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- PDB-4c5l: Structure of the pyridoxal kinase from Staphylococcus aureus in c... -

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Open data


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Basic information

Entry
Database: PDB / ID: 4c5l
TitleStructure of the pyridoxal kinase from Staphylococcus aureus in complex with pyridoxal
ComponentsPHOSPHOMETHYLPYRIMIDINE KINASE
KeywordsTRANSFERASE / RIBOKINASE
Function / homology
Function and homology information


phosphomethylpyrimidine kinase activity / hydroxymethylpyrimidine kinase activity / pyridoxal kinase / thiamine biosynthetic process / nucleotide binding / cytosol
Similarity search - Function
Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase / Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain / Pyridoxamine kinase/Phosphomethylpyrimidine kinase / Phosphomethylpyrimidine kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PXL / 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol / pyridoxal kinase / Phosphomethylpyrimidine kinase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNodwell, M. / Alte, F. / Sieber, S.A. / Schneider, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage.
Authors: Nodwell, M.B. / Koch, M.F. / Alte, F. / Schneider, S. / Sieber, S.A.
History
DepositionSep 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly_gen ...pdbx_database_status / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOMETHYLPYRIMIDINE KINASE
B: PHOSPHOMETHYLPYRIMIDINE KINASE
C: PHOSPHOMETHYLPYRIMIDINE KINASE
D: PHOSPHOMETHYLPYRIMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,30612
Polymers119,2474
Non-polymers1,0598
Water5,513306
1
A: PHOSPHOMETHYLPYRIMIDINE KINASE
D: PHOSPHOMETHYLPYRIMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2507
Polymers59,6242
Non-polymers6275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHOSPHOMETHYLPYRIMIDINE KINASE
C: PHOSPHOMETHYLPYRIMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0565
Polymers59,6242
Non-polymers4323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.440, 102.780, 83.520
Angle α, β, γ (deg.)90.00, 90.44, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9973, 0.0023, -0.0734), (-0.004, 0.9997, -0.0238), (0.0733, 0.024, 0.997)0.9407, -1.7557, 41.7491
2given(-0.998, 0.0112, 0.0626), (-0.0183, -0.9933, -0.1139), (0.0609, -0.1148, 0.9915)-27.3562, 5.6952, 42.1933
3given(-1, 0.0018, -0.0007), (-0.0017, -0.9888, -0.1496), (-0.001, -0.1496, 0.9888)-25.7177, 9.6722, 0.6748

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Components

#1: Protein
PHOSPHOMETHYLPYRIMIDINE KINASE / PYRIDOXAL KINASE


Mass: 29811.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q99W31, UniProt: A0A0H3JTP0*PLUS, pyridoxal kinase
#2: Chemical ChemComp-UEG / 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol


Mass: 169.178 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H11NO3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PXL / 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE / PYRIDOXAL


Mass: 167.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFIRST AMINO ACID IS A GLY INSTEAD OF MET DUE TO REMOVAL OF THE AFFINITY TAG

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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: 2.28 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 50MM HEPES PH 7.6, 2M NH4SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→43.81 Å / Num. obs: 90725 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.65
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.1 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C5J
Resolution: 1.85→43.81 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.071 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27485 4567 5 %RANDOM
Rwork0.2341 ---
obs0.23614 86158 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.128 Å2
Baniso -1Baniso -2Baniso -3
1-2.67 Å2-0 Å2-0.57 Å2
2---1.56 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.85→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8037 0 68 306 8411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198302
X-RAY DIFFRACTIONr_bond_other_d0.0010.027868
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.97111274
X-RAY DIFFRACTIONr_angle_other_deg0.763318151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30451078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27726.019319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.244151369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.823158
X-RAY DIFFRACTIONr_chiral_restr0.0770.21304
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029415
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021722
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_it00.24297
X-RAY DIFFRACTIONr_mcbond_other00.24296
X-RAY DIFFRACTIONr_mcangle_it00.35353
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.4010.2344005
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 328 -
Rwork0.384 6223 -
obs--97.35 %
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)
12.10460.2091-0.37271.68050.2912.05510.0189-0.2085-0.17030.1939-0.01560.06810.2485-0.0572-0.00330.2278-0.02750.01660.1394-0.00180.1677-16.39711.8661-20.9706
22.8281-0.2177-0.88013.8369-0.07977.3628-0.0069-0.27130.02950.3639-0.01350.1941-0.1896-0.33850.02040.2087-0.10220.01090.2149-0.0120.2231-25.6501-6.4398-18.9561
326.03860.70845.81515.22074.363524.3636-0.1195-0.0359-0.7801-0.0808-0.1153-0.7112-0.16190.55740.23480.2730.05270.01690.31130.05880.4255-5.4059-10.6849-21.5939
41.039-0.0497-0.90088.1768-17.48138.3554-0.2544-1.1096-0.3503-0.005-0.6658-0.27270.33512.52860.92020.81760.37-0.17011.26910.29940.7599-17.9532-17.4553-11.9759
53.3263-0.15460.54225.17871.15055.90070.1256-0.1325-0.43180.0434-0.07450.00930.86450.1778-0.05110.2674-0.0648-0.01080.20890.0310.2417-20.8389-20.4765-24.5786
63.50692.0619-4.69369.5834-0.224410.0769-0.03940.0602-0.18260.0288-0.0334-0.53910.48430.46280.07280.39930.0149-0.08120.2574-0.02260.2018-17.813-19.3294-36.1963
736.263411.315821.88824.23163.86817.82250.16281.6352-1.7629-1.07331.41640.00841.09751.4699-1.57920.50430.01290.020.3626-0.07220.4819-0.1929-9.6145-35.6331
85.44980.6591-0.16252.23720.16911.3660.05140.2472-0.2801-0.0989-0.0516-0.00380.4255-0.02350.00030.3473-0.0278-0.00020.1395-0.01890.1509-15.386-6.6211-36.1346
93.20041.83021.48541.74421.88492.97650.10540.3355-0.2599-0.04510.1048-0.24470.47080.2466-0.21020.51340.12120.00370.25330.00190.2025-6.676-6.4646-37.3923
102.64850.6022-0.57352.3927-0.37661.6577-0.04690.12690.0808-0.40870.03670.23970.1174-0.26380.01010.3077-0.0652-0.04920.1616-0.00290.1303-23.31923.2807-68.6538
117.9434-1.77910.0934.5122-0.44822.5417-0.1741-0.32040.0350.12650.0986-0.10890.32440.03340.07550.25320.0019-0.01750.15770.00740.1224-15.7921.111-54.308
122.0946-1.4740.14487.1472-0.77822.8620.0126-0.3338-0.10950.11190.10520.74640.1605-0.3613-0.11790.1482-0.0837-0.00730.29520.01930.3087-31.1838-3.0288-59.3043
1319.7389-5.64788.200611.8959-2.75023.4546-0.3757-0.08090.48880.56180.1565-1.144-0.13180.07860.21920.4347-0.0124-0.01750.5157-0.01020.3073-19.2843-16.8296-52.9484
143.4790.29390.11935.34750.75855.0929-0.2066-0.0274-0.2671-0.22310.08890.18660.43090.1810.11770.2455-0.1099-0.00230.23270.03780.2565-26.3414-20.031-64.6486
1528.1549-8.50623.81152.7318-0.14737.00230.4527-0.0401-0.8963-0.23990.16530.1547-0.07281.2635-0.6180.9232-0.15890.24830.7230.05580.8749-13.7116-20.8985-75.6655
1611.18964.21320.2988.6209-0.10683.0829-0.20330.6788-0.3416-0.53390.095-0.44420.5461-0.04290.10840.5213-0.0919-0.06330.2756-0.06270.2717-23.1258-18.8924-78.2748
174.07661.28770.23163.3143-0.10811.3924-0.18330.3102-0.2046-0.71260.1813-0.06070.43510.00210.0020.5701-0.09010.00310.2001-0.01610.1076-17.3455-5.1996-76.2414
188.778116.0249-8.2541.8861-17.68578.3015-0.35350.3164-0.7343-0.3182-0.1597-0.59570.2804-0.14510.51320.5611-0.0686-0.03170.3793-0.08680.2347-23.6969-19.2769-84.0797
191.48650.31950.39972.6945-0.14383.4472-0.08830.04320.0822-0.31390.05920.1129-0.066-0.15820.02910.2624-0.0274-0.04820.12140.02030.1332-17.889811.3094-64.6955
2012.2106-5.3581-3.11025.50492.54874.7450.0014-0.6230.20620.32650.0375-0.2377-0.15720.1317-0.03880.2638-0.0354-0.04160.15580.01750.1317-13.368610.3303-51.3184
211.68710.38520.43035.32850.29834.83130.0325-0.18810.11070.01060.0109-0.5609-0.10520.3819-0.04340.1315-0.0419-0.00020.19960.03460.2576-5.174916.2097-60.4204
2220.975815.17216.450311.53941.745118.5009-0.4385-0.70491.54880.0486-0.2621.2696-2.3921-0.66860.70040.64570.28560.01770.61770.06220.9014-20.092826.6577-55.4566
2321.099-3.1854-2.231712.56460.16119.3077-0.353-0.92490.74060.63350.1885-0.0871-0.99070.12010.16460.3197-0.0865-0.04120.2636-0.01160.2656-6.904628.0716-53.2082
243.5394-1.02771.61864.9745-0.17524.821-0.13090.03460.466-0.2378-0.112-0.082-0.763-0.22330.24290.2154-0.03220.04460.21260.03280.342-12.569234.6498-67.5891
254.22310.8335-0.38324.8789-1.75453.82070.07970.29560.4712-0.47180.10740.6882-0.3159-0.4567-0.18710.4447-0.0182-0.07320.22840.05120.2613-18.690222.0958-74.0446
2615.09313.38723.8347.2288-0.06312.4881-0.06420.45150.9799-0.53990.09090.05040.02190.0751-0.02670.4632-0.0096-0.0060.19620.08070.1757-13.808924.5641-78.292
271.23950.4253-0.14732.8149-0.94282.09840.12150.52050.4147-0.53410.14580.3818-0.1729-0.4909-0.26730.53870.0733-0.1390.41260.13230.4047-26.116721.0176-76.0467
281.21620.30231.13513.3644-0.64551.32750.0390.0296-0.00550.1555-0.0918-0.2727-0.0130.08550.05290.0098-0.01260.00780.1884-0.01710.2149-8.758311.03-26.0453
295.1002-2.0461-2.12588.43590.81770.88730.039-0.0619-0.021-0.4958-0.061-0.1378-0.00450.03960.0220.10220.01740.01230.20390.00820.1913-6.30458.9174-32.5357
306.9034-2.2584-0.71612.93580.48242.0357-0.0216-0.50740.18660.37450.0786-0.13210.0219-0.0085-0.0570.2576-0.0126-0.02080.1870.00850.1406-11.968610.2058-13.4441
311.62770.79660.81565.5605-0.62814.73180.0638-0.59710.30550.6323-0.013-0.153-0.31570.0358-0.05080.1435-0.05720.01920.3439-0.08170.3234-3.253223.378-17.3836
328.3621-0.91053.46344.70220.09796.1983-0.0146-0.07560.6644-0.0414-0.060.1757-0.6633-0.46890.07470.256-0.02810.06480.22040.01170.4714-7.926936.465-27.2665
3317.560516.1466-6.6814.8503-6.14662.5640.07570.2020.99670.01840.24440.94350.0011-0.1725-0.32010.5349-0.02220.02520.45270.04090.54-19.043230.0843-35.9923
348.24310.2155-0.32953.7833-0.34082.22580.32980.13670.4721-0.2021-0.1196-0.245-0.31120.1436-0.21030.2301-0.04410.00880.13070.01290.2286-6.342621.0637-32.5546
353.9505-0.3868-1.49742.4735-0.15461.46690.06020.02670.2489-0.1534-0.09540.1384-0.3307-0.13110.03520.24680.0192-0.02420.1627-0.00990.1337-19.811619.6863-32.9031
365.15168.48122.437616.76924.62811.7762-0.15960.39780.5612-0.22330.20210.4653-0.41040.0861-0.04250.39130.00680.02590.28560.05090.3036-13.579327.0578-41.0886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 81
2X-RAY DIFFRACTION2A82 - 108
3X-RAY DIFFRACTION3A109 - 115
4X-RAY DIFFRACTION4A116 - 123
5X-RAY DIFFRACTION5A124 - 172
6X-RAY DIFFRACTION6A173 - 203
7X-RAY DIFFRACTION7A204 - 208
8X-RAY DIFFRACTION8A209 - 249
9X-RAY DIFFRACTION9A250 - 276
10X-RAY DIFFRACTION10B1 - 34
11X-RAY DIFFRACTION11B35 - 64
12X-RAY DIFFRACTION12B65 - 107
13X-RAY DIFFRACTION13B108 - 123
14X-RAY DIFFRACTION14B124 - 176
15X-RAY DIFFRACTION15B177 - 188
16X-RAY DIFFRACTION16B189 - 207
17X-RAY DIFFRACTION17B208 - 269
18X-RAY DIFFRACTION18B270 - 276
19X-RAY DIFFRACTION19C1 - 50
20X-RAY DIFFRACTION20C51 - 65
21X-RAY DIFFRACTION21C66 - 107
22X-RAY DIFFRACTION22C108 - 119
23X-RAY DIFFRACTION23C120 - 128
24X-RAY DIFFRACTION24C129 - 199
25X-RAY DIFFRACTION25C200 - 228
26X-RAY DIFFRACTION26C229 - 243
27X-RAY DIFFRACTION27C244 - 276
28X-RAY DIFFRACTION28D1 - 27
29X-RAY DIFFRACTION29D28 - 35
30X-RAY DIFFRACTION30D36 - 71
31X-RAY DIFFRACTION31D72 - 149
32X-RAY DIFFRACTION32D150 - 197
33X-RAY DIFFRACTION33D198 - 208
34X-RAY DIFFRACTION34D209 - 233
35X-RAY DIFFRACTION35D234 - 264
36X-RAY DIFFRACTION36D265 - 276

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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