[English] 日本語
Yorodumi
- PDB-7oka: Crystal structure of Pseudomonas aeruginosa LpxA in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7oka
TitleCrystal structure of Pseudomonas aeruginosa LpxA in complex with compound 14
ComponentsAcyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
KeywordsTRANSFERASE / ACYLTRANSFERASE / FATTY ACIDS / LIPID A / LEFT-HANDED PARALLEL BETA-HELIX
Function / homology
Function and homology information


acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase / acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity / lipid A biosynthetic process / cytoplasm
Similarity search - Function
UDP N-acetylglucosamine O-acyltransferase, C-terminal / UDP-N-acetylglucosamine O-acyltransferase, C-terminal domain superfamily / Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
Chem-VFT / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.74 Å
AuthorsRyan, M.D. / Parkes, A.L. / Southey, M. / Andersen, O.A. / Zahn, M. / Barker, J. / DeJonge, B.L.M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of Novel UDP- N -Acetylglucosamine Acyltransferase (LpxA) Inhibitors with Activity against Pseudomonas aeruginosa .
Authors: Ryan, M.D. / Parkes, A.L. / Corbett, D. / Dickie, A.P. / Southey, M. / Andersen, O.A. / Stein, D.B. / Barbeau, O.R. / Sanzone, A. / Thommes, P. / Barker, J. / Cain, R. / Compper, C. / Dejob, ...Authors: Ryan, M.D. / Parkes, A.L. / Corbett, D. / Dickie, A.P. / Southey, M. / Andersen, O.A. / Stein, D.B. / Barbeau, O.R. / Sanzone, A. / Thommes, P. / Barker, J. / Cain, R. / Compper, C. / Dejob, M. / Dorali, A. / Etheridge, D. / Evans, S. / Faulkner, A. / Gadouleau, E. / Gorman, T. / Haase, D. / Holbrow-Wilshaw, M. / Krulle, T. / Li, X. / Lumley, C. / Mertins, B. / Napier, S. / Odedra, R. / Papadopoulos, K. / Roumpelakis, V. / Spear, K. / Trimby, E. / Williams, J. / Zahn, M. / Keefe, A.D. / Zhang, Y. / Soutter, H.T. / Centrella, P.A. / Clark, M.A. / Cuozzo, J.W. / Dumelin, C.E. / Deng, B. / Hunt, A. / Sigel, E.A. / Troast, D.M. / DeJonge, B.L.M.
History
DepositionMay 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
B: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
C: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
D: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
E: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
F: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
G: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
H: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
I: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
M: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
N: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
O: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
J: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
K: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
L: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
P: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
Q: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
R: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
S: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
T: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
U: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
V: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
W: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
X: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
Y: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
Z: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
a: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
b: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
c: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
d: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)869,402152
Polymers849,93030
Non-polymers19,472122
Water3,963220
1
A: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
B: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
C: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,06919
Polymers84,9933
Non-polymers2,07616
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
E: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
F: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,96316
Polymers84,9933
Non-polymers1,96913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
H: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
I: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,92715
Polymers84,9933
Non-polymers1,93412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
N: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
O: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,90216
Polymers84,9933
Non-polymers1,90913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
J: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
K: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
L: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,89214
Polymers84,9933
Non-polymers1,89911
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
P: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
Q: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
R: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,98815
Polymers84,9933
Non-polymers1,99512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
S: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
T: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
U: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,02316
Polymers84,9933
Non-polymers2,03013
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
V: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
W: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
X: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,92715
Polymers84,9933
Non-polymers1,93412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
Y: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
Z: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
a: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,85613
Polymers84,9933
Non-polymers1,86310
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
b: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
c: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
d: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,85613
Polymers84,9933
Non-polymers1,86310
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)377.003, 377.003, 263.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein ...
Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase / UDP-N-acetylglucosamine acyltransferase


Mass: 28331.010 Da / Num. of mol.: 30 / Fragment: full-length protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain PA7) (bacteria)
Strain: PA7 / Gene: lpxA, PSPA7_1495 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS
References: UniProt: A6V1E4, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Chemical...
ChemComp-VFT / 2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl)methyl]-~{N}-(1~{H}-imidazol-4-ylmethyl)ethanamide


Mass: 396.893 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C20H17ClN4OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cl
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 71 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.53 Å3/Da / Density % sol: 77.75 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 1.6 M (NH4)2SO4, 10% 1,4-Dioxane, 0.1 M MES pH 6.7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.74→113.47 Å / Num. obs: 489899 / % possible obs: 100 % / Redundancy: 27.7 % / Biso Wilson estimate: 49.993 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.399 / Rpim(I) all: 0.077 / Rrim(I) all: 0.406 / Net I/σ(I): 8.5
Reflection shellResolution: 2.74→2.81 Å / Redundancy: 28.3 % / Rmerge(I) obs: 3.879 / Num. unique obs: 35972 / CC1/2: 0.529 / Rpim(I) all: 0.741 / Rrim(I) all: 3.95 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DEM

5dem


Resolution: 2.74→113.45 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 22.016 / SU ML: 0.19 / SU R Cruickshank DPI: 0.2734 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 24562 5 %RANDOM
Rwork0.187 ---
obs0.189 464466 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.81 Å2 / Biso mean: 49.993 Å2 / Biso min: 22.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 2.74→113.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms59100 0 1312 220 60632
Biso mean--58.71 40.71 -
Num. residues----7725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01361838
X-RAY DIFFRACTIONr_bond_other_d0.0010.01757467
X-RAY DIFFRACTIONr_angle_refined_deg2.1991.65783975
X-RAY DIFFRACTIONr_angle_other_deg1.4441.591131631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8957741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41620.6273331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.075159609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.12215548
X-RAY DIFFRACTIONr_chiral_restr0.0830.28048
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0272167
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0215029
LS refinement shellResolution: 2.74→2.811 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 1752 -
Rwork0.377 33893 -
all-35645 -
obs--99.09 %
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)
10.7965-0.0384-0.61020.4955-0.10441.7957-0.06920.01030.00280.05690.0314-0.1336-0.0190.18160.03780.025-0.00360.02050.14720.02810.1607-18.957697.4528-34.2771
21.57470.4461-0.35260.7194-0.15770.5681-0.00630.0873-0.0515-0.07810.0165-0.10110.13220.014-0.01020.05960.02340.05250.1259-0.01810.1726-32.706277.8757-53.1464
31.3796-0.3699-0.5310.63520.10660.6425-0.00520.07970.106-0.0906-0.0024-0.0023-0.0680.10730.00760.0702-0.00810.060.13870.03340.1553-35.5751107.8482-57.5706
40.83480.00980.59530.45730.07751.4901-0.04250.02520.01430.04770.05910.1094-0.0035-0.1196-0.01660.0324-0.0105-0.04630.12520.00820.1748-172.857691.9464-31.4813
51.65040.45610.41560.58780.01950.62440.02290.10090.0736-0.08030.04110.0988-0.11880.0006-0.0640.07660.0074-0.050.10860.03150.1897-159.5603110.7925-51.3706
61.3516-0.36720.440.96050.00980.4601-0.00940.0661-0.1509-0.15750.00140.00560.0273-0.09750.00790.0948-0.0213-0.05920.1237-0.01350.1535-156.909480.6706-54.8846
71.0423-0.10410.42271.1261-0.15381.2430.1002-0.0070.2413-0.0139-0.13590.2406-0.3295-0.18090.03560.13950.06780.03170.0549-0.02130.2664-148.0015159.3305-15.317
81.3001-0.5337-0.3260.94060.26050.9175-0.01850.24010.1111-0.19760.070.1266-0.3486-0.1369-0.05150.2109-0.0165-0.06930.1060.10.1853-140.1336151.3617-43.6854
90.79850.09770.14711.616-0.30590.9747-0.09530.11110.1345-0.07030.05630.3104-0.0261-0.35010.0390.04310.0147-0.07820.24890.02260.2242-162.4892136.4597-29.2992
100.9312-0.1936-0.33190.9270.05111.40370.08640.0263-0.25240.0181-0.1503-0.20630.37840.22710.06390.15620.084-0.02390.08660.01430.2735-43.119430.6971-14.8026
111.2295-0.23330.18731.2038-0.00520.85860.04180.2447-0.104-0.21090.0407-0.16550.37680.1186-0.08250.21940.01420.03740.0803-0.08390.1507-51.946137.4922-43.2319
120.8405-0.0514-0.10011.61790.3760.9096-0.08450.1613-0.1327-0.07320.0381-0.30520.07390.35150.04640.0430.03630.07270.256-0.0050.1847-29.108152.9074-30.2083
130.7642-0.4327-0.2021.10370.56260.7563-0.00130.0021-0.1504-0.0359-0.0010.05030.0561-0.1160.00230.1005-0.0038-0.01950.0474-0.05370.2197-112.155223.6955-40.0069
140.49680.04170.09361.19040.17720.61980.06530.21570.0404-0.09370.0122-0.04970.05260.044-0.07750.07950.00890.01330.1389-0.05670.1473-94.408537.4953-60.6696
150.58140.13310.30750.72130.24091.35710.07890.0946-0.12730.0265-0.0996-0.04930.14360.18610.02070.12820.04990.00290.0947-0.05720.1473-81.777721.6934-37.8009
160.9065-0.00430.09431.07450.37691.33850.06160.2917-0.02-0.25260.01030.3049-0.0384-0.1467-0.07190.083-0.0023-0.11380.15060.02650.2013-130.165985.1977-75.8838
171.37910.31380.43690.82910.23171.002-0.01360.4085-0.0089-0.27270.0273-0.1920.09830.0551-0.01370.13230.02030.06110.1469-0.00110.0636-101.361477.1944-82.1061
180.74260.0371-0.10090.8989-0.22191.4316-0.12510.1662-0.2908-0.29240.05630.06820.1834-0.17490.06880.1311-0.0341-0.0050.0857-0.11640.2051-120.7356.8019-70.2131
190.8945-0.49460.43980.9691-0.59060.7662-0.0429-0.00160.2309-0.1029-0.0053-0.0409-0.01230.14160.04820.0886-0.00470.01390.07310.05750.2807-79.7663165.1945-43.2613
200.65610.2629-0.02631.7656-0.47610.32980.05410.1425-0.0271-0.1282-0.03310.0094-0.01850.0069-0.02110.08980.0003-0.00450.0960.08660.1679-98.237150.5562-62.6328
210.57680.2776-0.30471.0044-0.66141.30640.0360.03340.18620.0395-0.05020.0797-0.0823-0.10860.01430.05760.0105-0.02170.04520.0350.1816-110.0198167.5221-40.1848
220.9692-0.1550.08691.0517-0.3981.1140.06690.2881-0.0044-0.265-0.0057-0.3070.05370.0979-0.06110.1139-0.01010.13260.1542-0.01760.1922-63.1321102.5637-77.4828
231.28460.0688-0.49140.788-0.07981.02890.03060.3753-0.0393-0.3214-0.01070.183-0.114-0.0203-0.01990.16010.0196-0.06120.16090.00370.0663-92.1659110.3443-82.8095
240.5743-0.05690.09650.92330.16611.5648-0.07530.1810.2737-0.31380.0395-0.1209-0.16360.08560.03580.136-0.0240.02280.12190.15080.2222-72.4202131.1214-72.3026
251.57250.1669-0.48060.80040.17390.9789-0.0224-0.08850.15620.02610.0625-0.3544-0.28090.1424-0.040.1235-0.0457-0.04880.0603-0.00770.3197-26.083143.07316.3588
261.06160.2587-0.24611.352-0.27170.7506-0.0633-0.03580.14760.07470.0299-0.33130.06050.26390.03350.02590.0274-0.07120.1938-0.03480.2709-13.9031115.13727.3764
270.9289-0.10010.2950.75230.21680.95550.01510.14490.0772-0.2273-0.0116-0.2711-0.08870.3031-0.00350.07280.0010.10590.18240.07420.298-20.3495127.9657-19.4413
281.46930.10840.11090.93840.00050.9740.03140.17150.4135-0.002-0.1073-0.1265-0.2783-0.04290.07590.16960.02260.02870.04080.08160.27-75.6598176.2739-11.1355
290.74970.1149-0.05651.1172-0.39491.174-0.0737-0.19330.27240.0813-0.04-0.1444-0.32470.080.11370.1410.0051-0.08890.0588-0.0950.3168-61.7469170.982515.504
300.81270.0726-0.06921.84770.36090.98840.02470.0630.3346-0.1241-0.0386-0.2101-0.13760.3630.01390.0351-0.05220.01370.17350.06270.2924-47.7297163.947-10.5409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 258
2X-RAY DIFFRACTION2B1 - 258
3X-RAY DIFFRACTION3C1 - 258
4X-RAY DIFFRACTION4D1 - 258
5X-RAY DIFFRACTION5E1 - 258
6X-RAY DIFFRACTION6F1 - 258
7X-RAY DIFFRACTION7G2 - 258
8X-RAY DIFFRACTION8H2 - 258
9X-RAY DIFFRACTION9I2 - 258
10X-RAY DIFFRACTION10M2 - 258
11X-RAY DIFFRACTION11N2 - 258
12X-RAY DIFFRACTION12O2 - 258
13X-RAY DIFFRACTION13J1 - 258
14X-RAY DIFFRACTION14K1 - 258
15X-RAY DIFFRACTION15L1 - 258
16X-RAY DIFFRACTION16P2 - 258
17X-RAY DIFFRACTION17Q2 - 258
18X-RAY DIFFRACTION18R2 - 258
19X-RAY DIFFRACTION19S1 - 258
20X-RAY DIFFRACTION20T1 - 258
21X-RAY DIFFRACTION21U1 - 258
22X-RAY DIFFRACTION22V2 - 258
23X-RAY DIFFRACTION23W2 - 258
24X-RAY DIFFRACTION24X2 - 258
25X-RAY DIFFRACTION25Y1 - 258
26X-RAY DIFFRACTION26Z1 - 258
27X-RAY DIFFRACTION27a2 - 258
28X-RAY DIFFRACTION28b2 - 258
29X-RAY DIFFRACTION29c1 - 258
30X-RAY DIFFRACTION30d2 - 258

+
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