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- PDB-5c3y: Structure of human ribokinase crystallized with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 5c3y
TitleStructure of human ribokinase crystallized with AMPPNP
ComponentsRibokinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


ribokinase / ribokinase activity / Pentose phosphate pathway / D-ribose catabolic process / pentose-phosphate shunt / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AMP PHOSPHORAMIDATE / Ribokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPark, J. / Chakrabarti, J. / Singh, B. / Gupta, R.S. / Junop, M.S.
CitationJournal: To Be Published
Title: Structure of human ribokinase crystallized with AMPPNP
Authors: Park, J. / Chakrabarti, J. / Singh, B. / Gupta, R.S. / Junop, M.S.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references / Structure summary
Revision 1.2Sep 27, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_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: Ribokinase
B: Ribokinase
C: Ribokinase
D: Ribokinase
E: Ribokinase
F: Ribokinase
G: Ribokinase
H: Ribokinase
I: Ribokinase
J: Ribokinase
K: Ribokinase
L: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,55848
Polymers422,89212
Non-polymers5,66636
Water14,592810
1
A: Ribokinase
B: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4268
Polymers70,4822
Non-polymers9446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-20 kcal/mol
Surface area26090 Å2
MethodPISA
2
C: Ribokinase
D: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4268
Polymers70,4822
Non-polymers9446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-20 kcal/mol
Surface area25830 Å2
MethodPISA
3
E: Ribokinase
F: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4268
Polymers70,4822
Non-polymers9446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-19 kcal/mol
Surface area25730 Å2
MethodPISA
4
G: Ribokinase
H: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4268
Polymers70,4822
Non-polymers9446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-19 kcal/mol
Surface area26040 Å2
MethodPISA
5
I: Ribokinase
J: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4268
Polymers70,4822
Non-polymers9446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-19 kcal/mol
Surface area26050 Å2
MethodPISA
6
K: Ribokinase
L: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4268
Polymers70,4822
Non-polymers9446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-20 kcal/mol
Surface area25630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.310, 168.140, 161.500
Angle α, β, γ (deg.)90.00, 90.82, 90.00
Int Tables number4
Space group name H-MP1211
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
110A
210K
111A
211L
112B
212C
113B
213D
114B
214E
115B
215F
116B
216G
117B
217H
118B
218I
119B
219J
120B
220K
121B
221L
122C
222D
123C
223E
124C
224F
125C
225G
126C
226H
127C
227I
128C
228J
129C
229K
130C
230L
131D
231E
132D
232F
133D
233G
134D
234H
135D
235I
136D
236J
137D
237K
138D
238L
139E
239F
140E
240G
141E
241H
142E
242I
143E
243J
144E
244K
145E
245L
146F
246G
147F
247H
148F
248I
149F
249J
150F
250K
151F
251L
152G
252H
153G
253I
154G
254J
155G
255K
156G
256L
157H
257I
158H
258J
159H
259K
160H
260L
161I
261J
162I
262K
163I
263L
164J
264K
165J
265L
166K
266L

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLEULEUAA15 - 31915 - 319
21VALVALLEULEUBB15 - 31915 - 319
12VALVALLEULEUAA15 - 31915 - 319
22VALVALLEULEUCC15 - 31915 - 319
13VALVALLEULEUAA15 - 31915 - 319
23VALVALLEULEUDD15 - 31915 - 319
14VALVALLEULEUAA15 - 31915 - 319
24VALVALLEULEUEE15 - 31915 - 319
15VALVALLEULEUAA15 - 31915 - 319
25VALVALLEULEUFF15 - 31915 - 319
16VALVALLEULEUAA15 - 31915 - 319
26VALVALLEULEUGG15 - 31915 - 319
17VALVALLEULEUAA15 - 31915 - 319
27VALVALLEULEUHH15 - 31915 - 319
18VALVALLEULEUAA15 - 31915 - 319
28VALVALLEULEUII15 - 31915 - 319
19VALVALLEULEUAA15 - 31915 - 319
29VALVALLEULEUJJ15 - 31915 - 319
110VALVALLEULEUAA15 - 31915 - 319
210VALVALLEULEUKK15 - 31915 - 319
111VALVALLEULEUAA15 - 31915 - 319
211VALVALLEULEULL15 - 31915 - 319
112GLUGLUHISHISBB14 - 32514 - 325
212GLUGLUHISHISCC14 - 32514 - 325
113GLUGLULEULEUBB14 - 32314 - 323
213GLUGLULEULEUDD14 - 32314 - 323
114GLUGLULEULEUBB14 - 32314 - 323
214GLUGLULEULEUEE14 - 32314 - 323
115VALVALHISHISBB15 - 32515 - 325
215VALVALHISHISFF15 - 32515 - 325
116GLUGLUHISHISBB14 - 32714 - 327
216GLUGLUHISHISGG14 - 32714 - 327
117GLUGLULEULEUBB14 - 32314 - 323
217GLUGLULEULEUHH14 - 32314 - 323
118VALVALHISHISBB15 - 32615 - 326
218VALVALHISHISII15 - 32615 - 326
119GLUGLUHISHISBB14 - 32714 - 327
219GLUGLUHISHISJJ14 - 32714 - 327
120VALVALHISHISBB15 - 32515 - 325
220VALVALHISHISKK15 - 32515 - 325
121GLUGLULEULEUBB14 - 32314 - 323
221GLUGLULEULEULL14 - 32314 - 323
122GLUGLULEULEUCC14 - 32314 - 323
222GLUGLULEULEUDD14 - 32314 - 323
123GLUGLULEULEUCC14 - 32314 - 323
223GLUGLULEULEUEE14 - 32314 - 323
124VALVALHISHISCC15 - 32515 - 325
224VALVALHISHISFF15 - 32515 - 325
125GLUGLUHISHISCC14 - 32514 - 325
225GLUGLUHISHISGG14 - 32514 - 325
126GLUGLULEULEUCC14 - 32314 - 323
226GLUGLULEULEUHH14 - 32314 - 323
127VALVALHISHISCC15 - 32515 - 325
227VALVALHISHISII15 - 32515 - 325
128GLUGLUHISHISCC14 - 32514 - 325
228GLUGLUHISHISJJ14 - 32514 - 325
129VALVALHISHISCC15 - 32515 - 325
229VALVALHISHISKK15 - 32515 - 325
130GLUGLULEULEUCC14 - 32314 - 323
230GLUGLULEULEULL14 - 32314 - 323
131GLUGLUGLUGLUDD14 - 32414 - 324
231GLUGLUGLUGLUEE14 - 32414 - 324
132VALVALLEULEUDD15 - 32315 - 323
232VALVALLEULEUFF15 - 32315 - 323
133GLUGLULEULEUDD14 - 32314 - 323
233GLUGLULEULEUGG14 - 32314 - 323
134GLUGLUGLUGLUDD14 - 32414 - 324
234GLUGLUGLUGLUHH14 - 32414 - 324
135VALVALLEULEUDD15 - 32315 - 323
235VALVALLEULEUII15 - 32315 - 323
136GLUGLULEULEUDD14 - 32314 - 323
236GLUGLULEULEUJJ14 - 32314 - 323
137VALVALLEULEUDD15 - 32315 - 323
237VALVALLEULEUKK15 - 32315 - 323
138GLUGLUGLUGLUDD14 - 32414 - 324
238GLUGLUGLUGLULL14 - 32414 - 324
139VALVALLEULEUEE15 - 32315 - 323
239VALVALLEULEUFF15 - 32315 - 323
140GLUGLULEULEUEE14 - 32314 - 323
240GLUGLULEULEUGG14 - 32314 - 323
141GLUGLUGLUGLUEE14 - 32414 - 324
241GLUGLUGLUGLUHH14 - 32414 - 324
142VALVALLEULEUEE15 - 32315 - 323
242VALVALLEULEUII15 - 32315 - 323
143GLUGLULEULEUEE14 - 32314 - 323
243GLUGLULEULEUJJ14 - 32314 - 323
144VALVALLEULEUEE15 - 32315 - 323
244VALVALLEULEUKK15 - 32315 - 323
145GLUGLUGLUGLUEE14 - 32414 - 324
245GLUGLUGLUGLULL14 - 32414 - 324
146VALVALHISHISFF15 - 32515 - 325
246VALVALHISHISGG15 - 32515 - 325
147VALVALLEULEUFF15 - 32315 - 323
247VALVALLEULEUHH15 - 32315 - 323
148VALVALHISHISFF15 - 32515 - 325
248VALVALHISHISII15 - 32515 - 325
149VALVALHISHISFF15 - 32515 - 325
249VALVALHISHISJJ15 - 32515 - 325
150VALVALHISHISFF15 - 32615 - 326
250VALVALHISHISKK15 - 32615 - 326
151VALVALLEULEUFF15 - 32315 - 323
251VALVALLEULEULL15 - 32315 - 323
152GLUGLULEULEUGG14 - 32314 - 323
252GLUGLULEULEUHH14 - 32314 - 323
153VALVALHISHISGG15 - 32615 - 326
253VALVALHISHISII15 - 32615 - 326
154GLUGLUHISHISGG14 - 32714 - 327
254GLUGLUHISHISJJ14 - 32714 - 327
155VALVALHISHISGG15 - 32515 - 325
255VALVALHISHISKK15 - 32515 - 325
156GLUGLULEULEUGG14 - 32314 - 323
256GLUGLULEULEULL14 - 32314 - 323
157VALVALLEULEUHH15 - 32315 - 323
257VALVALLEULEUII15 - 32315 - 323
158GLUGLULEULEUHH14 - 32314 - 323
258GLUGLULEULEUJJ14 - 32314 - 323
159VALVALLEULEUHH15 - 32315 - 323
259VALVALLEULEUKK15 - 32315 - 323
160GLUGLUGLUGLUHH14 - 32414 - 324
260GLUGLUGLUGLULL14 - 32414 - 324
161VALVALHISHISII15 - 32615 - 326
261VALVALHISHISJJ15 - 32615 - 326
162VALVALHISHISII15 - 32515 - 325
262VALVALHISHISKK15 - 32515 - 325
163VALVALLEULEUII15 - 32315 - 323
263VALVALLEULEULL15 - 32315 - 323
164VALVALHISHISJJ15 - 32515 - 325
264VALVALHISHISKK15 - 32515 - 325
165GLUGLULEULEUJJ14 - 32314 - 323
265GLUGLULEULEULL14 - 32314 - 323
166VALVALLEULEUKK15 - 32315 - 323
266VALVALLEULEULL15 - 32315 - 323

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
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

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Components

#1: Protein
Ribokinase /


Mass: 35241.008 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBKS, RBSK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H477, ribokinase
#2: Chemical
ChemComp-AN2 / AMP PHOSPHORAMIDATE


Mass: 426.216 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N6O9P2
#3: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 810 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.1M sodium HEPES, 7% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→51.26 Å / Num. obs: 130659 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.521 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 2 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FV7
Resolution: 2.6→51.26 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.904 / SU B: 24.881 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.939 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23205 6493 5 %RANDOM
Rwork0.2047 ---
obs0.20609 124139 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.583 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20 Å20.21 Å2
2--0.58 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.6→51.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27417 0 348 810 28575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01928250
X-RAY DIFFRACTIONr_bond_other_d0.0150.0226927
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.98238549
X-RAY DIFFRACTIONr_angle_other_deg2.117361873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08153748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02925.6681041
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.833154471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3871582
X-RAY DIFFRACTIONr_chiral_restr0.1040.24722
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0232327
X-RAY DIFFRACTIONr_gen_planes_other0.0110.025955
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_it0.5821.1915001
X-RAY DIFFRACTIONr_mcbond_other0.5821.1915000
X-RAY DIFFRACTIONr_mcangle_it1.0221.78418746
X-RAY DIFFRACTIONr_mcangle_other1.0221.78418747
X-RAY DIFFRACTIONr_scbond_it0.9071.32313249
X-RAY DIFFRACTIONr_scbond_other0.9071.32313250
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4191.9619804
X-RAY DIFFRACTIONr_long_range_B_refined3.8069.99130082
X-RAY DIFFRACTIONr_long_range_B_other3.8069.99230083
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)
11A349860.06
12B349860.06
21A351800.06
22C351800.06
31A350460.07
32D350460.07
41A350800.06
42E350800.06
51A351820.07
52F351820.07
61A351080.06
62G351080.06
71A352640.06
72H352640.06
81A350080.06
82I350080.06
91A352940.05
92J352940.05
101A349020.06
102K349020.06
111A348360.06
112L348360.06
121B363240.07
122C363240.07
131B356000.07
132D356000.07
141B354720.07
142E354720.07
151B358560.07
152F358560.07
161B357560.07
162G357560.07
171B358400.06
172H358400.06
181B364640.06
182I364640.06
191B359400.06
192J359400.06
201B359100.06
202K359100.06
211B355520.06
212L355520.06
221C356480.08
222D356480.08
231C358020.07
232E358020.07
241C360180.07
242F360180.07
251C359280.08
252G359280.08
261C359340.07
262H359340.07
271C363540.06
272I363540.06
281C361040.06
282J361040.06
291C361400.07
292K361400.07
301C358020.07
302L358020.07
311D355460.08
312E355460.08
321D360160.07
322F360160.07
331D353720.08
332G353720.08
341D359420.07
342H359420.07
351D358660.06
352I358660.06
361D359040.06
362J359040.06
371D357740.06
372K357740.06
381D358580.06
382L358580.06
391E355280.08
392F355280.08
401E357100.07
402G357100.07
411E361880.06
412H361880.06
421E354080.07
422I354080.07
431E359020.06
432J359020.06
441E354380.07
442K354380.07
451E355180.07
452L355180.07
461F356240.08
462G356240.08
471F357320.07
472H357320.07
481F360240.07
482I360240.07
491F357760.07
492J357760.07
501F359120.07
502K359120.07
511F355480.07
512L355480.07
521G355720.07
522H355720.07
531G354200.08
532I354200.08
541G356140.07
542J356140.07
551G355120.07
552K355120.07
561G351520.08
562L351520.08
571H356980.06
572I356980.06
581H360800.06
582J360800.06
591H355200.06
592K355200.06
601H355320.07
602L355320.07
611I357900.06
612J357900.06
621I362040.06
622K362040.06
631I357780.06
632L357780.06
641J357100.06
642K357100.06
651J356880.06
652L356880.06
661K359820.06
662L359820.06
LS refinement shellResolution: 2.602→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 512 -
Rwork0.321 8916 -
obs--97.32 %
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)
14.31811.59241.28632.1061-0.05572.5347-0.24830.06650.3607-0.04290.04040.0454-0.31150.23210.20790.14210.0178-0.0470.07420.06030.21876.015346.8562-17.5474
23.47712.0215-0.218312.96848.685113.9858-0.10390.0348-0.3195-0.2451-0.1166-0.09760.00520.43690.22050.3727-0.0424-0.08110.56380.1210.273282.647856.1622-33.8103
33.3767-1.0583-2.21933.3830.96737.7343-0.09741.5246-0.0903-1.14940.112-0.4598-0.29661.1994-0.01450.5018-0.40790.08361.61420.01470.434392.518848.1973-34.1984
46.28610.75290.95532.90690.06624.3368-0.14631.1422-0.1773-0.16240.2233-0.3234-0.03160.9809-0.0770.1043-0.0303-0.050.5382-0.02070.298795.452642.6281-18.6591
53.2453.0452-1.33463.9271-2.65342.3968-0.01780.09710.1302-0.14840.02440.12230.16040.0933-0.00660.16310.0453-0.04510.08960.04530.262658.431334.3927-21.3695
63.13020.3925-0.05162.0824-0.09561.3621-0.0784-0.2467-0.04650.13690.0431-0.02940.2191-0.05430.03530.11540.023-0.00860.04830.05590.201652.116225.3414-9.421
72.4757-0.07380.19494.4423-0.18192.3396-0.00530.3489-0.3279-0.5170.05030.38350.3583-0.4135-0.0450.1918-0.0749-0.04450.24350.04120.285237.690121.7993-21.2262
86.2653-2.35334.27896.11292.6566.40490.1523-0.7391-0.42420.2499-0.37010.8230.4243-0.93720.21780.17230.0738-0.01230.68070.04280.500422.38532.2257-11.9896
94.72232.06580.41372.76120.27580.06260.0060.0271-0.3503-0.17510.0259-0.06870.0141-0.0322-0.03190.1681-0.0226-0.02770.06150.02970.2824-14.8882-9.7275-8.0522
103.68160.9864-0.48272.9135-0.17261.819-0.14290.38060.2087-0.3580.08420.0754-0.1109-0.02390.05870.22110.0124-0.04450.0470.04540.2842-5.73226.17-14.0985
111.72861.93160.47326.509-0.01540.5575-0.05260.2902-0.1091-0.34820.1811-0.35340.06230.2546-0.12850.30320.00850.0210.3249-0.04430.30068.5046-0.9407-22.3569
123.83260.32161.09912.64480.43833.57490.00320.3768-0.6485-0.28160.1362-0.45640.21560.2465-0.13940.16160.0184-0.03720.0496-0.0960.42856.148-10.0524-10.6007
133.62763.32770.05946.3016-0.10950.03580.02540.27040.2349-0.558-0.01710.2964-0.00460.0762-0.00830.26950.0018-0.07940.1777-0.04320.306-31.5402-14.8896-14.395
143.68051.95920.00633.59850.35551.3390.0839-0.1788-0.2061-0.0373-0.0741-0.16560.03310.0903-0.00980.10840.0144-0.08610.0175-0.00990.2883-35.4273-26.2175-6.7414
153.10420.76440.26383.31220.85852.9950.11530.5323-0.0304-0.5925-0.0650.4501-0.0909-0.3145-0.05020.17620.0571-0.1250.1397-0.03480.376-52.88-27.7459-17.2104
166.17170.9890.06923.6042-1.33383.24190.1787-0.25720.33620.3282-0.08680.3563-0.3321-0.4273-0.0920.17540.0340.00940.0859-0.05010.4292-54.9805-17.1859-3.5206
173.629-0.03472.73790.12610.67896.06670.1032-0.4904-0.0268-0.15330.025-0.0295-0.7322-0.1958-0.12830.2408-0.03310.02820.10570.08470.254728.148416.099321.7841
181.8206-0.90840.28877.3669-0.48352.38730.0416-0.29960.19670.2185-0.01360.2217-0.11930.0029-0.02790.28380.0193-0.0190.2324-0.03330.265438.891330.658533.2701
193.561.07782.02341.1179-0.3362.31940.03360.0956-0.1295-0.1395-0.0158-0.09130.13680.1117-0.01780.1410.01210.05380.00870.02290.179427.181612.391714.1278
202.5425-0.0541.91992.7188-0.69924.547-0.1363-0.37170.36350.03420.00730.2442-0.4633-0.48330.1290.1240.04250.00530.0685-0.05110.23189.844219.519416.9165
213.8757-0.5850.69031.0982-0.231.9411-0.1077-0.3194-0.2748-0.01720.12650.0553-0.00730.0908-0.01880.1624-0.04690.02280.07540.01540.272448.559818.84932.102
223.8758-1.3931-0.24616.322-3.20252.3134-0.0941-0.8362-0.14070.45950.1268-0.07820.1688-0.0047-0.03270.46470.0055-0.08250.701-0.02960.306558.100416.453150.4684
233.7606-0.18280.27964.30561.30293.84690.0591-0.51641.13540.09260.0942-0.368-0.58690.4727-0.15330.2687-0.08490.12210.4503-0.20730.662367.386230.415440.7063
248.3417-0.7685-0.08441.5540.39010.57560.12620.1679-0.0626-0.0771-0.0105-0.0504-0.09970.1163-0.11570.3113-0.0180.05550.2922-0.01430.213971.057718.048827.8244
253.4171-0.3378-2.51310.4018-0.40843.0708-0.0917-0.2326-0.0134-0.03980.170.11210.1275-0.0734-0.07820.21090.0096-0.05850.10640.01660.26564.6255-20.506554.0284
264.0310.3355-0.06591.6079-0.40222.683-0.0170.12330.4117-0.04510.06120.2142-0.0806-0.2535-0.04420.12840.0408-0.02560.0634-0.06180.27448.6272-12.894444.6598
273.05880.27670.42543.09040.60752.53620.09210.0812-0.28750.09740.0372-0.15970.29840.2313-0.12930.08750.0141-0.03470.0549-0.01840.17624.5031-23.78141.9553
289.2232-1.53873.36486.31020.27224.0927-0.1559-0.1552-0.0991-0.268-0.0576-0.16890.25020.31520.21360.2674-0.0132-0.06840.185-0.04240.240137.6562-9.961251.1478
293.48410.3606-1.96340.041-0.22846.4597-0.17570.60040.03370.00470.0419-0.01050.57780.11910.13380.2366-0.0649-0.02360.19990.11580.2722-12.9944-11.92859.0939
304.4770.5830.634711.9384-2.57331.1681-0.14920.5381-0.4881-0.32570.27950.04780.4168-0.2663-0.13030.4331-0.11080.0240.4189-0.08460.2359-2.3274-26.842647.9041
314.52-1.2501-0.92071.9848-0.8651.9515-0.01340.04910.30190.1154-0.071-0.2592-0.14090.2190.08450.1057-0.0509-0.0610.05490.05530.2083-12.5871-7.961565.757
322.6227-0.1953-0.21622.1554-0.29823.9473-0.01720.0882-0.28970.0657-0.10260.13310.3289-0.2440.11980.0767-0.02070.01030.025-0.01010.2076-30.6666-14.876265.1662
338.0153-5.88484.38714.9187-3.24833.1167-0.3487-1.1255-0.96630.590.7420.4977-0.1905-0.1095-0.39330.29870.03660.08560.64310.36840.522617.4318-29.3102102.5792
345.5356-0.4911-0.29113.96-0.07571.7415-0.1971-0.1861-0.0798-0.05650.0582-0.1669-0.16670.16710.13890.1217-0.04220.01720.17280.14540.22210.1514-19.084791.168
353.13581.3038-0.18064.1664-0.16241.9634-0.0536-0.68910.31460.71040.08730.5951-0.3087-0.2456-0.03370.27470.1010.0940.38190.1290.4046-4.4196-17.9691103.0968
3613.6944-0.1372-9.35421.72581.63417.7723-0.42790.4671-0.3472-0.4367-0.20560.4496-0.1455-0.48240.63350.3957-0.0291-0.08410.42250.0720.5083-20.3887-25.259892.0535
374.6827-1.64110.75272.4553-1.56291.0754-0.0981-0.0696-0.28480.00350.17140.13780.0826-0.227-0.07320.1659-0.10060.03090.38650.21330.372232.8543-37.577296.3251
384.5932-0.69490.51261.3784-1.41323.386-0.1768-0.2259-0.50670.11310.27180.16040.5537-0.2887-0.09490.2817-0.06370.04240.3110.21990.454439.4383-49.2542104.3457
392.7536-0.28911.01864.3057-2.1965.0421-0.0256-0.47130.1730.3827-0.0337-0.4139-0.17870.30420.05930.1706-0.00060.03750.33950.0680.370453.7063-39.8533110.6007
404.40221.3836-0.31094.0021-0.70735.74890.03570.34380.1217-0.3728-0.0678-0.53890.1890.54540.03210.13950.01280.09650.25780.08990.3455.0447-37.101292.9
415.5809-3.3663-0.97243.43590.74530.2065-0.3695-0.60660.63970.73040.4427-0.25690.14170.0536-0.07330.37480.0668-0.02180.2861-0.12390.394321.23216.995895.6993
424.0303-1.5377-0.19953.7024-0.19150.8486-0.1246-0.13150.11230.16280.1097-0.03810.1311-0.10740.01490.1251-0.04270.01480.0929-0.04130.258127.86495.989287.4064
432.9886-0.13-0.34943.7378-0.75271.7279-0.1795-0.91630.38910.7870.1379-0.6233-0.14380.22280.04160.27760.0661-0.0960.3062-0.15330.446443.34247.298198.3071
445.4286-1.47733.45690.95920.52786.08360.21530.50250.2041-0.1442-0.2275-0.1218-0.08890.11250.01220.3218-0.07820.07720.2752-0.00320.588955.971815.134785.1658
454.6598-3.06380.35854.59730.09310.786-0.0451-0.07570.02040.2595-0.0705-0.01320.05950.24170.11560.141-0.02410.09630.1317-0.04880.31474.394223.032188.963
463.4495-2.3-0.01543.34681.05491.69540.00570.01490.34390.11050.0061-0.2405-0.09980.0742-0.01180.1069-0.03840.07930.1196-0.04620.38784.233332.586487.9097
474.6139-0.8099-0.98554.15080.42054.5062-0.0465-0.55340.09350.8073-0.12070.51220.1459-0.28170.16730.3595-0.0190.17560.1844-0.12880.4436-14.042435.366299.8057
483.7562-0.7287-0.25556.19060.17593.61980.00290.0259-0.47280.0624-0.20110.82320.3323-0.44880.19820.1241-0.0590.09250.154-0.12860.4957-15.29322.364285.7966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 181
2X-RAY DIFFRACTION2A182 - 189
3X-RAY DIFFRACTION3A190 - 226
4X-RAY DIFFRACTION4A227 - 320
5X-RAY DIFFRACTION5B14 - 50
6X-RAY DIFFRACTION6B51 - 168
7X-RAY DIFFRACTION7B169 - 319
8X-RAY DIFFRACTION8B320 - 327
9X-RAY DIFFRACTION9C14 - 116
10X-RAY DIFFRACTION10C117 - 229
11X-RAY DIFFRACTION11C230 - 259
12X-RAY DIFFRACTION12C260 - 326
13X-RAY DIFFRACTION13D14 - 45
14X-RAY DIFFRACTION14D46 - 167
15X-RAY DIFFRACTION15D168 - 282
16X-RAY DIFFRACTION16D283 - 324
17X-RAY DIFFRACTION17E14 - 34
18X-RAY DIFFRACTION18E35 - 48
19X-RAY DIFFRACTION19E49 - 180
20X-RAY DIFFRACTION20E181 - 324
21X-RAY DIFFRACTION21F15 - 133
22X-RAY DIFFRACTION22F134 - 171
23X-RAY DIFFRACTION23F172 - 289
24X-RAY DIFFRACTION24F290 - 326
25X-RAY DIFFRACTION25G14 - 47
26X-RAY DIFFRACTION26G48 - 137
27X-RAY DIFFRACTION27G138 - 314
28X-RAY DIFFRACTION28G315 - 327
29X-RAY DIFFRACTION29H14 - 34
30X-RAY DIFFRACTION30H35 - 48
31X-RAY DIFFRACTION31H49 - 167
32X-RAY DIFFRACTION32H168 - 324
33X-RAY DIFFRACTION33I15 - 50
34X-RAY DIFFRACTION34I51 - 186
35X-RAY DIFFRACTION35I187 - 321
36X-RAY DIFFRACTION36I322 - 327
37X-RAY DIFFRACTION37J14 - 114
38X-RAY DIFFRACTION38J115 - 189
39X-RAY DIFFRACTION39J190 - 276
40X-RAY DIFFRACTION40J277 - 327
41X-RAY DIFFRACTION41K15 - 45
42X-RAY DIFFRACTION42K46 - 188
43X-RAY DIFFRACTION43K189 - 318
44X-RAY DIFFRACTION44K319 - 326
45X-RAY DIFFRACTION45L14 - 78
46X-RAY DIFFRACTION46L79 - 167
47X-RAY DIFFRACTION47L168 - 252
48X-RAY DIFFRACTION48L253 - 324

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