[English] 日本語
Yorodumi
- PDB-2jd7: Crystal Structure of the Fe-soaked Ferritin from the Hyperthermop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jd7
TitleCrystal Structure of the Fe-soaked Ferritin from the Hyperthermophilic Archaeal Anaerobe Pyrococcus furiosus
ComponentsFERRITIN HOMOLOG
KeywordsMETAL TRANSPORT / IRON / PORES / FERRITIN / ARCHAEON / ENTRY CHANNELS / THERMOSTABILITY / HYPERTHERMOPHILE / FERROXIDASE CENTER METAL TRANSPORT
Function / homology
Function and homology information


ferric iron binding / iron ion transport / intracellular iron ion homeostasis
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Ferritin homolog
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTatur, J. / Hagen, W.R. / Matias, P.M.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2007
Title: Crystal Structure of the Ferritin from the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus
Authors: Tatur, J. / Hagen, W.R. / Matias, P.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization and Preliminary X-Ray Characterization of a Ferritin from the Hyperthermophilic Archaeon and Anaerobe Pyrococcus Furiosus
Authors: Matias, P.M. / Tatur, J. / Carrondo, M.A. / Hagen, W.R.
History
DepositionJan 5, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: FERRITIN HOMOLOG
1: FERRITIN HOMOLOG
2: FERRITIN HOMOLOG
3: FERRITIN HOMOLOG
4: FERRITIN HOMOLOG
5: FERRITIN HOMOLOG
6: FERRITIN HOMOLOG
7: FERRITIN HOMOLOG
8: FERRITIN HOMOLOG
9: FERRITIN HOMOLOG
A: FERRITIN HOMOLOG
B: FERRITIN HOMOLOG
C: FERRITIN HOMOLOG
D: FERRITIN HOMOLOG
E: FERRITIN HOMOLOG
F: FERRITIN HOMOLOG
G: FERRITIN HOMOLOG
H: FERRITIN HOMOLOG
I: FERRITIN HOMOLOG
J: FERRITIN HOMOLOG
K: FERRITIN HOMOLOG
L: FERRITIN HOMOLOG
M: FERRITIN HOMOLOG
N: FERRITIN HOMOLOG
O: FERRITIN HOMOLOG
P: FERRITIN HOMOLOG
Q: FERRITIN HOMOLOG
R: FERRITIN HOMOLOG
S: FERRITIN HOMOLOG
T: FERRITIN HOMOLOG
U: FERRITIN HOMOLOG
V: FERRITIN HOMOLOG
W: FERRITIN HOMOLOG
X: FERRITIN HOMOLOG
Y: FERRITIN HOMOLOG
Z: FERRITIN HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)740,521170
Polymers731,99236
Non-polymers8,529134
Water6,630368
1
0: FERRITIN HOMOLOG
1: FERRITIN HOMOLOG
2: FERRITIN HOMOLOG
3: FERRITIN HOMOLOG
4: FERRITIN HOMOLOG
5: FERRITIN HOMOLOG
6: FERRITIN HOMOLOG
7: FERRITIN HOMOLOG
8: FERRITIN HOMOLOG
9: FERRITIN HOMOLOG
G: FERRITIN HOMOLOG
H: FERRITIN HOMOLOG
I: FERRITIN HOMOLOG
J: FERRITIN HOMOLOG
K: FERRITIN HOMOLOG
L: FERRITIN HOMOLOG
M: FERRITIN HOMOLOG
N: FERRITIN HOMOLOG
O: FERRITIN HOMOLOG
P: FERRITIN HOMOLOG
Q: FERRITIN HOMOLOG
R: FERRITIN HOMOLOG
Y: FERRITIN HOMOLOG
Z: FERRITIN HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)493,457111
Polymers487,99524
Non-polymers5,46287
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: FERRITIN HOMOLOG
B: FERRITIN HOMOLOG
C: FERRITIN HOMOLOG
D: FERRITIN HOMOLOG
E: FERRITIN HOMOLOG
F: FERRITIN HOMOLOG
S: FERRITIN HOMOLOG
T: FERRITIN HOMOLOG
U: FERRITIN HOMOLOG
V: FERRITIN HOMOLOG
W: FERRITIN HOMOLOG
X: FERRITIN HOMOLOG
hetero molecules

A: FERRITIN HOMOLOG
B: FERRITIN HOMOLOG
C: FERRITIN HOMOLOG
D: FERRITIN HOMOLOG
E: FERRITIN HOMOLOG
F: FERRITIN HOMOLOG
S: FERRITIN HOMOLOG
T: FERRITIN HOMOLOG
U: FERRITIN HOMOLOG
V: FERRITIN HOMOLOG
W: FERRITIN HOMOLOG
X: FERRITIN HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)494,129118
Polymers487,99524
Non-polymers6,13494
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)254.301, 342.878, 266.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T
211U
221V
231W
241X
251Y
261Z
2710
2811
2912
3013
3114
3215
3316
3417
3518
3619

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLUAK1717
21GLUGLUGLUGLUBL1717
31GLUGLUGLUGLUCM1717
41GLUGLUGLUGLUDN1717
51GLUGLUGLUGLUEO1717
61GLUGLUGLUGLUFP1717
71GLUGLUGLUGLUGQ1717
81GLUGLUGLUGLUHR1717
91GLUGLUGLUGLUIS1717
101GLUGLUGLUGLUJT1717
111GLUGLUGLUGLUKU1717
121GLUGLUGLUGLULV1717
131GLUGLUGLUGLUMW1717
141GLUGLUGLUGLUNX1717
151GLUGLUGLUGLUOY1717
161GLUGLUGLUGLUPZ1717
171GLUGLUGLUGLUQAA1717
181GLUGLUGLUGLURBA1717
194GLUGLUGLUGLUSCA1717
204GLUGLUGLUGLUTDA1717
214GLUGLUGLUGLUUEA1717
224GLUGLUGLUGLUVFA1717
234GLUGLUGLUGLUWGA1717
244GLUGLUGLUGLUXHA1717
254GLUGLUGLUGLUYIA1717
264GLUGLUGLUGLUZJA1717
274GLUGLUGLUGLU0A1717
284GLUGLUGLUGLU1B1717
294GLUGLUGLUGLU2C1717
304GLUGLUGLUGLU3D1717
314GLUGLUGLUGLU4E1717
324GLUGLUGLUGLU5F1717
334GLUGLUGLUGLU6G1717
344GLUGLUGLUGLU7H1717
354GLUGLUGLUGLU8I1717
364GLUGLUGLUGLU9J1717
12GLUGLUHISHISAK49 - 5349 - 53
22GLUGLUHISHISBL49 - 5349 - 53
32GLUGLUHISHISCM49 - 5349 - 53
42GLUGLUHISHISDN49 - 5349 - 53
52GLUGLUHISHISEO49 - 5349 - 53
62GLUGLUHISHISFP49 - 5349 - 53
72GLUGLUHISHISGQ49 - 5349 - 53
82GLUGLUHISHISHR49 - 5349 - 53
92GLUGLUHISHISIS49 - 5349 - 53
102GLUGLUHISHISJT49 - 5349 - 53
112GLUGLUHISHISKU49 - 5349 - 53
122GLUGLUHISHISLV49 - 5349 - 53
132GLUGLUHISHISMW49 - 5349 - 53
142GLUGLUHISHISNX49 - 5349 - 53
152GLUGLUHISHISOY49 - 5349 - 53
162GLUGLUHISHISPZ49 - 5349 - 53
172GLUGLUHISHISQAA49 - 5349 - 53
182GLUGLUHISHISRBA49 - 5349 - 53
195GLUGLUHISHISSCA49 - 5349 - 53
205GLUGLUHISHISTDA49 - 5349 - 53
215GLUGLUHISHISUEA49 - 5349 - 53
225GLUGLUHISHISVFA49 - 5349 - 53
235GLUGLUHISHISWGA49 - 5349 - 53
245GLUGLUHISHISXHA49 - 5349 - 53
255GLUGLUHISHISYIA49 - 5349 - 53
265GLUGLUHISHISZJA49 - 5349 - 53
275GLUGLUHISHIS0A49 - 5349 - 53
285GLUGLUHISHIS1B49 - 5349 - 53
295GLUGLUHISHIS2C49 - 5349 - 53
305GLUGLUHISHIS3D49 - 5349 - 53
315GLUGLUHISHIS4E49 - 5349 - 53
325GLUGLUHISHIS5F49 - 5349 - 53
335GLUGLUHISHIS6G49 - 5349 - 53
345GLUGLUHISHIS7H49 - 5349 - 53
355GLUGLUHISHIS8I49 - 5349 - 53
365GLUGLUHISHIS9J49 - 5349 - 53
13GLUGLUGLUGLUAK126 - 130126 - 130
23GLUGLUGLUGLUBL126 - 130126 - 130
33GLUGLUGLUGLUCM126 - 130126 - 130
43GLUGLUGLUGLUDN126 - 130126 - 130
53GLUGLUGLUGLUEO126 - 130126 - 130
63GLUGLUGLUGLUFP126 - 130126 - 130
73GLUGLUGLUGLUGQ126 - 130126 - 130
83GLUGLUGLUGLUHR126 - 130126 - 130
93GLUGLUGLUGLUIS126 - 130126 - 130
103GLUGLUGLUGLUJT126 - 130126 - 130
113GLUGLUGLUGLUKU126 - 130126 - 130
123GLUGLUGLUGLULV126 - 130126 - 130
133GLUGLUGLUGLUMW126 - 130126 - 130
143GLUGLUGLUGLUNX126 - 130126 - 130
153GLUGLUGLUGLUOY126 - 130126 - 130
163GLUGLUGLUGLUPZ126 - 130126 - 130
173GLUGLUGLUGLUQAA126 - 130126 - 130
183GLUGLUGLUGLURBA126 - 130126 - 130
196GLUGLUGLUGLUSCA126 - 130126 - 130
206GLUGLUGLUGLUTDA126 - 130126 - 130
216GLUGLUGLUGLUUEA126 - 130126 - 130
226GLUGLUGLUGLUVFA126 - 130126 - 130
236GLUGLUGLUGLUWGA126 - 130126 - 130
246GLUGLUGLUGLUXHA126 - 130126 - 130
256GLUGLUGLUGLUYIA126 - 130126 - 130
266GLUGLUGLUGLUZJA126 - 130126 - 130
276GLUGLUGLUGLU0A126 - 130126 - 130
286GLUGLUGLUGLU1B126 - 130126 - 130
296GLUGLUGLUGLU2C126 - 130126 - 130
306GLUGLUGLUGLU3D126 - 130126 - 130
316GLUGLUGLUGLU4E126 - 130126 - 130
326GLUGLUGLUGLU5F126 - 130126 - 130
336GLUGLUGLUGLU6G126 - 130126 - 130
346GLUGLUGLUGLU7H126 - 130126 - 130
356GLUGLUGLUGLU8I126 - 130126 - 130
366GLUGLUGLUGLU9J126 - 130126 - 130
17GLUGLUGLUGLUAK9494
27GLUGLUGLUGLUBL9494
37GLUGLUGLUGLUCM9494
47GLUGLUGLUGLUDN9494
57GLUGLUGLUGLUEO9494
67GLUGLUGLUGLUFP9494
77GLUGLUGLUGLUGQ9494
87GLUGLUGLUGLUHR9494
97GLUGLUGLUGLUIS9494
107GLUGLUGLUGLUJT9494
117GLUGLUGLUGLUKU9494
127GLUGLUGLUGLULV9494
137GLUGLUGLUGLUMW9494
147GLUGLUGLUGLUNX9494
157GLUGLUGLUGLUOY9494
167GLUGLUGLUGLUPZ9494
177GLUGLUGLUGLUQAA9494
187GLUGLUGLUGLURBA9494
198GLUGLUGLUGLUSCA9494
208GLUGLUGLUGLUTDA9494
218GLUGLUGLUGLUUEA9494
228GLUGLUGLUGLUVFA9494
238GLUGLUGLUGLUWGA9494
248GLUGLUGLUGLUXHA9494
258GLUGLUGLUGLUYIA9494
268GLUGLUGLUGLUZJA9494
278GLUGLUGLUGLU0A9494
288GLUGLUGLUGLU1B9494
298GLUGLUGLUGLU2C9494
308GLUGLUGLUGLU3D9494
318GLUGLUGLUGLU4E9494
328GLUGLUGLUGLU5F9494
338GLUGLUGLUGLU6G9494
348GLUGLUGLUGLU7H9494
358GLUGLUGLUGLU8I9494
368GLUGLUGLUGLU9J9494
19FEFEFEFEATB - VB201 - 203
29FEFEFEFEBXB - ZB201 - 203
39FEFEFEFECCC - EC201 - 203
49FEFEFEFEDIC - KC201 - 203
59FEFEFEFEELC - NC201 - 203
69FEFEFEFEFOC - QC201 - 203
79FEFEFEFEGRC - TC201 - 203
89FEFEFEFEHWC - YC201 - 203
99FEFEFEFEIAD - CD201 - 203
109FEFEFEFEJFD - HD201 - 203
119FEFEFEFEKJD - LD201 - 203
129FEFEFEFELMD - OD201 - 203
139FEFEFEFEMPD - RD201 - 203
149FEFEFEFENSD - UD201 - 203
159FEFEFEFEOVD - XD201 - 203
169FEFEFEFEPZD - BE201 - 203
179FEFEFEFEQCE - EE201 - 203
189FEFEFEFERFE - HE201 - 203
1910FEFEFEFESJE - LE201 - 203
2010FEFEFEFETNE - PE201 - 203
2110FEFEFEFEURE - TE201 - 203
2210FEFEFEFEVUE - WE201 - 203
2310FEFEFEFEWZE - BF201 - 203
2410FEFEFEFEXDF - FF201 - 203
2510FEFEFEFEYGF - IF201 - 203
2610FEFEFEFEZLF - NF201 - 203
2710FEFEFEFE0KA - MA201 - 203
2810FEFEFEFE1NA - PA201 - 203
2910FEFEFEFE2RA - TA201 - 203
3010FEFEFEFE3VA - XA201 - 203
3110FEFEFEFE4AB - CB201 - 203
3210FEFEFEFE5DB - FB201 - 203
3310FEFEFEFE6GB - IB201 - 203
3410FEFEFEFE7JB - LB201 - 203
3510FEFEFEFE8MB - OB201 - 203
3610FEFEFEFE9QB - SB201 - 203

-
Components

#1: Protein ...
FERRITIN HOMOLOG / FERRITIN


Mass: 20333.123 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8U2T8
#2: Chemical...
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 108 / Source method: obtained synthetically / Formula: Fe
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69 %
Crystal growDetails: THE CRYSTALS USED FOR DATA COLLECTION WERE GROWN AGAINST 0.5 ML OF 2 M AMMONIUM SULPHATE RESERVOIR SOLUTION, WITH DROPS CONTAINING 2 MICRO-L OF 5 MG/ML PROTEIN SOLUTION IN 50 MM HEPES, PH 7 ...Details: THE CRYSTALS USED FOR DATA COLLECTION WERE GROWN AGAINST 0.5 ML OF 2 M AMMONIUM SULPHATE RESERVOIR SOLUTION, WITH DROPS CONTAINING 2 MICRO-L OF 5 MG/ML PROTEIN SOLUTION IN 50 MM HEPES, PH 7 AND EQUAL AMOUNT OF THE RESERVOIR SOLUTION. IRON SOAKING OF FERRITIN CRYSTALS WAS PERFORMED BY TRANSFERRING THEM TO A 10-20 MICRO-L DROP OF A SOLUTION WITH COMPOSITION 20 MM FESO4, 2 MM NA2S2O4, 25 % GLYCEROL AND 2 M AMMONIUM SULFATE, FOR 15 MINUTES.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.4585
DetectorType: MARRSEARCH / Detector: CCD / Date: Jun 25, 2006 / Details: COLLIMATING AND FOCUSSING MIRRO
RadiationMonochromator: CHANNEL-CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4585 Å / Relative weight: 1
ReflectionResolution: 2.8→42 Å / Num. obs: 280407 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 60.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 94.1

-
Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: REFINED 2JD6 COORDINATES

2jd6


Resolution: 2.8→204.12 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.888 / SU B: 11.01 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.503 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ELECTRON DENSITY FOR C-TERMINAL RESIDU BEYOND 167 (667) WAS NOT VISIBLE.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 14187 5.1 %RANDOM
Rwork0.199 ---
obs0.201 266173 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2---1.4 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.8→204.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49788 0 238 368 50394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02251170
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.97868946
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46955982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27124.7362667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.208159363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.23915252
X-RAY DIFFRACTIONr_chiral_restr0.1010.26987
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0239300
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.225167
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.234930
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.21605
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.2133
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.084330917
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3744.548006
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.847623570
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.241920937
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 208 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.050.05
3Ctight positional0.050.05
4Dtight positional0.050.05
5Etight positional0.050.05
6Ftight positional0.050.05
7Gtight positional0.050.05
8Htight positional0.050.05
9Itight positional0.050.05
10Jtight positional0.050.05
11Ktight positional0.050.05
12Ltight positional0.050.05
13Mtight positional0.050.05
14Ntight positional0.050.05
15Otight positional0.050.05
16Ptight positional0.050.05
17Qtight positional0.050.05
18Rtight positional0.050.05
19Stight positional0.050.05
20Ttight positional0.050.05
21Utight positional0.050.05
22Vtight positional0.050.05
23Wtight positional0.050.05
24Xtight positional0.050.05
25Ytight positional0.050.05
26Ztight positional0.050.05
270tight positional0.050.05
281tight positional0.050.05
292tight positional0.050.05
303tight positional0.050.05
314tight positional0.050.05
325tight positional0.050.05
336tight positional0.050.05
347tight positional0.050.05
358tight positional0.050.05
369tight positional0.050.05
1Atight thermal0.190.5
2Btight thermal0.180
3Ctight thermal0.190
4Dtight thermal0.160
5Etight thermal0.210
6Ftight thermal0.170
7Gtight thermal0.190
8Htight thermal0.240
9Itight thermal0.150
10Jtight thermal0.130
11Ktight thermal0.170
12Ltight thermal0.120
13Mtight thermal0.180
14Ntight thermal0.160
15Otight thermal0.230
16Ptight thermal0.180
17Qtight thermal0.150
18Rtight thermal0.180
19Stight thermal0.190.5
20Ttight thermal0.180
21Utight thermal0.190
22Vtight thermal0.160
23Wtight thermal0.210
24Xtight thermal0.170
25Ytight thermal0.190
26Ztight thermal0.240
270tight thermal0.150
281tight thermal0.130
292tight thermal0.170
303tight thermal0.120
314tight thermal0.180
325tight thermal0.160
336tight thermal0.230
347tight thermal0.180
358tight thermal0.150
369tight thermal0.180
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 983
Rwork0.314 17823

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more