[English] 日本語
Yorodumi
- PDB-2vat: Crystal structure of deacetylcephalosporin C acetyltransferase in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vat
TitleCrystal structure of deacetylcephalosporin C acetyltransferase in complex with coenzyme A
ComponentsACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
KeywordsTRANSFERASE / ACETYL TRANSFERASE / A/B- HYDROLASE FOLD / ACYLTRANSFERASE / ACETYL COENZYME A / ANTIBIOTIC BIOSYNTHESIS / CEPHALOSPORIN BIOSYNTHESIS
Function / homology
Function and homology information


deacetylcephalosporin-C acetyltransferase / deacetylcephalosporin-C acetyltransferase activity / homoserine metabolic process / homoserine O-acetyltransferase activity / methionine biosynthetic process / antibiotic biosynthetic process
Similarity search - Function
Homoserine/serine acetyltransferase MetX-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / COENZYME A / Acetyl-CoA--deacetylcephalosporin C acetyltransferase
Similarity search - Component
Biological speciesACREMONIUM CHRYSOGENUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsLejon, S. / Ellis, J. / Valegard, K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The Last Step in Cephalosporin C Formation Revealed: Crystal Structures of Deacetylcephalosporin C Acetyltransferase from Acremonium Chrysogenum in Complexes with Reaction Intermediates.
Authors: Lejon, S. / Ellis, J. / Valegard, K.
History
DepositionSep 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
B: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
C: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
D: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
E: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
F: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
G: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
H: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
I: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
J: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
K: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
L: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)600,71538
Polymers590,61212
Non-polymers10,10326
Water28,3381573
1
A: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
I: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1817
Polymers98,4352
Non-polymers1,7455
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-38.9 kcal/mol
Surface area31460 Å2
MethodPISA
2
B: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
E: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1817
Polymers98,4352
Non-polymers1,7455
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-30.1 kcal/mol
Surface area31280 Å2
MethodPISA
3
D: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
K: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0886
Polymers98,4352
Non-polymers1,6534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-24.4 kcal/mol
Surface area31170 Å2
MethodPISA
4
F: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
H: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0886
Polymers98,4352
Non-polymers1,6534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-30.2 kcal/mol
Surface area30580 Å2
MethodPISA
5
G: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
L: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0886
Polymers98,4352
Non-polymers1,6534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-24 kcal/mol
Surface area30380 Å2
MethodPISA
6
C: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
J: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0886
Polymers98,4352
Non-polymers1,6534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-23.5 kcal/mol
Surface area31320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.959, 109.278, 197.001
Angle α, β, γ (deg.)90.00, 90.23, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
12A
22B
32C
42D
52E
62F
72G
82H
92I
102J
112K
122L
13A
23B
33C
43D
53E
63F
73G
83H
93I
103J
113K
123L
14A
24B
34C
44D
54E
64F
74G
84H
94I
104J
114K
124L
15A
25B
35C
45D
55E
65F
75G
85H
95I
105J
115K
125L
16A
26B
36C
46D
56E
66F
76G
86H
96I
106J
116K
126L
17A
27B
37C
47D
57E
67F
77G
87H
97I
107J
117K
127L
18A
28B
38C
48D
58E
68F
78G
88H
98I
108J
118K
128L
19A
29B
39C
49D
59E
69F
79G
89H
99I
109J
119K
129L
110A
210B
310C
410D
510E
610F
710G
810H
910I
1010J
1110K
1210L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A7 - 32
2111B7 - 32
3111C7 - 32
4111D7 - 32
5111E7 - 32
6111F7 - 32
7111G7 - 32
8111H7 - 32
9111I7 - 32
10111J7 - 32
11111K7 - 32
12111L7 - 32
1121A35 - 46
2121B35 - 46
3121C35 - 46
4121D35 - 46
5121E35 - 46
6121F35 - 46
7121G35 - 46
8121H35 - 46
9121I35 - 46
10121J35 - 46
11121K35 - 46
12121L35 - 46
1131A48 - 127
2131B48 - 127
3131C48 - 127
4131D48 - 127
5131E48 - 127
6131F48 - 127
7131G48 - 127
8131H48 - 127
9131I48 - 127
10131J48 - 127
11131K48 - 127
12131L48 - 127
1141A129 - 139
2141B129 - 139
3141C129 - 139
4141D129 - 139
5141E129 - 139
6141F129 - 139
7141G129 - 139
8141H129 - 139
9141I129 - 139
10141J129 - 139
11141K129 - 139
12141L129 - 139
1151A141 - 268
2151B141 - 268
3151C141 - 268
4151D141 - 268
5151E141 - 268
6151F141 - 268
7151G141 - 268
8151H141 - 268
9151I141 - 268
10151J141 - 268
11151K141 - 268
12151L141 - 268
1161A272 - 309
2161B272 - 309
3161C272 - 309
4161D272 - 309
5161E272 - 309
6161F272 - 309
7161G272 - 309
8161H272 - 309
9161I272 - 309
10161J272 - 309
11161K272 - 309
12161L272 - 309
1171A311 - 330
2171B311 - 330
3171C311 - 330
4171D311 - 330
5171E311 - 330
6171F311 - 330
7171G311 - 330
8171H311 - 330
9171I311 - 330
10171J311 - 330
11171K311 - 330
12171L311 - 330
1181A332 - 345
2181B332 - 345
3181C332 - 345
4181D332 - 345
5181E332 - 345
6181F332 - 345
7181G332 - 345
8181H332 - 345
9181I332 - 345
10181J332 - 345
11181K332 - 345
12181L332 - 345
1191A347 - 359
2191B347 - 359
3191C347 - 359
4191D347 - 359
5191E347 - 359
6191F347 - 359
7191G347 - 359
8191H347 - 359
9191I347 - 359
10191J347 - 359
11191K347 - 359
12191L347 - 359
11101A361 - 382
21101B361 - 382
31101C361 - 382
41101D361 - 382
51101E361 - 382
61101F361 - 382
71101G361 - 382
81101H361 - 382
91101I361 - 382
101101J361 - 382
111101K361 - 382
121101L361 - 382

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

NCS oper:
IDCodeMatrixVector
1given(-0.9998, -0.009359, -0.01501), (0.009254, -0.9999, 0.007044), (-0.01507, 0.006904, 0.9999)152.4, 21.19, 1.126
2given(-0.7844, 0.1134, -0.6098), (0.0845, 0.9935, 0.0761), (0.6145, 0.008163, -0.7889)146.4, 0.03458, -20.22
3given(0.7874, -0.116, -0.6054), (-0.08718, -0.9932, 0.07694), (-0.6102, -0.007808, -0.7922)58.8, -24.09, 169.2
4given(1, 0.000224, 0.00149), (0.000226, -1, -0.000907), (0.001489, 0.000907, -1)60.92, 22.17, 98.46
5given(-0.5174, 0.487, 0.7037), (0.3435, 0.8713, -0.3504), (-0.7838, 0.06045, -0.6181)109.6, -8.064, 56.55
6given(0.537, 0.481, 0.693), (0.364, -0.8732, 0.3241), (0.761, 0.07818, -0.644)-9.027, -42.79, 58.66
7given(0.5363, -0.4796, -0.6945), (0.3637, 0.8739, -0.3226), (0.7616, -0.07962, 0.6431)37.05, -52.5, -49.85
8given(-0.9999, 0.0103, 0.01302), (0.01022, 0.9999, -0.006346), (-0.01309, -0.006212, -0.9999)211.7, -0.9462, 100.5
9given(-0.7692, -0.1268, -0.6263), (-0.09399, 0.9919, -0.08534), (0.6321, -0.00677, -0.7749)154.9, 65.11, 42.63
10given(-0.7763, 0.1269, 0.6175), (-0.09495, -0.9919, 0.08441), (0.6232, 0.006894, 0.7821)152.3, -23.86, -70.99
11given(-0.5181, -0.4888, -0.7019), (0.342, -0.8706, 0.3538), (-0.784, -0.05677, 0.6182)220.9, -44.32, 44.42

-
Components

#1: Protein
ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE / DCPC-ATF / DAC ACETYLTRANSFERASE / DAC-AT / DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE


Mass: 49217.633 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACREMONIUM CHRYSOGENUM (fungus) / Plasmid: PTWIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P39058, deacetylcephalosporin-C acetyltransferase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1573 / 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: 2.56 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growDetails: 18-19% PEG 4000, 0.1M IMIDAZOLE, 0.5M NACL, 0.2M SODIUM ACETATE

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-110.934
SYNCHROTRONMAX II I911-320.978
Detector
TypeIDDetectorDateDetails
ADSC CCD1CCDApr 22, 2004TOROIDAL MIRROR
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DIAMOND (111), GE(220)SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
20.9781
ReflectionResolution: 2.2→60.97 Å / Num. obs: 258318 / % possible obs: 98.6 % / Observed criterion σ(I): 6 / Redundancy: 3.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.7 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
autoSHARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.2→122.17 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.616 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 242-267 ARE DISORDERED. ACETYL MOIETY WAS LEFT UNMODELLED. RESIDUAL DENSITY NEAR SER149, POSSIBLY INDICATING MULTIPLE REACTION ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 242-267 ARE DISORDERED. ACETYL MOIETY WAS LEFT UNMODELLED. RESIDUAL DENSITY NEAR SER149, POSSIBLY INDICATING MULTIPLE REACTION STATES WITH PARTIAL OCCUPANCIES, WAS LEFT UNMODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 4405 1.7 %RANDOM
Rwork0.2 ---
obs0.201 253887 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å2-0.09 Å2
2--2.1 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.2→122.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32569 0 636 1573 34778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02234275
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9646567
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22354170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.78222.5821650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.607155393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.72915342
X-RAY DIFFRACTIONr_chiral_restr0.1260.24929
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0226450
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.215329
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.223387
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.21832
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.2274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2810.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0871.521221
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.731233347
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.749314840
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3214.513186
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A194tight positional0.080.05
12B194tight positional0.220.05
13C194tight positional0.090.05
14D194tight positional0.180.05
15E194tight positional0.090.05
16F194tight positional0.080.05
17G194tight positional0.090.05
18H194tight positional0.10.05
19I194tight positional0.090.05
110J194tight positional0.170.05
111K194tight positional0.090.05
112L194tight positional0.080.05
21A98tight positional0.060.05
22B98tight positional0.070.05
23C98tight positional0.060.05
24D98tight positional0.070.05
25E98tight positional0.070.05
26F98tight positional0.080.05
27G98tight positional0.080.05
28H98tight positional0.090.05
29I98tight positional0.070.05
210J98tight positional0.080.05
211K98tight positional0.070.05
212L98tight positional0.080.05
31A557tight positional0.070.05
32B557tight positional0.060.05
33C557tight positional0.090.05
34D557tight positional0.090.05
35E557tight positional0.070.05
36F557tight positional0.080.05
37G557tight positional0.090.05
38H557tight positional0.090.05
39I557tight positional0.060.05
310J557tight positional0.070.05
311K557tight positional0.070.05
312L557tight positional0.080.05
41A75tight positional0.070.05
42B75tight positional0.070.05
43C75tight positional0.070.05
44D75tight positional0.080.05
45E75tight positional0.060.05
46F75tight positional0.090.05
47G75tight positional0.090.05
48H75tight positional0.070.05
49I75tight positional0.070.05
410J75tight positional0.10.05
411K75tight positional0.10.05
412L75tight positional0.090.05
51A757tight positional0.120.05
52B757tight positional0.180.05
53C757tight positional0.170.05
54D757tight positional0.110.05
55E757tight positional0.10.05
56F757tight positional0.160.05
57G757tight positional0.110.05
58H757tight positional0.110.05
59I757tight positional0.10.05
510J757tight positional0.110.05
511K757tight positional0.10.05
512L757tight positional0.090.05
61A295tight positional0.090.05
62B295tight positional0.090.05
63C295tight positional0.10.05
64D295tight positional0.10.05
65E295tight positional0.090.05
66F295tight positional0.090.05
67G295tight positional0.150.05
68H295tight positional0.140.05
69I295tight positional0.080.05
610J295tight positional0.080.05
611K295tight positional0.080.05
612L295tight positional0.090.05
71A136tight positional0.230.05
72B136tight positional0.060.05
73C136tight positional0.060.05
74D136tight positional0.060.05
75E136tight positional0.070.05
76F136tight positional0.060.05
77G136tight positional0.080.05
78H136tight positional0.090.05
79I136tight positional0.060.05
710J136tight positional0.070.05
711K136tight positional0.070.05
712L136tight positional0.060.05
81A110tight positional0.070.05
82B110tight positional0.060.05
83C110tight positional0.070.05
84D110tight positional0.260.05
85E110tight positional0.080.05
86F110tight positional0.080.05
87G110tight positional0.070.05
88H110tight positional0.070.05
89I110tight positional0.060.05
810J110tight positional0.060.05
811K110tight positional0.070.05
812L110tight positional0.070.05
91A97tight positional0.090.05
92B97tight positional0.060.05
93C97tight positional0.080.05
94D97tight positional0.070.05
95E97tight positional0.090.05
96F97tight positional0.080.05
97G97tight positional0.080.05
98H97tight positional0.070.05
99I97tight positional0.060.05
910J97tight positional0.060.05
911K97tight positional0.070.05
912L97tight positional0.080.05
101A163tight positional0.070.05
102B163tight positional0.230.05
103C163tight positional0.210.05
104D163tight positional0.070.05
105E163tight positional0.070.05
106F163tight positional0.070.05
107G163tight positional0.070.05
108H163tight positional0.070.05
109I163tight positional0.080.05
1010J163tight positional0.080.05
1011K163tight positional0.090.05
1012L163tight positional0.070.05
11A194tight thermal0.460.5
12B194tight thermal0.480.5
13C194tight thermal0.250.5
14D194tight thermal0.260.5
15E194tight thermal0.470.5
16F194tight thermal0.40.5
17G194tight thermal0.230.5
18H194tight thermal0.240.5
19I194tight thermal0.490.5
110J194tight thermal0.670.5
111K194tight thermal0.630.5
112L194tight thermal0.40.5
21A98tight thermal0.340.5
22B98tight thermal0.350.5
23C98tight thermal0.380.5
24D98tight thermal0.380.5
25E98tight thermal0.310.5
26F98tight thermal0.320.5
27G98tight thermal0.360.5
28H98tight thermal0.330.5
29I98tight thermal0.370.5
210J98tight thermal0.720.5
211K98tight thermal0.660.5
212L98tight thermal0.310.5
31A557tight thermal0.340.5
32B557tight thermal0.410.5
33C557tight thermal0.360.5
34D557tight thermal0.330.5
35E557tight thermal0.350.5
36F557tight thermal0.330.5
37G557tight thermal0.290.5
38H557tight thermal0.310.5
39I557tight thermal0.40.5
310J557tight thermal0.70.5
311K557tight thermal0.650.5
312L557tight thermal0.330.5
41A75tight thermal0.380.5
42B75tight thermal0.550.5
43C75tight thermal0.350.5
44D75tight thermal0.340.5
45E75tight thermal0.360.5
46F75tight thermal0.290.5
47G75tight thermal0.30.5
48H75tight thermal0.290.5
49I75tight thermal0.510.5
410J75tight thermal0.750.5
411K75tight thermal0.710.5
412L75tight thermal0.320.5
51A757tight thermal0.370.5
52B757tight thermal0.360.5
53C757tight thermal0.280.5
54D757tight thermal0.280.5
55E757tight thermal0.350.5
56F757tight thermal0.280.5
57G757tight thermal0.270.5
58H757tight thermal0.270.5
59I757tight thermal0.370.5
510J757tight thermal0.490.5
511K757tight thermal0.470.5
512L757tight thermal0.290.5
61A295tight thermal0.390.5
62B295tight thermal0.380.5
63C295tight thermal0.30.5
64D295tight thermal0.30.5
65E295tight thermal0.390.5
66F295tight thermal0.320.5
67G295tight thermal0.260.5
68H295tight thermal0.270.5
69I295tight thermal0.430.5
610J295tight thermal0.510.5
611K295tight thermal0.510.5
612L295tight thermal0.360.5
71A136tight thermal0.260.5
72B136tight thermal0.310.5
73C136tight thermal0.260.5
74D136tight thermal0.210.5
75E136tight thermal0.270.5
76F136tight thermal0.20.5
77G136tight thermal0.220.5
78H136tight thermal0.260.5
79I136tight thermal0.310.5
710J136tight thermal0.440.5
711K136tight thermal0.420.5
712L136tight thermal0.240.5
81A110tight thermal0.290.5
82B110tight thermal0.270.5
83C110tight thermal0.270.5
84D110tight thermal0.270.5
85E110tight thermal0.330.5
86F110tight thermal0.250.5
87G110tight thermal0.260.5
88H110tight thermal0.260.5
89I110tight thermal0.290.5
810J110tight thermal0.410.5
811K110tight thermal0.40.5
812L110tight thermal0.260.5
91A97tight thermal0.250.5
92B97tight thermal0.290.5
93C97tight thermal0.250.5
94D97tight thermal0.230.5
95E97tight thermal0.260.5
96F97tight thermal0.20.5
97G97tight thermal0.210.5
98H97tight thermal0.220.5
99I97tight thermal0.240.5
910J97tight thermal0.330.5
911K97tight thermal0.340.5
912L97tight thermal0.220.5
101A163tight thermal0.220.5
102B163tight thermal0.370.5
103C163tight thermal0.270.5
104D163tight thermal0.240.5
105E163tight thermal0.220.5
106F163tight thermal0.240.5
107G163tight thermal0.230.5
108H163tight thermal0.240.5
109I163tight thermal0.350.5
1010J163tight thermal0.450.5
1011K163tight thermal0.490.5
1012L163tight thermal0.210.5
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 321
Rwork0.243 18133

+
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