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- PDB-6aqo: Crystal structure of hypoxanthine-guanine-xanthine phosphorybosyl... -

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Basic information

Entry
Database: PDB / ID: 6aqo
TitleCrystal structure of hypoxanthine-guanine-xanthine phosphorybosyltranferase in complex with {[(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid)
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE/INHIBITOR / Purine salvage / Trypanosoma brucei / acyclic nucleoside phosphonates / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


xanthine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / glycosome / phosphate ion binding / magnesium ion binding ...xanthine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / glycosome / phosphate ion binding / magnesium ion binding / cytosol / cytoplasm
Similarity search - Function
Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-45T / Hypoxanthine-guanine phosphoribosyltransferase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsTeran, D. / Gudday, L.W.
CitationJournal: PLoS Negl Trop Dis / Year: 2018
Title: Evaluation of the Trypanosoma brucei 6-oxopurine salvage pathway as a potential target for drug discovery.
Authors: Dolezelova, E. / Teran, D. / Gahura, O. / Kotrbova, Z. / Prochazkova, M. / Keough, D. / Spacek, P. / Hockova, D. / Guddat, L. / Zikova, A.
History
DepositionAug 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_label_seq_id
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase
E: Hypoxanthine-guanine phosphoribosyltransferase
F: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,62614
Polymers183,9306
Non-polymers2,6968
Water84747
1
A: Hypoxanthine-guanine phosphoribosyltransferase
E: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2175
Polymers61,3102
Non-polymers9073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-13 kcal/mol
Surface area17970 Å2
MethodPISA
2
B: Hypoxanthine-guanine phosphoribosyltransferase
F: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1934
Polymers61,3102
Non-polymers8832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-5 kcal/mol
Surface area18090 Å2
MethodPISA
3
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2175
Polymers61,3102
Non-polymers9073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-15 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.321, 107.841, 117.693
Angle α, β, γ (deg.)90.00, 96.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypoxanthine-guanine phosphoribosyltransferase /


Mass: 30654.998 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb10.70.6660 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38CA1
#2: Chemical
ChemComp-45T / {[(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid)


Mass: 441.271 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H21N5O9P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25% PEG 3350, 0.2 M lithium sulfate and 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9536 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.638→41.32 Å / Num. obs: 44654 / % possible obs: 99.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.048 / Net I/σ(I): 8.8
Reflection shellResolution: 2.64→2.74 Å / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 1.3 / Rpim(I) all: 0.411 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AP3

6ap3
PDB Unreleased entry


Resolution: 2.64→41.32 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.01
RfactorNum. reflection% reflection
Rfree0.249 1999 4.48 %
Rwork0.191 --
obs0.194 44601 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.64→41.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10037 0 170 47 10254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310403
X-RAY DIFFRACTIONf_angle_d0.59414078
X-RAY DIFFRACTIONf_dihedral_angle_d9.4856319
X-RAY DIFFRACTIONf_chiral_restr0.0461577
X-RAY DIFFRACTIONf_plane_restr0.0031774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6384-2.70440.38931340.31082847X-RAY DIFFRACTION94
2.7044-2.77750.34041420.29083044X-RAY DIFFRACTION100
2.7775-2.85920.35231430.27593046X-RAY DIFFRACTION100
2.8592-2.95150.30371430.2643035X-RAY DIFFRACTION100
2.9515-3.0570.31421420.23693044X-RAY DIFFRACTION100
3.057-3.17930.26161430.22473042X-RAY DIFFRACTION100
3.1793-3.3240.33781430.22123058X-RAY DIFFRACTION100
3.324-3.49910.27931430.23033X-RAY DIFFRACTION100
3.4991-3.71820.26981440.19053082X-RAY DIFFRACTION100
3.7182-4.00510.20761440.17093067X-RAY DIFFRACTION100
4.0051-4.40770.22651440.15473058X-RAY DIFFRACTION100
4.4077-5.04450.20741420.14813042X-RAY DIFFRACTION100
5.0445-6.35190.22111460.18433085X-RAY DIFFRACTION100
6.3519-41.32510.21291460.17663119X-RAY DIFFRACTION99
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)
15.45632.02080.02692.37860.11861.10930.00730.0460.06970.0142-0.0598-0.2346-0.049-0.08460.08110.45890.0771-0.04950.29070.02160.32812.5348-6.9455-47.5318
25.40332.68531.24731.84371.48332.2890.02570.29120.4141-0.6629-0.09220.4442-0.3018-0.03570.07740.59310.0434-0.0450.37010.04880.51691.09914.0068-55.8694
32.49650.45680.39972.48261.08264.5849-0.01980.16110.4153-0.188-0.05840.6706-0.4616-0.570.12350.48920.105-0.05410.47830.00980.5661-17.4469-5.2178-48.3781
46.33550.8751-0.35039.07730.87548.44990.0509-0.1146-0.11450.03150.25890.34890.1267-1.3078-0.31460.6173-0.0261-0.09730.57840.12450.5186-5.5762-33.3149-26.4121
54.86014.77145.46395.06375.42176.24270.15750.5902-0.60760.2220.1455-0.49870.27560.4589-0.23640.7998-0.0042-0.05130.61950.05560.467517.3186-27.7597-20.0848
68.4083-0.7316-1.79392.06730.2072.9581-0.444-0.00820.79250.760.2364-0.7879-0.2830.82870.21440.75-0.1623-0.15210.6151-0.01320.546535.4282-30.4025-3.4191
75.04550.48381.04093.67391.29320.6748-0.1445-0.288-0.0840.1580.0247-0.1286-0.0346-0.1980.11950.57470.0034-0.0820.44950.03280.370917.6896-34.6395-5.8035
84.8341-2.17792.6581.5464-0.86441.87340.1319-0.50760.26480.3505-0.0028-0.2723-0.2012-0.0323-0.14620.6748-0.0728-0.03620.58680.00290.495512.5433-22.617-2.4674
93.42360.70020.62112.52230.89741.19370.0043-0.44260.07570.2101-0.08460.2443-0.135-0.33440.08340.56870.04380.00610.51070.02940.42122.2456-30.0573-13.5136
100.24610.8998-1.19724.2978-5.51527.1743-0.6239-0.5412-0.5970.82280.7347-0.0295-0.5592-1.5685-0.27390.59940.12960.02080.9950.13630.6578-10.0002-34.117-11.3911
118.0971-2.67463.27733.2926-1.3293.5614-0.43420.11640.05380.2230.27740.4419-0.7499-0.49540.19590.52790.0846-0.00580.59610.00360.5334-30.6459-11.4705-70.8914
125.9963-1.30711.86762.6954-0.72384.4571-0.03270.0588-0.145-0.0105-0.0221-0.20990.08810.11680.02810.3945-0.0310.05990.3231-0.00630.3978-6.627-25.4366-72.1096
138.0453-0.5192-0.94082.40410.1922.27890.15020.0442-0.76630.427-0.04160.34040.3263-0.4761-0.11380.4877-0.05640.0130.47050.02140.573-17.8847-32.0898-65.7931
142.75020.2789-0.79542.7352-0.16710.74820.0413-0.0174-0.1953-0.00530.0550.69840.1843-0.1926-0.15370.4193-0.05670.00120.70060.01760.505-32.7903-24.2879-72.6871
154.9193-1.9602-0.39916.1633-0.25275.9821-0.1741-0.46440.12390.5451-0.0287-0.5766-0.02160.23990.29830.6477-0.0939-0.13380.57340.12240.4706-0.273-4.2829-81.8934
164.88375.30754.83245.88765.39184.916-0.5806-0.02610.6174-1.0303-0.04970.7573-1.3883-0.4630.74050.81360.0405-0.13610.5820.0230.6738-20.9137-7.3663-90.912
173.51-0.44581.51283.8581.12564.35-0.12240.0117-0.0045-0.07440.04970.55210.1221-0.8160.04550.5046-0.0928-0.08140.65810.03430.4474-30.3206-21.6525-90.8815
182.84180.3257-0.5361.08750.16342.56490.05680.0887-0.3750.0057-0.10220.01080.2214-0.23740.01520.7318-0.0259-0.11950.5546-0.04370.6229-22.2767-26.7236-94.7572
193.07510.59251.79961.05790.77012.8721-0.01470.316-0.3831-0.45820.1342-0.05390.2315-0.0014-0.10830.6907-0.0089-0.02670.4673-0.00770.4067-13.0098-21.6778-97.281
201.4653-1.7390.90524.8703-0.95871.3454-0.2349-0.3184-0.3625-0.07840.1968-0.20950.28760.43480.11210.470.10890.02950.60070.0490.51480.7112-17.7712-82.7476
216.09980.459-0.20087.39761.57045.8256-0.36390.31980.40680.16880.24-0.6535-0.11470.32820.0770.46050.09070.03070.37540.09260.449615.6797-22.0523-34.1596
223.6039-1.2480.07153.4224-0.11791.87740.2039-0.3632-0.3683-0.1807-0.05570.7638-0.044-0.4313-0.13190.51790.06540.01020.4667-0.0020.5235-16.8202-8.8645-30.4866
233.14920.35910.2881.4202-0.02483.0661-0.0746-0.30410.25050.0443-0.03910.202-0.1846-0.360.14410.52480.1134-0.04070.4941-0.04560.489-9.9404-4.1969-33.8988
242.9543-0.06791.05561.1624-0.47712.1123-0.1829-0.36750.46590.5240.10.0218-0.4122-0.31580.04980.70350.1282-0.04730.5561-0.05260.5315-3.0354-4.8502-21.3185
255.57361.63080.40345.227-2.05393.8698-0.2573-0.04460.66750.06160.1959-0.0253-0.19080.28530.03080.48410.0462-0.03230.3852-0.03120.39415.0152-7.7297-33.2789
268.7832.18811.27636.5386-0.40025.4061-0.6927-0.30850.6972-0.34620.3493-0.3123-0.34410.2720.33750.6203-0.0064-0.00620.4741-0.06630.563331.9992-47.4172-22.5731
273.47351.7371-3.6961.4899-1.62424.1232-0.19190.296-0.0197-0.2448-0.05610.20390.5275-0.49520.25250.73860.0479-0.03740.4709-0.05010.45578.3962-53.0879-21.3587
283.52660.34021.88037.6410.40645.82080.0140.4712-0.04540.55560.3950.44920.0009-0.9251-0.2230.6607-0.12450.08930.91840.01520.5086-12.9435-50.8249-8.5406
291.80131.3964-1.14032.1709-0.99940.73340.0485-0.07770.1916-0.1122-0.0574-0.07010.303-0.1045-0.06260.5622-0.03690.01120.5438-0.01140.36798.3502-46.1491-11.5593
305.3315-1.5725-1.72145.2169-2.51022.4699-0.07530.1415-0.19580.2331-0.3428-0.2582-0.3295-0.37690.42850.5359-0.0013-0.03090.49520.08150.49482.691-45.8338-10.0155
316.5395-3.6236-0.97363.2354-1.04852.5139-0.5876-1.4799-0.20960.43030.799-0.1954-0.6571-0.66430.02060.9145-0.01210.21460.7275-0.01120.608-0.26-47.65371.8832
328.1059-2.751-1.111.6519-0.18050.88930.5263-0.6103-0.11010.182-0.1029-0.04080.53780.3856-0.30530.7654-0.05210.03210.63780.0040.49098.2171-56.9246-0.9253
335.2919-0.808-0.10093.5464-0.37460.41010.1204-0.0362-0.4570.4079-0.17730.030.22720.00550.04910.6974-0.0205-0.03340.50430.03030.489913.9935-59.9008-8.8113
345.42340.01110.18956.40490.88533.48120.1418-0.76080.2705-0.1421-0.00060.2924-0.6220.0612-0.15390.4735-0.0191-0.01940.4560.01240.408824.9769-45.5182-11.9365
352.5926-2.0794-2.49256.21794.73454.079-0.1023-0.9614-0.3591-0.60850.14190.5625-1.02461.2471-0.11530.6121-0.0346-0.19910.7381-0.0260.765134.4809-45.5843-4.1893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 9 THROUGH 141 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 142 THROUGH 193 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 194 THROUGH 234 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 9 THROUGH 36 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 37 THROUGH 55 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 56 THROUGH 79 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 80 THROUGH 141 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 142 THROUGH 188 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 189 THROUGH 218 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 219 THROUGH 234 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 9 THROUGH 54 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 55 THROUGH 141 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 142 THROUGH 183 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 184 THROUGH 234 )
15X-RAY DIFFRACTION15CHAIN 'D' AND (RESID 9 THROUGH 36 )
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESID 37 THROUGH 53 )
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESID 54 THROUGH 113 )
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 114 THROUGH 153 )
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 154 THROUGH 213 )
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESID 214 THROUGH 234 )
21X-RAY DIFFRACTION21CHAIN 'E' AND (RESID 9 THROUGH 36 )
22X-RAY DIFFRACTION22CHAIN 'E' AND (RESID 37 THROUGH 87 )
23X-RAY DIFFRACTION23CHAIN 'E' AND (RESID 88 THROUGH 141 )
24X-RAY DIFFRACTION24CHAIN 'E' AND (RESID 142 THROUGH 206 )
25X-RAY DIFFRACTION25CHAIN 'E' AND (RESID 207 THROUGH 234 )
26X-RAY DIFFRACTION26CHAIN 'F' AND (RESID 9 THROUGH 36 )
27X-RAY DIFFRACTION27CHAIN 'F' AND (RESID 37 THROUGH 55 )
28X-RAY DIFFRACTION28CHAIN 'F' AND (RESID 56 THROUGH 79 )
29X-RAY DIFFRACTION29CHAIN 'F' AND (RESID 80 THROUGH 101 )
30X-RAY DIFFRACTION30CHAIN 'F' AND (RESID 102 THROUGH 113 )
31X-RAY DIFFRACTION31CHAIN 'F' AND (RESID 114 THROUGH 141 )
32X-RAY DIFFRACTION32CHAIN 'F' AND (RESID 142 THROUGH 167 )
33X-RAY DIFFRACTION33CHAIN 'F' AND (RESID 168 THROUGH 203 )
34X-RAY DIFFRACTION34CHAIN 'F' AND (RESID 204 THROUGH 222 )
35X-RAY DIFFRACTION35CHAIN 'F' AND (RESID 223 THROUGH 234 )

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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

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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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