-0.23030.1847-0.1157-0.98390.3173-0.3592-0.18120.124-0.08710.0687-0.0130.04720.20370.00180.1324-46.8791-39.21319.9048
22.37961.43540.36981.3174-0.21470.9875-0.0191-0.0125-0.1952-0.1196-0.0012-0.2719-0.05210.07580.02040.0922-0.01060.04310.0992-0.03820.1211-45.8092-40.648825.3521
32.48071.7670.7243.36330.13253.18060.0316-0.07040.00460.1564-0.034-0.0765-0.0275-0.03370.00240.03170.01070.01260.1044-0.04260.0424-56.6728-40.546627.0193
40.19930.07060.89910.05950.21927.48970.03730.10740.0327-0.04290.04640.1098-0.2445-0.4225-0.08370.30910.0817-0.07340.374-0.04410.3465-55.7888-76.576614.7323
51.47730.14480.0422.7715-0.2831.29920.0146-0.11120.13460.2196-0.03830.0859-0.136-0.13020.02370.05830.02390.00290.229-0.05110.0346-61.6626-42.023227.7686
62.87174.6609-0.506312.8468-0.29794.7381-0.0441-0.03110.26630.6377-0.0794-0.7288-0.56590.83540.12350.2904-0.046-0.07950.48890.07680.459-52.8861-22.59573.9386
72.3550.7408-0.1953.0061-1.75584.6521-0.0232-0.21250.24520.2454-0.1485-0.2575-0.55470.31780.17180.14940.0352-0.02770.206-0.01760.1518-64.4528-24.99270.9918
80.2822-0.724-1.37622.10843.89837.2757-0.03590.06040.033-0.10890.06770.0167-0.02730.0997-0.03180.50860.0435-0.09430.398-0.00080.2831-67.8926-60.634810.8394
91.29670.5005-0.01472.6612-1.76213.5794-0.0044-0.00070.23650.00530.0780.1545-0.4555-0.2928-0.07350.14660.0916-0.00770.2435-0.06420.1535-73.7413-28.2493-0.5306
109.9422-1.1648-0.86328.27221.13433.9591-0.3305-0.10321.05560.31620.158-0.9805-0.6528-0.07940.17250.842-0.1157-0.06920.56320.11150.6762-55.4717-9.2315-3.771
114.22131.6016-0.65013.2001-0.13854.99270.0133-0.26130.06620.4283-0.0606-0.341-0.07840.29960.04730.10380.047-0.05230.29470.02710.1994-47.9472-24.3396-24.7772
123.72690.766-0.58352.59470.20893.1928-0.0191-0.28770.04910.0691-0.1795-0.04780.01350.1480.19860.07020.062-0.00890.10990.02660.0581-58.4912-28.3112-29.1661
131.974-5.0561-0.22913.09090.44220.18710.01660.0367-0.0482-0.2775-0.03510.06760.2853-0.04110.01850.5293-0.0218-0.0380.3493-0.02360.235-74.0797-50.3608-5.9266
143.37761.1658-0.93241.7143-0.47342.2666-0.07720.25240.0475-0.19710.0001-0.0385-0.0533-0.15720.07710.13150.0897-0.02240.09540.0030.0894-64.8217-30.6456-35.2493
154.5295-0.737.34520.1338-1.213212.0731-0.2382-0.18640.14910.08790.1291-0.0095-0.6434-0.3580.10910.42010.04130.05240.56690.1030.4148-41.6882-18.8333-32.9987
165.75461.8386-2.70164.1067-2.0322.93110.2539-0.58040.650.3921-0.2828-0.5869-0.87310.57480.02890.5677-0.0301-0.00020.6131-0.12490.7119-33.3276-39.914-40.5785
173.34590.1623-0.83781.8011-0.13112.84220.2959-0.27161.1204-0.0349-0.0554-0.3866-0.80450.3339-0.24040.4180.03860.13960.2701-0.01140.5771-38.1984-40.4171-46.6594
184.1887-0.05161.69343.8876-0.21431.22780.2171-0.28730.4246-0.3529-0.1388-0.2536-0.06140.2033-0.07830.27380.01210.19080.3005-0.09360.2785-40.1513-50.6198-49.0847
190.1704-1.0660.64638.4072-5.34863.4614-0.035-0.0362-0.1127-0.2783-0.0030.05280.34050.02090.0380.49060.06210.11250.29170.02230.3785-68.8012-52.545-26.1443
204.3121-0.8163-1.51832.18730.43592.51080.22230.31220.3601-0.3391-0.162-0.4972-0.28310.2101-0.06030.32850.08310.05250.2010.07780.2259-41.152-50.9274-53.7795
217.53683.68720.28663.62190.3452.64460.0875-0.16740.87530.0764-0.2097-0.3573-0.54640.4450.12220.4112-0.0323-0.07790.34440.05970.6175-16.8838-60.7137-37.5533
222.99330.11131.53692.8637-0.31082.102-0.07640.06850.7006-0.0896-0.2116-0.6031-0.1980.41020.2880.16340.0550.06760.19110.05910.3392-19.7573-70.7283-42.118
230.41560.3551-1.45140.5469-1.66766.0459-0.0312-0.0973-0.11250.03640.14450.16740.32440.0139-0.11320.45650.09840.07030.35240.11710.4678-56.0681-66.0048-37.1101
243.4719-0.4240.73882.6957-0.74742.42550.0250.3084-0.0416-0.3502-0.2071-0.41080.11840.3830.18210.21430.03860.09110.11890.0440.0829-24.1324-79.8257-44.8326
2548.49344.9058-3.9910.5953-0.37160.35650.4994-1.35421.3887-0.1001-0.2704-0.1853-0.17930.248-0.2290.9314-0.55790.1131.61260.58581.3693-2.484-68.6893-40.0439
265.71570.81940.77382.8715-0.9524.305-0.04140.20470.9231-0.1143-0.1013-0.1589-0.5030.12040.14270.3028-0.016-0.02230.0797-0.02340.2842-8.0568-77.2582-14.3519
273.62821.17381.34912.11980.09973.5177-0.11230.10220.3756-0.1219-0.0445-0.051-0.1826-0.0230.15680.09860.04120.00680.02570.0190.0679-13.7445-87.8627-16.2924
287.5908-2.3549-5.99540.75021.8224.8971-0.1217-0.2794-0.17220.07280.12830.13320.0797-0.0169-0.00670.30740.03670.07930.39140.1360.3535-44.6632-81.9409-32.2517
293.82660.22322.57861.0266-0.23933.06070.12170.0048-0.1238-0.063-0.0341-0.05520.20860.1113-0.08760.10260.03280.04530.02130.00380.0439-15.5903-96.2879-15.3448
307.4489-1.70560.07179.54772.00863.63160.0289-0.09931.12880.2503-0.0715-0.7193-0.27210.29050.04260.2399-0.0519-0.00610.32150.0090.31053.5234-82.6803-6.6883
317.19351.36061.89613.56151.54625.6213-0.04210.23010.5695-0.0407-0.0358-0.4799-0.4071.01310.07790.3567-0.16620.010.4046-0.01450.326-11.4444-77.989312.8572
322.98560.3619-0.2482.5630.57424.2960.0647-0.02050.00680.03110.0144-0.3012-0.25080.6713-0.07910.0919-0.0472-0.02840.1624-0.02340.0569-19.1382-87.032614.456
337.3062-5.7241-2.41354.49261.88530.83050.15810.2118-0.0211-0.0939-0.14740.0479-0.0747-0.1826-0.01080.23340.03790.02330.39790.07810.1757-40.4719-90.4319-15.3992
342.0861-0.00880.44691.39970.17213.73960.0638-0.1986-0.10190.1740.0532-0.24090.330.393-0.1170.10390.0202-0.01740.12480.03090.0946-25.7701-94.111615.662
357.3196-0.3103-0.24279.3599-5.55236.64130.1728-0.45210.04230.4956-0.3748-0.5706-0.32950.96620.2020.5406-0.1687-0.18230.8192-0.13720.4401-7.0455-78.157627.4816
364.48021.89494.38265.22842.68236.2015-0.15260.32290.2695-0.21270.1808-0.6212-0.47860.4566-0.02820.3289-0.076-0.030.23090.01120.3337-26.9793-61.148826.6853
372.42050.1920.18313.68760.50621.8211-0.2866-0.08950.17880.10340.2005-0.3574-0.17030.11670.08610.22480.0007-0.06410.0972-0.0480.0716-35.4324-65.777532.7242
383.0371-0.45870.72584.71290.107511.010.1814-0.04930.03620.0858-0.1725-0.1337-0.12280.107-0.00890.1599-0.00740.03780.3080.03840.1748-48.2478-85.19920.7347
390.266-0.5046-0.08381.98291.46491.7728-0.0106-0.0653-0.01350.04720.09280.0052-0.0279-0.0351-0.08220.1279-0.04880.01570.10370.03120.0618-41.3463-86.852519.9146
403.60480.95350.73953.77270.67031.5424-0.1947-0.41650.45260.33970.03-0.2238-0.2378-0.0090.16470.33210.0925-0.10140.2393-0.07150.1467-41.5258-61.682138.5539
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A56 - 85
2X-RAY DIFFRACTION2A86 - 122
3X-RAY DIFFRACTION3A123 - 174
4X-RAY DIFFRACTION4A175 - 210
5X-RAY DIFFRACTION5A211 - 291
6X-RAY DIFFRACTION6B57 - 103
7X-RAY DIFFRACTION7B104 - 173
8X-RAY DIFFRACTION8B174 - 210
9X-RAY DIFFRACTION9B211 - 277
10X-RAY DIFFRACTION10B278 - 290
11X-RAY DIFFRACTION11C57 - 109
12X-RAY DIFFRACTION12C110 - 175
13X-RAY DIFFRACTION13C176 - 215
14X-RAY DIFFRACTION14C216 - 277
15X-RAY DIFFRACTION15C278 - 295
16X-RAY DIFFRACTION16D57 - 99
17X-RAY DIFFRACTION17D100 - 132
18X-RAY DIFFRACTION18D133 - 175
19X-RAY DIFFRACTION19D176 - 215
20X-RAY DIFFRACTION20D216 - 290
21X-RAY DIFFRACTION21E57 - 99
22X-RAY DIFFRACTION22E100 - 173
23X-RAY DIFFRACTION23E174 - 215
24X-RAY DIFFRACTION24E216 - 277
25X-RAY DIFFRACTION25E278 - 290
26X-RAY DIFFRACTION26F57 - 109
27X-RAY DIFFRACTION27F110 - 175
28X-RAY DIFFRACTION28F176 - 215
29X-RAY DIFFRACTION29F216 - 277
30X-RAY DIFFRACTION30F278 - 291
31X-RAY DIFFRACTION31G57 - 108
32X-RAY DIFFRACTION32G109 - 174
33X-RAY DIFFRACTION33G175 - 209
34X-RAY DIFFRACTION34G210 - 276
35X-RAY DIFFRACTION35G277 - 291
36X-RAY DIFFRACTION36H56 - 99
37X-RAY DIFFRACTION37H100 - 173
38X-RAY DIFFRACTION38H174 - 191
39X-RAY DIFFRACTION39H192 - 236
40X-RAY DIFFRACTION40H237 - 291

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  • 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

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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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