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- PDB-4w91: Crystal structure of a cysteine desulfurase SufS from Brucella su... -

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Basic information

Entry
Database: PDB / ID: 4w91
TitleCrystal structure of a cysteine desulfurase SufS from Brucella suis bound to PLP
ComponentsAminotransferase
KeywordsTRANSFERASE / structural genomics / National Institute for Allergy and Infectious Disease / NIAID / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / pyridoxal-5-phosphate / PLP / LLP
Function / homologyAspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta / Aminotransferase / Aminotransferase
Function and homology information
Biological speciesBrucella suis bv. 4 str. 40 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a cysteine desulfurase SufS from Brucella suis bound to PLP
Authors: Seattle Structural Genomics Center for Infectious Disease
History
DepositionAug 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 2.0Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords / struct_ncs_dom_lim
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_keywords.text / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase
B: Aminotransferase
C: Aminotransferase
D: Aminotransferase
E: Aminotransferase
F: Aminotransferase
G: Aminotransferase
H: Aminotransferase
I: Aminotransferase
J: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,97117
Polymers470,72310
Non-polymers2487
Water6,377354
1
A: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2164
Polymers94,1452
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-53 kcal/mol
Surface area24940 Å2
MethodPISA
2
C: Aminotransferase
D: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2164
Polymers94,1452
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-52 kcal/mol
Surface area25160 Å2
MethodPISA
3
E: Aminotransferase
F: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1803
Polymers94,1452
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-43 kcal/mol
Surface area24740 Å2
MethodPISA
4
G: Aminotransferase
H: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1803
Polymers94,1452
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-44 kcal/mol
Surface area24790 Å2
MethodPISA
5
I: Aminotransferase
J: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1803
Polymers94,1452
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-42 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.850, 121.910, 133.720
Angle α, β, γ (deg.)111.49, 106.53, 89.81
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110B
210C
111B
211D
112B
212E
113B
213F
114B
214G
115B
215H
116B
216I
117B
217J
118C
218D
119C
219E
120C
220F
121C
221G
122C
222H
123C
223I
124C
224J
125D
225E
126D
226F
127D
227G
128D
228H
129D
229I
130D
230J
131E
231F
132E
232G
133E
233H
134E
234I
135E
235J
136F
236G
137F
237H
138F
238I
139F
239J
140G
240H
141G
241I
142G
242J
143H
243I
144H
244J
145I
245J

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEAA11 - 41319 - 421
21PHEPHEBB11 - 41319 - 421
12GLYGLYAA11 - 41419 - 422
22GLYGLYCC11 - 41419 - 422
13GLYGLYAA11 - 41419 - 422
23GLYGLYDD11 - 41419 - 422
14GLYGLYAA11 - 41419 - 422
24GLYGLYEE11 - 41419 - 422
15GLYGLYAA11 - 41419 - 422
25GLYGLYFF11 - 41419 - 422
16PHEPHEAA11 - 41219 - 420
26PHEPHEGG11 - 41219 - 420
17GLYGLYAA11 - 41419 - 422
27GLYGLYHH11 - 41419 - 422
18GLYGLYAA11 - 41419 - 422
28GLYGLYII11 - 41419 - 422
19TYRTYRAA11 - 39319 - 401
29TYRTYRJJ11 - 39319 - 401
110PHEPHEBB11 - 41319 - 421
210PHEPHECC11 - 41319 - 421
111PHEPHEBB11 - 41319 - 421
211PHEPHEDD11 - 41319 - 421
112PHEPHEBB11 - 41319 - 421
212PHEPHEEE11 - 41319 - 421
113PHEPHEBB11 - 41319 - 421
213PHEPHEFF11 - 41319 - 421
114PHEPHEBB11 - 41219 - 420
214PHEPHEGG11 - 41219 - 420
115GLYGLYBB11 - 41419 - 422
215GLYGLYHH11 - 41419 - 422
116GLYGLYBB11 - 41419 - 422
216GLYGLYII11 - 41419 - 422
117TYRTYRBB11 - 39319 - 401
217TYRTYRJJ11 - 39319 - 401
118GLYGLYCC11 - 41419 - 422
218GLYGLYDD11 - 41419 - 422
119GLYGLYCC11 - 41419 - 422
219GLYGLYEE11 - 41419 - 422
120GLYGLYCC11 - 41419 - 422
220GLYGLYFF11 - 41419 - 422
121PHEPHECC11 - 41219 - 420
221PHEPHEGG11 - 41219 - 420
122GLYGLYCC11 - 41419 - 422
222GLYGLYHH11 - 41419 - 422
123GLYGLYCC11 - 41419 - 422
223GLYGLYII11 - 41419 - 422
124TYRTYRCC11 - 39319 - 401
224TYRTYRJJ11 - 39319 - 401
125GLYGLYDD11 - 41419 - 422
225GLYGLYEE11 - 41419 - 422
126GLYGLYDD11 - 41419 - 422
226GLYGLYFF11 - 41419 - 422
127PHEPHEDD11 - 41219 - 420
227PHEPHEGG11 - 41219 - 420
128GLYGLYDD11 - 41419 - 422
228GLYGLYHH11 - 41419 - 422
129GLYGLYDD11 - 41419 - 422
229GLYGLYII11 - 41419 - 422
130TYRTYRDD11 - 39319 - 401
230TYRTYRJJ11 - 39319 - 401
131GLYGLYEE11 - 41419 - 422
231GLYGLYFF11 - 41419 - 422
132PHEPHEEE11 - 41219 - 420
232PHEPHEGG11 - 41219 - 420
133GLYGLYEE11 - 41419 - 422
233GLYGLYHH11 - 41419 - 422
134GLYGLYEE11 - 41419 - 422
234GLYGLYII11 - 41419 - 422
135TYRTYREE11 - 39319 - 401
235TYRTYRJJ11 - 39319 - 401
136PHEPHEFF11 - 41219 - 420
236PHEPHEGG11 - 41219 - 420
137GLYGLYFF11 - 41419 - 422
237GLYGLYHH11 - 41419 - 422
138GLYGLYFF11 - 41419 - 422
238GLYGLYII11 - 41419 - 422
139TYRTYRFF11 - 39319 - 401
239TYRTYRJJ11 - 39319 - 401
140PHEPHEGG11 - 41319 - 421
240PHEPHEHH11 - 41319 - 421
141PHEPHEGG11 - 41319 - 421
241PHEPHEII11 - 41319 - 421
142TYRTYRGG11 - 39319 - 401
242TYRTYRJJ11 - 39319 - 401
143GLYGLYHH11 - 41419 - 422
243GLYGLYII11 - 41419 - 422
144TYRTYRHH11 - 39319 - 401
244TYRTYRJJ11 - 39319 - 401
145TYRTYRII11 - 39319 - 401
245TYRTYRJJ11 - 39319 - 401

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

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Components

#1: Protein
Aminotransferase


Mass: 47072.312 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis bv. 4 str. 40 (bacteria) / Gene: BAVG_0632 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0BBJ1, UniProt: A0A7U8IVA5*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: BrsuA.01104.a.B1.PS01850 at 25.1 mg/mL against JCSG+ screen condition D3, 0.2 M NaCl, 0.1 M NaK Phosphate pH 6.2, 50% PEG 200, crystal tracking ID 246776d3, unique puck ID thi5-2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 178399 / % possible obs: 96.3 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.87
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.04 / % possible all: 95.8

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementResolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.911 / SU B: 24.705 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.477 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25215 8955 5 %RANDOM
Rwork0.23733 ---
obs0.23807 169402 96.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.904 Å2
Baniso -1Baniso -2Baniso -3
1--3.43 Å2-0.46 Å20.8 Å2
2---4.69 Å20.95 Å2
3---4.41 Å2
Refinement stepCycle: 1 / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29981 0 7 354 30342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01930691
X-RAY DIFFRACTIONr_bond_other_d0.0060.0228418
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.94341792
X-RAY DIFFRACTIONr_angle_other_deg1.205364763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05153974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40822.9811352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.868154416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6815222
X-RAY DIFFRACTIONr_chiral_restr0.0750.24696
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02135668
X-RAY DIFFRACTIONr_gen_planes_other0.0060.027386
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_it00.215920
X-RAY DIFFRACTIONr_mcbond_other00.215919
X-RAY DIFFRACTIONr_mcangle_it00.319874
X-RAY DIFFRACTIONr_mcangle_other00.319875
X-RAY DIFFRACTIONr_scbond_it00.214771
X-RAY DIFFRACTIONr_scbond_other00.214772
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other00.321915
X-RAY DIFFRACTIONr_long_range_B_refined4.6261.73834240
X-RAY DIFFRACTIONr_long_range_B_other4.6221.70434207
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A248200.05
12B248200.05
21A247240.05
22C247240.05
31A249330.06
32D249330.06
41A246640.05
42E246640.05
51A245560.06
52F245560.06
61A240340.06
62G240340.06
71A241710.05
72H241710.05
81A197550.06
82I197550.06
91A175660.05
92J175660.05
101B248270.06
102C248270.06
111B249010.05
112D249010.05
121B244870.05
122E244870.05
131B243770.07
132F243770.07
141B239680.06
142G239680.06
151B240540.06
152H240540.06
161B196810.06
162I196810.06
171B175070.06
172J175070.06
181C247940.06
182D247940.06
191C243150.06
192E243150.06
201C243830.07
202F243830.07
211C240910.06
212G240910.06
221C240560.06
222H240560.06
231C195990.06
232I195990.06
241C174750.06
242J174750.06
251D245160.05
252E245160.05
261D245270.06
262F245270.06
271D241710.06
272G241710.06
281D241760.05
282H241760.05
291D197360.06
292I197360.06
301D174950.06
302J174950.06
311E243290.06
312F243290.06
321E237640.06
322G237640.06
331E237350.05
332H237350.05
341E197370.05
342I197370.05
351E174440.06
352J174440.06
361F238390.07
362G238390.07
371F237270.07
372H237270.07
381F196150.06
382I196150.06
391F174650.06
392J174650.06
401G233900.06
402H233900.06
411G193230.06
412I193230.06
421G172690.06
422J172690.06
431H195870.06
432I195870.06
441H172430.06
442J172430.06
451I153350.05
452J153350.05
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 657 -
Rwork0.323 12432 -
obs--95.57 %
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)
11.512-0.3385-0.15090.9956-0.48591.50090.2062-0.09930.09460.04010.08810.2805-0.2011-0.3075-0.29420.75880.00240.03930.69580.06390.116815.4603-6.671-35.5108
21.6061-0.09750.09131.7106-0.23361.28960.20480.0217-0.0617-0.1146-0.1034-0.13560.07570.2826-0.10130.73780.0123-0.01990.6890.0260.027743.4495-18.0245-42.3512
30.60350.05770.11211.44990.06720.8989-0.00390.1334-0.07880.0260.0397-0.07890.3355-0.178-0.03580.8896-0.117-0.04140.78180.050.021969.4426-79.3137-15.7834
40.7709-0.1199-0.04551.4301-0.08051.1142-0.0080.09150.13340.11840.0336-0.0509-0.0662-0.2041-0.02560.7344-0.0258-0.04490.74180.11370.03968.9692-48.4232-12.396
50.9878-0.031-0.04751.23210.06791.6560.0654-0.0792-0.0743-0.02970.1451-0.16720.26680.2538-0.21050.81350.065-0.09390.6820.0210.066241.1633-19.8365-83.9012
61.0554-0.1611-0.42081.4469-0.09151.87020.15480.05010.2141-0.10040.1760.0775-0.3676-0.2762-0.33080.84470.0667-0.00080.69560.12970.099423.43634.4587-90.325
71.66320.411-0.04461.9256-0.28280.82310.1949-0.0265-0.07670.5316-0.11740.4279-0.3036-0.0579-0.07751.1118-0.09740.19780.749-0.06360.16618.08110.02844.6417
82.20720.7613-0.39071.21890.02260.72010.3318-0.2917-0.17860.5148-0.2933-0.2011-0.20460.2293-0.03851.2237-0.2376-0.08080.87810.04390.074647.93327.17698.1396
90.51530.53420.24263.46691.35561.5764-0.22690.274-0.0769-1.16140.2804-0.2925-0.43990.3798-0.05351.4715-0.09250.13051.20980.03910.264280.8025-56.8222-66.2424
101.5704-0.09270.24022.89350.16281.3314-0.0799-0.0366-0.3038-0.28750.03670.08920.3239-0.020.04321.32190.05260.04841.0953-0.00090.310669.0406-80.1696-55.6433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 414
2X-RAY DIFFRACTION2B10 - 414
3X-RAY DIFFRACTION3C11 - 414
4X-RAY DIFFRACTION4D11 - 414
5X-RAY DIFFRACTION5E11 - 414
6X-RAY DIFFRACTION6F11 - 414
7X-RAY DIFFRACTION7G11 - 413
8X-RAY DIFFRACTION8H11 - 414
9X-RAY DIFFRACTION9I11 - 414
10X-RAY DIFFRACTION10J11 - 393

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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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