[English] 日本語
Yorodumi
- PDB-3sqb: Structure of the major type 1 pilus subunit FimA bound to the Fim... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sqb
TitleStructure of the major type 1 pilus subunit FimA bound to the FimC chaperone
Components
  • Chaperone protein fimC
  • Type-1 fimbrial protein, A chain
KeywordsSTRUCTURAL PROTEIN/CHAPERONE / immunoglobin-like fold / involved in type 1 pilus assembly / STRUCTURAL PROTEIN-CHAPERONE complex
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / : / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion / identical protein binding
Similarity search - Function
Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily ...Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Type-1 fimbrial protein, A chain / Chaperone protein FimC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsScharer, M.A. / Eidam, O. / Grutter, M.G. / Glockshuber, R. / Capitani, G.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: Quality control of disulfide bond formation in pilus subunits by the chaperone FimC.
Authors: Crespo, M.D. / Puorger, C. / Scharer, M.A. / Eidam, O. / Grutter, M.G. / Capitani, G. / Glockshuber, R.
History
DepositionJul 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chaperone protein fimC
B: Type-1 fimbrial protein, A chain
C: Chaperone protein fimC
D: Type-1 fimbrial protein, A chain
E: Chaperone protein fimC
F: Type-1 fimbrial protein, A chain
G: Chaperone protein fimC
H: Type-1 fimbrial protein, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,52915
Polymers155,8428
Non-polymers6877
Water86548
1
A: Chaperone protein fimC
B: Type-1 fimbrial protein, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2795
Polymers38,9612
Non-polymers3183
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-7 kcal/mol
Surface area15760 Å2
MethodPISA
2
C: Chaperone protein fimC
D: Type-1 fimbrial protein, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3296
Polymers38,9612
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-9 kcal/mol
Surface area15750 Å2
MethodPISA
3
E: Chaperone protein fimC
F: Type-1 fimbrial protein, A chain


Theoretical massNumber of molelcules
Total (without water)38,9612
Polymers38,9612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-13 kcal/mol
Surface area13500 Å2
MethodPISA
4
G: Chaperone protein fimC
H: Type-1 fimbrial protein, A chain


Theoretical massNumber of molelcules
Total (without water)38,9612
Polymers38,9612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-7 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.620, 142.180, 171.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
12D
22B
13C
23E
33G
14D
24F
15D
25H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain C and (resseq 5:23 or resseq 31:93 or resseq...C5 - 23
121chain C and (resseq 5:23 or resseq 31:93 or resseq...C31 - 93
131chain C and (resseq 5:23 or resseq 31:93 or resseq...C110 - 122
141chain C and (resseq 5:23 or resseq 31:93 or resseq...C130 - 175
151chain C and (resseq 5:23 or resseq 31:93 or resseq...C185 - 203
211chain A and (resseq 5:23 or resseq 31:93 or resseq...A5 - 23
221chain A and (resseq 5:23 or resseq 31:93 or resseq...A31 - 93
231chain A and (resseq 5:23 or resseq 31:93 or resseq...A110 - 122
241chain A and (resseq 5:23 or resseq 31:93 or resseq...A130 - 175
251chain A and (resseq 5:23 or resseq 31:93 or resseq...A185 - 203
112chain D and (resseq 17:24 or resseq 29:123 or resseq...D17 - 24
122chain D and (resseq 17:24 or resseq 29:123 or resseq...D29 - 123
132chain D and (resseq 17:24 or resseq 29:123 or resseq...D129 - 139
212chain B and (resseq 17:24 or resseq 29:123 or resseq...B17 - 24
222chain B and (resseq 17:24 or resseq 29:123 or resseq...B29 - 123
232chain B and (resseq 17:24 or resseq 29:123 or resseq...B129 - 139
113chain C and (resseq 1:73 or resseq 83:92 or resseq 101:136 )C1 - 73
123chain C and (resseq 1:73 or resseq 83:92 or resseq 101:136 )C83 - 92
133chain C and (resseq 1:73 or resseq 83:92 or resseq 101:136 )C101 - 136
213chain E and (resseq 1:70 or resseq 83:92 or resseq 101:136 )E1 - 70
223chain E and (resseq 1:70 or resseq 83:92 or resseq 101:136 )E83 - 92
233chain E and (resseq 1:70 or resseq 83:92 or resseq 101:136 )E101 - 136
313chain G and (resseq 1:73 or resseq 83:92 or resseq 102:117 )G1 - 73
323chain G and (resseq 1:73 or resseq 83:92 or resseq 102:117 )G83 - 92
333chain G and (resseq 1:73 or resseq 83:92 or resseq 102:117 )G102 - 117
114chain D and (resseq 18:25 or resseq 29:37 or resseq 48:119 or resseq 129:137 or resseq 149:158 )D18 - 25
124chain D and (resseq 18:25 or resseq 29:37 or resseq 48:119 or resseq 129:137 or resseq 149:158 )D29 - 37
134chain D and (resseq 18:25 or resseq 29:37 or resseq 48:119 or resseq 129:137 or resseq 149:158 )D48 - 119
144chain D and (resseq 18:25 or resseq 29:37 or resseq 48:119 or resseq 129:137 or resseq 149:158 )D129 - 137
154chain D and (resseq 18:25 or resseq 29:37 or resseq 48:119 or resseq 129:137 or resseq 149:158 )D149 - 158
214chain F and (resseq 18:25 or resseq 29:37 or resseq 48:119 or resseq 129:137 or resseq 149:158 )F18 - 25
224chain F and (resseq 18:25 or resseq 29:37 or resseq 48:119 or resseq 129:137 or resseq 149:158 )F29 - 37
234chain F and (resseq 18:25 or resseq 29:37 or resseq 48:119 or resseq 129:137 or resseq 149:158 )F48 - 119
244chain F and (resseq 18:25 or resseq 29:37 or resseq 48:119 or resseq 129:137 or resseq 149:158 )F129 - 137
254chain F and (resseq 18:25 or resseq 29:37 or resseq 48:119 or resseq 129:137 or resseq 149:158 )F149 - 158
115chain D and (resseq 18:25 or resseq 29:37 or resseq...D18 - 25
125chain D and (resseq 18:25 or resseq 29:37 or resseq...D29 - 37
135chain D and (resseq 18:25 or resseq 29:37 or resseq...D48 - 119
145chain D and (resseq 18:25 or resseq 29:37 or resseq...D123 - 124
155chain D and (resseq 18:25 or resseq 29:37 or resseq...D129 - 137
165chain D and (resseq 18:25 or resseq 29:37 or resseq...D149 - 159
215chain H and (resseq 18:25 or resseq 29:37 or resseq...H18 - 25
225chain H and (resseq 18:25 or resseq 29:37 or resseq...H29 - 37
235chain H and (resseq 18:25 or resseq 29:37 or resseq...H48 - 119
245chain H and (resseq 18:25 or resseq 29:37 or resseq...H123 - 124
255chain H and (resseq 18:25 or resseq 29:37 or resseq...H129 - 137
265chain H and (resseq 18:25 or resseq 29:37 or resseq...H149 - 159

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(-0.613277, 0.507624, 0.605152), (-0.404084, 0.456663, -0.792575), (-0.678681, -0.7306, -0.074938)57.580898, -29.633699, 5.34699
2given(-0.560904, 0.514493, 0.648602), (-0.417791, 0.500459, -0.758282), (-0.714729, -0.696303, -0.065759)56.660702, -27.167101, 8.0676
3given(0.584875, 0.669279, -0.458244), (0.397537, 0.255923, 0.881174), (0.707026, -0.697545, -0.11638)10.0167, 29.8234, -19.8197
4given(-0.99998, -0.000225, -0.006376), (-0.002046, 0.957876, 0.287175), (0.006043, 0.287182, -0.957857)23.0611, 22.693899, -72.037804
5given(0.561011, 0.678382, -0.47441), (0.401726, 0.277976, 0.872551), (0.723798, -0.680093, -0.116576)8.82329, 29.993299, -18.8909
6given(-0.999935, 0.011444, 3.96102), (0.010942, 0.954976, 0.296482), (0.003355, 0.296463, -0.955038)24.318899, 23.1724, -71.3563

-
Components

-
Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Chaperone protein fimC


Mass: 23582.914 Da / Num. of mol.: 4 / Fragment: UNP residues 37-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b4316, fimC, JW4279 / Plasmid: pfimChis-cyt / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31697
#2: Protein
Type-1 fimbrial protein, A chain / Type-1A pilin


Mass: 15377.686 Da / Num. of mol.: 4 / Fragment: UNP residues 37-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b4314, fimA, JW4277, pilA / Plasmid: pfimAt-cyt / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04128

-
Non-polymers , 4 types, 55 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsFOR CHAINS B,D,F,H: THE FIRST 13 RESIDUES OF FIMA WERE REMOVED FROM THE CONSTRUCT AND REPLACED BY A ...FOR CHAINS B,D,F,H: THE FIRST 13 RESIDUES OF FIMA WERE REMOVED FROM THE CONSTRUCT AND REPLACED BY A (HIS)6-TAG DIRECTLY BEFORE RESIDUE 14.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium acetate, 0.2 M magnesium chloride, 13% PEG 4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 90.6 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.071 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2006 / Details: dynamically bendable mirror
RadiationMonochromator: LN2-cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071 Å / Relative weight: 1
ReflectionResolution: 3.2→60 Å / Num. obs: 32913 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 10.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.2-3.30.7692.3419430284099.9
3.3-3.80.4364.61745351022499.9
3.8-40.2777.719635274099.7
4-50.12613.82600358218100
5-60.09817.29259433662100
6-80.08418.63204112972100
8-100.06822.4668571084100
10-200.05823.346113103499.3
20-300.0592254410793
30-400.0616.29652365.7
40-500.05714.158440
500.07910.677527.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å29.61 Å
Translation3.2 Å29.61 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BWU

3bwu


Resolution: 3.2→58.386 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.96 / Isotropic thermal model: isotropic / σ(F): 1.99 / Phase error: 29.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3004 1021 3.11 %random
Rwork0.2605 ---
obs0.2617 32880 99.84 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 86.253 Å2 / ksol: 0.296 e/Å3
Displacement parametersBiso max: 264.09 Å2 / Biso mean: 103.8051 Å2 / Biso min: 27.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.6446 Å20 Å2-0 Å2
2--3.8113 Å2-0 Å2
3----3.1667 Å2
Refinement stepCycle: LAST / Resolution: 3.2→58.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7747 0 45 48 7840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057878
X-RAY DIFFRACTIONf_angle_d0.82710743
X-RAY DIFFRACTIONf_chiral_restr0.0711331
X-RAY DIFFRACTIONf_plane_restr0.0031407
X-RAY DIFFRACTIONf_dihedral_angle_d13.6612630
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C1178X-RAY DIFFRACTIONPOSITIONAL0.046
12A1178X-RAY DIFFRACTIONPOSITIONAL0.046
21D778X-RAY DIFFRACTIONPOSITIONAL0.066
22B778X-RAY DIFFRACTIONPOSITIONAL0.066
31C748X-RAY DIFFRACTIONPOSITIONAL0.09
32E748X-RAY DIFFRACTIONPOSITIONAL0.09
33G480X-RAY DIFFRACTIONPOSITIONAL0.063
41D528X-RAY DIFFRACTIONPOSITIONAL0.033
42F528X-RAY DIFFRACTIONPOSITIONAL0.033
51D402X-RAY DIFFRACTIONPOSITIONAL0.024
52H402X-RAY DIFFRACTIONPOSITIONAL0.024
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
3.2-3.36870.32621420.2822444245844584100
3.3687-3.57970.35741450.2839450946544654100
3.5797-3.85610.32271430.2946448646294629100
3.8561-4.2440.28441440.2414450446484648100
4.244-4.85790.25481460.208455547014703100
4.8579-6.11940.25471480.2395460947574757100
6.1194-58.39570.33991530.291547544907490799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2099-0.786-0.95761.4734-1.37932.91940.00880.8356-0.5641-0.90030.39550.15160.4077-0.337-0.1770.7022-0.0840.03560.5624-0.25610.278332.8558-32.8936-33.0924
20.55510.9771-0.62533.0170.90893.6614-0.36450.3885-0.0998-0.78880.3168-0.0426-0.1468-0.10740.02910.5629-0.0198-0.00160.3566-0.03090.202237.118-25.7983-26.133
30.0938-0.0103-0.0750.00070.00880.062-0.19420.40340.2083-0.1591-0.05690.05860.07790.0294-0.04421.5922-0.4561-0.57091.33990.23750.760422.1994-23.3217-50.8583
42.6481.8998-1.74075.708-1.93014.6688-0.0911.23451.7761-0.2522-0.08230.10370.0472-0.15050.09481.03410.0498-0.47640.87780.47821.215921.9513-6.0207-44.2048
57.0748-5.33530.60874.44150.34331.63890.00721.51461.3362-2.2304-0.0776-0.4195-0.4443-0.32360.03611.1706-0.1866-0.27941.14010.36340.703730.9483-11.9734-47.2336
63.69210.78740.85213.31061.24595.03420.07170.3410.053-0.537-0.0453-0.7499-0.07880.58-0.0280.4545-0.05480.08870.26290.11160.429949.8809-10.6924-17.9016
74.62913.23634.43095.21415.68359.32310.1370.11050.0771-0.75190.0869-0.00820.2347-0.6253-0.3230.62940.01990.05490.46370.12950.405342.2525-14.1932-26.1497
81.2547-1.6841-1.4335.18160.52842.3184-0.0054-0.4575-0.0770.74080.1234-0.0695-0.2326-0.3433-0.09240.313-0.0686-0.0410.35240.06140.53280.5478-31.80459.6651
93.0848-0.4264-1.83690.941-1.47345.15850.0952-0.0333-0.1947-0.02990.09650.22180.40570.0956-0.17390.38690.0678-0.07670.20450.09650.56376.104-34.81271.6301
109.11084.9057-7.89996.6566-2.11238.29921.0889-0.83330.9281.8983-0.21650.6504-2.0025-0.9003-0.89480.8675-0.23760.25120.7383-0.08790.73810.994-8.719910.7081
112.06790.90850.21244.10980.13152.6115-0.08390.25440.5487-0.11660.1128-0.2104-0.59790.3637-0.09320.8235-0.32890.19520.2346-0.24331.020914.3916-6.0024-3.2602
121.77071.1251-1.35128.3527-3.97827.03210.34410.08031.4710.18770.36280.8826-0.5316-0.3064-0.6330.41550.04920.00230.45990.01661.1395.1501-8.8415-4.6972
139.0676-2.8842-4.11813.96142.25235.0187-0.01970.686-0.9327-0.6089-0.22150.69880.3494-0.42980.17080.666-0.179-0.1870.53650.03610.486411.3612-39.5599-18.5815
148.5341-5.3949-2.78925.53384.27574.408-0.1877-0.43750.651-0.77490.4314-0.4582-0.1141-0.3991-0.17790.6815-0.0499-0.02130.33770.13650.59428.9207-32.1226-10.7096
153.7532-2.9019-3.37583.13441.77823.8206-0.27610.8876-1.51310.21170.50520.1402-0.09480.4459-0.24310.82670.01430.04432.189-0.25650.8138-11.2467-41.9922-53.8106
161.9630.06982.91281.2552-0.19716.9721-0.0942-0.3131-0.0840.08210.1620.65130.2433-0.72190.35070.9572-0.14920.04672.6402-0.46240.1251-14.6484-33.714-58.8752
172.6912.3348-0.63046.1941-6.58188.8885-0.3963-0.1987-0.23640.17540.4855-0.25110.93482.22130.04570.8464-0.01920.10243.34370.2510.7851.4658-37.5339-34.3478
182.893-3.0516-0.18294.7315-0.00290.0342-0.1245-0.10840.68531.8368-0.9319-1.1218-0.90570.26111.01411.2353-0.155-0.30352.16910.08880.66121.3433-20.6258-36.0683
192.4023-0.25941.0528.42845.33284.00050.6006-0.5743-0.16290.972-1.59890.5802-0.2554-0.13960.92691.17140.05950.00281.6753-0.15890.5091-7.5685-25.4529-33.8441
202.2047-0.89330.13212.9846-0.49135.3478-0.6817-0.0357-0.14470.50670.69380.4479-1.793-0.04250.04261.24890.0954-0.03981.703-0.20470.6201-27.3189-21.3466-55.0779
214.3042-2.72665.14027.8232-6.01188.44930.2949-0.01310.04941.1039-0.1079-0.3826-1.68520.5157-0.20011.2148-0.22450.08351.7436-0.18870.5635-18.5071-23.4651-53.7921
221.598-0.0953-0.75410.26420.97883.64640.3226-0.9219-0.04380.0997-0.2424-0.3524-0.2431.8629-0.09730.7840.03280.10213.2181-0.61850.816424.3821-31.8901-93.1697
233.43851.6837-3.61590.9568-1.74319.784-0.5012-1.2615-0.05650.37970.0134-0.51220.70472.04540.1320.9484-0.1310.09572.3776-0.77690.833217.6498-36.8122-86.1883
242.237-0.4619-1.35123.97570.13330.8452-0.462-0.3258-1.12520.39120.0027-0.7030.05571.68940.57130.78940.0890.12142.7698-0.07020.8659.8987-45.5553-68.6758
251.30550.2293-0.76921.52540.99842.2628-0.6524-0.7413-0.60490.16670.3956-0.30160.07970.93390.24460.9163-0.13690.46362.2682-0.36140.82413.0822-39.0277-75.2463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and (resid 1: 25 or resid 46: 52 or resid 60: 75))A1 - 25
2X-RAY DIFFRACTION1(chain A and (resid 1: 25 or resid 46: 52 or resid 60: 75))A46 - 52
3X-RAY DIFFRACTION1(chain A and (resid 1: 25 or resid 46: 52 or resid 60: 75))A60 - 75
4X-RAY DIFFRACTION2(chain A and (resid 53: 59 or resid 26: 45 or resid 76:116))A53 - 59
5X-RAY DIFFRACTION2(chain A and (resid 53: 59 or resid 26: 45 or resid 76:116))A26 - 45
6X-RAY DIFFRACTION2(chain A and (resid 53: 59 or resid 26: 45 or resid 76:116))A76 - 116
7X-RAY DIFFRACTION3(chain A and (resid 117:130))A117 - 130
8X-RAY DIFFRACTION4(chain A and (resid 131:147 or resid 168:182))A131 - 147
9X-RAY DIFFRACTION4(chain A and (resid 131:147 or resid 168:182))A168 - 182
10X-RAY DIFFRACTION5(chain A and (resid 148:167 or resid 183:206))A148 - 167
11X-RAY DIFFRACTION5(chain A and (resid 148:167 or resid 183:206))A183 - 206
12X-RAY DIFFRACTION6(chain B and (resid 1: 59 or resid 79:110 or resid 121:144))B1 - 59
13X-RAY DIFFRACTION6(chain B and (resid 1: 59 or resid 79:110 or resid 121:144))B79 - 110
14X-RAY DIFFRACTION6(chain B and (resid 1: 59 or resid 79:110 or resid 121:144))B121 - 144
15X-RAY DIFFRACTION7(chain B and (resid 60: 76 or resid 111:120 or resid 145:159))B60 - 76
16X-RAY DIFFRACTION7(chain B and (resid 60: 76 or resid 111:120 or resid 145:159))B111 - 120
17X-RAY DIFFRACTION7(chain B and (resid 60: 76 or resid 111:120 or resid 145:159))B145 - 159
18X-RAY DIFFRACTION8(chain C and (resid 1: 25 or resid 46: 52 or resid 60: 75))C1 - 25
19X-RAY DIFFRACTION8(chain C and (resid 1: 25 or resid 46: 52 or resid 60: 75))C46 - 52
20X-RAY DIFFRACTION8(chain C and (resid 1: 25 or resid 46: 52 or resid 60: 75))C60 - 75
21X-RAY DIFFRACTION9(chain C and (resid 53: 59 or resid 26: 45 or resid 76:116))C53 - 59
22X-RAY DIFFRACTION9(chain C and (resid 53: 59 or resid 26: 45 or resid 76:116))C26 - 45
23X-RAY DIFFRACTION9(chain C and (resid 53: 59 or resid 26: 45 or resid 76:116))C76 - 116
24X-RAY DIFFRACTION10(chain C and (resid 117:130))C117 - 130
25X-RAY DIFFRACTION11(chain C and (resid 131:147 or resid 168:182))C131 - 147
26X-RAY DIFFRACTION11(chain C and (resid 131:147 or resid 168:182))C168 - 182
27X-RAY DIFFRACTION12(chain C and (resid 148:167 or resid 183:206))C148 - 167
28X-RAY DIFFRACTION12(chain C and (resid 148:167 or resid 183:206))C183 - 206
29X-RAY DIFFRACTION13(chain D and (resid 1: 59 or resid 79:110 or resid 121:144))D1 - 59
30X-RAY DIFFRACTION13(chain D and (resid 1: 59 or resid 79:110 or resid 121:144))D79 - 110
31X-RAY DIFFRACTION13(chain D and (resid 1: 59 or resid 79:110 or resid 121:144))D121 - 144
32X-RAY DIFFRACTION14(chain D and (resid 60: 76 or resid 111:120 or resid 145:159))D60 - 76
33X-RAY DIFFRACTION14(chain D and (resid 60: 76 or resid 111:120 or resid 145:159))D111 - 120
34X-RAY DIFFRACTION14(chain D and (resid 60: 76 or resid 111:120 or resid 145:159))D145 - 159
35X-RAY DIFFRACTION15(chain E and (resid 1: 25 or resid 46: 52 or resid 60: 75))E1 - 25
36X-RAY DIFFRACTION15(chain E and (resid 1: 25 or resid 46: 52 or resid 60: 75))E46 - 52
37X-RAY DIFFRACTION15(chain E and (resid 1: 25 or resid 46: 52 or resid 60: 75))E60 - 75
38X-RAY DIFFRACTION16(chain E and (resid 53: 59 or resid 26: 45 or resid 76:116))E53 - 59
39X-RAY DIFFRACTION16(chain E and (resid 53: 59 or resid 26: 45 or resid 76:116))E26 - 45
40X-RAY DIFFRACTION16(chain E and (resid 53: 59 or resid 26: 45 or resid 76:116))E76 - 116
41X-RAY DIFFRACTION17(chain E and (resid 117:130))E117 - 130
42X-RAY DIFFRACTION18(chain E and (resid 131:147 or resid 168:182))E131 - 147
43X-RAY DIFFRACTION18(chain E and (resid 131:147 or resid 168:182))E168 - 182
44X-RAY DIFFRACTION19(chain E and (resid 148:167 or resid 183:206))E148 - 167
45X-RAY DIFFRACTION19(chain E and (resid 148:167 or resid 183:206))E183 - 206
46X-RAY DIFFRACTION20(chain F and (resid 1: 59 or resid 79:110 or resid 121:144))F1 - 59
47X-RAY DIFFRACTION20(chain F and (resid 1: 59 or resid 79:110 or resid 121:144))F79 - 110
48X-RAY DIFFRACTION20(chain F and (resid 1: 59 or resid 79:110 or resid 121:144))F121 - 144
49X-RAY DIFFRACTION21(chain F and (resid 60: 76 or resid 111:120 or resid 145:159))F60 - 76
50X-RAY DIFFRACTION21(chain F and (resid 60: 76 or resid 111:120 or resid 145:159))F111 - 120
51X-RAY DIFFRACTION21(chain F and (resid 60: 76 or resid 111:120 or resid 145:159))F145 - 159
52X-RAY DIFFRACTION22(chain G and (resid 1: 25 or resid 46: 52 or resid 60: 75))G1 - 25
53X-RAY DIFFRACTION22(chain G and (resid 1: 25 or resid 46: 52 or resid 60: 75))G46 - 52
54X-RAY DIFFRACTION22(chain G and (resid 1: 25 or resid 46: 52 or resid 60: 75))G60 - 75
55X-RAY DIFFRACTION23(chain G and (resid 53: 59 or resid 26: 45 or resid 76:116))G53 - 59
56X-RAY DIFFRACTION23(chain G and (resid 53: 59 or resid 26: 45 or resid 76:116))G26 - 45
57X-RAY DIFFRACTION23(chain G and (resid 53: 59 or resid 26: 45 or resid 76:116))G76 - 116
58X-RAY DIFFRACTION24(chain H and (resid 1: 59 or resid 79:110 or resid 121:144))H1 - 59
59X-RAY DIFFRACTION24(chain H and (resid 1: 59 or resid 79:110 or resid 121:144))H79 - 110
60X-RAY DIFFRACTION24(chain H and (resid 1: 59 or resid 79:110 or resid 121:144))H121 - 144
61X-RAY DIFFRACTION25(chain H and (resid 60: 76 or resid 111:120 or resid 145:159))H60 - 76
62X-RAY DIFFRACTION25(chain H and (resid 60: 76 or resid 111:120 or resid 145:159))H111 - 120
63X-RAY DIFFRACTION25(chain H and (resid 60: 76 or resid 111:120 or resid 145:159))H145 - 159

+
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