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- PDB-4v0h: Human metallo beta lactamase domain containing protein 1 (hMBLAC1) -

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Basic information

Entry
Database: PDB / ID: 4v0h
TitleHuman metallo beta lactamase domain containing protein 1 (hMBLAC1)
ComponentsMETALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1
KeywordsHYDROLASE / GLYOXALASE II FAMILY / NON-HEME IRON
Function / homology
Function and homology information


Hydrolases / hydrolase activity / metal ion binding
Similarity search - Function
Metallo-beta-lactamase domain-containing protein 1 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Metallo-beta-lactamase domain-containing protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsPettinati, I. / McDonough, M.A. / Brem, J. / Schofield, C.J.
CitationJournal: Elife / Year: 2018
Title: Biosynthesis of histone messenger RNA employs a specific 3' end endonuclease.
Authors: Pettinati, I. / Grzechnik, P. / Ribeiro de Almeida, C. / Brem, J. / McDonough, M.A. / Dhir, S. / Proudfoot, N.J. / Schofield, C.J.
History
DepositionSep 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Nov 20, 2019Group: Database references / Other / Category: citation / citation_author / pdbx_database_status
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_database_status.status_code_sf
Revision 1.3May 8, 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_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.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.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.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_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: METALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1
B: METALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1
C: METALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1
D: METALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,63615
Polymers108,9134
Non-polymers72311
Water9,260514
1
C: METALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1
hetero molecules

D: METALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8648
Polymers54,4562
Non-polymers4086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area4000 Å2
ΔGint-69.3 kcal/mol
Surface area15940 Å2
MethodPISA
2
B: METALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1
hetero molecules

A: METALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7727
Polymers54,4562
Non-polymers3155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3630 Å2
ΔGint-68.5 kcal/mol
Surface area16250 Å2
MethodPISA
3
A: METALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1
hetero molecules

B: METALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7727
Polymers54,4562
Non-polymers3155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3630 Å2
ΔGint-68.5 kcal/mol
Surface area16250 Å2
MethodPISA
4
D: METALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1
hetero molecules

C: METALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8648
Polymers54,4562
Non-polymers4086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area4000 Å2
ΔGint-69.3 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.950, 67.130, 67.900
Angle α, β, γ (deg.)109.31, 105.40, 90.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
METALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1


Mass: 27228.221 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCOLD I / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4D2B0, Hydrolases
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Description: SEARCH MODEL GENERATED AS AN ENSEMBLE FROM 12 STRUCTURES PDB CODES 3LVZ, 2ZO4, 3AJ3, 2YZ3, 3VQZ,1P9E, 4AWY, 3ESH, 2Q0I, 4LE6, 4AD9, 2XF4
Crystal growpH: 5.5
Details: 0.1 M BIS-TRIS PH5.5 0.18 M AMMONIUM ACETATE 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.28268
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2013 / Details: COMPOUND REFRACTIVE LENSES
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28268 Å / Relative weight: 1
ReflectionResolution: 1.79→45.96 Å / Num. obs: 90649 / % possible obs: 95.5 % / Observed criterion σ(I): 3 / Redundancy: 6.9 % / Biso Wilson estimate: 21.81 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.4
Reflection shellResolution: 1.79→1.84 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.6 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→45.958 Å / SU ML: 0.23 / σ(F): 1.55 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 4544 5 %
Rwork0.1823 --
obs0.1837 90641 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.87 Å2
Refinement stepCycle: LAST / Resolution: 1.79→45.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6235 0 26 514 6775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116408
X-RAY DIFFRACTIONf_angle_d1.3628781
X-RAY DIFFRACTIONf_dihedral_angle_d11.5992210
X-RAY DIFFRACTIONf_chiral_restr0.0541013
X-RAY DIFFRACTIONf_plane_restr0.0061176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.81030.42061530.36172808X-RAY DIFFRACTION93
1.8103-1.83160.37991750.32542770X-RAY DIFFRACTION93
1.8316-1.8540.34511560.30442789X-RAY DIFFRACTION93
1.854-1.87740.32561540.26242758X-RAY DIFFRACTION93
1.8774-1.90220.22941510.2112821X-RAY DIFFRACTION94
1.9022-1.92820.22191660.17882788X-RAY DIFFRACTION94
1.9282-1.95580.1731340.17012845X-RAY DIFFRACTION94
1.9558-1.9850.23331560.17272815X-RAY DIFFRACTION94
1.985-2.0160.20831510.17482810X-RAY DIFFRACTION95
2.016-2.0490.20441460.16672915X-RAY DIFFRACTION95
2.049-2.08440.18881520.16752809X-RAY DIFFRACTION95
2.0844-2.12230.22681410.17512851X-RAY DIFFRACTION95
2.1223-2.16310.22311260.17872912X-RAY DIFFRACTION95
2.1631-2.20720.22541520.17462838X-RAY DIFFRACTION95
2.2072-2.25520.20511410.17742913X-RAY DIFFRACTION95
2.2552-2.30770.19671490.17222865X-RAY DIFFRACTION96
2.3077-2.36540.2181650.16082882X-RAY DIFFRACTION96
2.3654-2.42930.20591460.17482906X-RAY DIFFRACTION96
2.4293-2.50080.22531270.17222910X-RAY DIFFRACTION96
2.5008-2.58150.21291550.18482861X-RAY DIFFRACTION97
2.5815-2.67380.22331540.17992924X-RAY DIFFRACTION97
2.6738-2.78080.20281720.17312899X-RAY DIFFRACTION97
2.7808-2.90740.1981580.18222917X-RAY DIFFRACTION97
2.9074-3.06060.23591410.18582952X-RAY DIFFRACTION97
3.0606-3.25230.18211590.1812903X-RAY DIFFRACTION97
3.2523-3.50340.19491570.18392915X-RAY DIFFRACTION97
3.5034-3.85580.18931560.17132942X-RAY DIFFRACTION98
3.8558-4.41330.18491350.1662959X-RAY DIFFRACTION98
4.4133-5.55880.1941670.16392908X-RAY DIFFRACTION97
5.5588-45.97280.21231490.20172912X-RAY DIFFRACTION97
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)
10.85720.9778-0.05261.2408-0.71882.937-0.01370.39070.047-0.0173-0.1955-0.5371-0.35740.79850.14960.2215-0.0819-0.02670.35450.01930.390711.957672.72274.3591
20.6563-1.1181-0.71916.03971.06781.4176-0.27410.1279-0.1190.38230.3705-0.66180.42310.592-0.12490.19230.0665-0.00250.2706-0.03410.304211.486248.776-0.3502
31.6354-0.7859-0.14772.16780.80141.7382-0.2484-0.0280.29420.47750.2013-0.0689-0.00160.20920.02020.1053-0.0648-0.00860.15120.01850.19473.756665.8584.8374
42.8363-1.19010.11863.53730.21361.67380.0986-0.10430.5007-0.09140.0499-0.0423-0.30620.0581-0.15840.1819-0.02670.02720.1558-0.01170.2801-6.220474.11454.1656
51.84841.22171.04215.31542.52582.3970.2312-0.2311-0.19360.6497-0.25960.00750.3857-0.03160.03550.2369-0.0265-0.02420.1842-0.00880.21332.440861.222713.7116
62.06740.02160.17621.6753-0.13270.96880.04760.07890.1135-0.1042-0.06350.059-0.11180.00330.01080.16210.00730.00430.1405-0.0010.1859-8.292768.52661.4291
72.6610.07260.32472.2995-0.41182.58560.02870.41440.0911-0.3454-0.0587-0.3365-0.02810.34740.05710.2157-0.00510.05010.25430.04820.18793.923368.6044-7.0452
81.6168-0.33040.44072.8482-0.52812.92360.22260.82780.1297-0.6905-0.258-0.6162-0.09180.38060.05170.29340.05710.11110.41190.06960.24237.876265.657-10.9187
91.12080.6348-0.24451.06460.56322.9098-0.01380.3156-0.2265-0.1256-0.18390.33310.1724-0.65560.15440.2083-0.0410.02740.3161-0.02980.258934.984442.89663.6061
101.0607-1.74830.9835.6748-0.74571.1498-0.04420.15650.27420.03330.01010.4993-0.3313-0.4554-0.00120.20730.06220.00230.22690.01820.24935.815966.8016-0.3114
111.6829-0.7190.41062.4147-0.78511.6871-0.1571-0.0498-0.04560.26770.1246-0.1132-0.0039-0.09740.01360.124-0.0302-0.00220.1637-0.01050.167443.556149.76714.9282
121.5503-0.1767-0.70390.64410.24371.31620.0174-0.0521-0.08730.1812-0.0158-0.060.04430.0227-0.00590.1838-0.0208-0.01130.14250.00660.167949.366147.45248.5356
132.333-0.3455-0.35061.45310.15860.90190.0730.0463-0.0469-0.0693-0.065-0.0660.06650.0099-0.00580.15280.0072-0.00910.14270.00080.160755.585947.06221.4797
142.49050.1844-0.44872.16830.39212.28240.06460.3220.1201-0.254-0.02990.1178-0.1102-0.3388-0.01210.1960.0187-0.0150.2317-0.01450.118743.438448.836-8.1426
151.47630.5086-0.62172.1545-0.51591.9673-0.03420.4073-0.0369-0.29150.06020.15690.2227-0.263-0.01740.18560.0027-0.03490.2781-0.02880.145138.607347.7297-10.2453
161.2094-0.59580.24450.7032-0.38172.6873-0.0175-0.1785-0.33080.1177-0.2101-0.29040.25420.66540.17610.22620.04460.04230.30360.04230.276843.240576.369915.6105
171.64151.12810.25982.69570.38821.6293-0.11440.0353-0.0482-0.18970.074-0.1916-0.17890.24360.06190.10180.0014-0.01440.17170.01350.1638.562691.080817.2609
181.6335-0.3162-0.45310.57890.38941.34010.02330.0319-0.1358-0.2377-0.05650.11020.10890.033-0.00090.17810.0268-0.0140.1518-0.01240.179829.20580.974211.1311
192.09960.3551-0.05351.614-0.04750.84660.0569-0.0585-0.0930.0875-0.06390.09370.1307-0.02720.01460.1638-0.0093-0.00670.1391-0.0030.159923.134680.643118.2505
202.6771-0.4457-0.59372.2226-0.16012.5812-0.0247-0.40510.02550.30430.0373-0.148-0.06360.26480.00910.2155-0.0007-0.0260.22250.02870.137135.498882.526227.9435
211.2769-0.0607-0.67091.94670.23962.46730.0033-0.4492-0.14030.37460.0106-0.28640.22240.4235-0.01790.21460.0121-0.05620.30740.04190.19340.294881.159229.6768
220.9603-0.7471-0.14930.79020.92983.21320.0153-0.21940.2050.0219-0.23870.3545-0.2538-0.66090.18790.21850.0537-0.04360.2911-0.0320.30894.108739.237915.505
231.71740.6098-0.22672.3318-0.59611.6698-0.14720.083-0.0186-0.28210.11980.20220.1612-0.32030.01960.09530.01050.00070.1621-0.01680.14298.799725.206716.9707
242.37370.23770.67711.96810.31830.98190.03030.00360.090.0181-0.0464-0.0645-0.0740.00490.01410.14520.00540.0170.13370.00820.133222.013534.819215.7501
252.19890.480.60342.18450.37462.83340.0599-0.4990.06080.4588-0.08280.2488-0.0191-0.42680.02220.2210.00290.05510.2809-0.03610.141310.006333.798228.6559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 6 THROUGH 28 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 29 THROUGH 40 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 41 THROUGH 70 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 71 THROUGH 89 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 90 THROUGH 103 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 104 THROUGH 161 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 162 THROUGH 205 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 206 THROUGH 241 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 5 THROUGH 28 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 29 THROUGH 40 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 41 THROUGH 70 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 71 THROUGH 103 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 104 THROUGH 161 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 162 THROUGH 212 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 213 THROUGH 241 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 5 THROUGH 28 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 29 THROUGH 70 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 71 THROUGH 103 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 104 THROUGH 161 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 162 THROUGH 212 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 213 THROUGH 241 )
22X-RAY DIFFRACTION22CHAIN D AND (RESID 5 THROUGH 28 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 29 THROUGH 70 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 71 THROUGH 161 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 162 THROUGH 242 )

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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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