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- PDB-5dg3: Structure of Pseudomonas aeruginosa LpxA in complex with UDP-3-O-... -

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Basic information

Entry
Database: PDB / ID: 5dg3
TitleStructure of Pseudomonas aeruginosa LpxA in complex with UDP-3-O-(R-3-hydroxydecanoyl)-GlcNAc
ComponentsAcyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
KeywordsTRANSFERASE / Acyltransferases / Catalytic Domain / UDP-GlcNAc / Fatty Acids / Lipid A / Substrate Specificity / Uridine Diphosphate N-Acetylglucosamine / Hydrocarbon Rulers
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 / membrane / cytoplasm
Similarity search - Function
Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / 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 / Hexapeptide repeat proteins ...Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / 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 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Chem-U21 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSmith, E.W. / Chen, Y.
CitationJournal: Biochemistry / Year: 2015
Title: Structures of Pseudomonas aeruginosa LpxA Reveal the Basis for Its Substrate Selectivity.
Authors: Smith, E.W. / Zhang, X. / Behzadi, C. / Andrews, L.D. / Cohen, F. / Chen, Y.
History
DepositionAug 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Derived calculations
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Oct 14, 2015Group: Database references
Revision 1.4Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.5Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,49811
Polymers168,2926
Non-polymers3,2055
Water4,161231
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)85,7015
Polymers84,1463
Non-polymers1,5552
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules

F: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase

E: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7966
Polymers84,1463
Non-polymers1,6503
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Unit cell
Length a, b, c (Å)79.963, 83.328, 220.369
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUTHRTHRAA3 - 2573 - 257
21LEULEUTHRTHRBB3 - 2573 - 257
12LEULEUARGARGAA3 - 2583 - 258
22LEULEUARGARGCC3 - 2583 - 258
13LEULEUARGARGAA3 - 2583 - 258
23LEULEUARGARGDD3 - 2583 - 258
14LEULEUARGARGAA3 - 2583 - 258
24LEULEUARGARGEE3 - 2583 - 258
15LEULEUTHRTHRAA3 - 2573 - 257
25LEULEUTHRTHRFF3 - 2573 - 257
16LEULEUTHRTHRBB3 - 2573 - 257
26LEULEUTHRTHRCC3 - 2573 - 257
17LEULEUARGARGBB3 - 2583 - 258
27LEULEUARGARGDD3 - 2583 - 258
18LEULEUTHRTHRBB3 - 2573 - 257
28LEULEUTHRTHREE3 - 2573 - 257
19SERSERARGARGBB2 - 2582 - 258
29SERSERARGARGFF2 - 2582 - 258
110LEULEUARGARGCC3 - 2583 - 258
210LEULEUARGARGDD3 - 2583 - 258
111LEULEUARGARGCC3 - 2583 - 258
211LEULEUARGARGEE3 - 2583 - 258
112LEULEUTHRTHRCC3 - 2573 - 257
212LEULEUTHRTHRFF3 - 2573 - 257
113LEULEUARGARGDD3 - 2583 - 258
213LEULEUARGARGEE3 - 2583 - 258
114LEULEUARGARGDD3 - 2583 - 258
214LEULEUARGARGFF3 - 2583 - 258
115LEULEUTHRTHREE3 - 2573 - 257
215LEULEUTHRTHRFF3 - 2573 - 257

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.320813, 0.191648, -0.927551), (0.656625, 0.750774, -0.071985), (0.682585, -0.632147, -0.366699)44.186859, -2.56039, 44.751732
3given(1), (1), (1)
4given(-0.35211, 0.680981, 0.642093), (0.222899, 0.7273, -0.649115), (-0.909029, -0.085438, -0.40788)-13.26099, 22.214331, 58.62532
5given(1), (1), (1)
6given(0.026005, 0.997878, 0.059692), (-0.999405, 0.027306, -0.021084), (-0.02267, -0.059108, 0.997994)19.828171, 18.89175, 55.368038
7given(1), (1), (1)
8given(-0.72233, 0.363667, -0.588205), (-0.687318, -0.283597, 0.668705), (0.076373, 0.88731, 0.454806)71.82132, 19.567869, 50.481312
9given(1), (1), (1)
10given(0.199744, 0.280149, -0.938946), (0.707773, -0.703932, -0.059463), (-0.677613, -0.652683, -0.338888)86.090958, -1.35003, 89.476517
11given(1), (1), (1)
12given(-0.361069, 0.200972, -0.910626), (0.674646, 0.730448, -0.106294), (0.643803, -0.65273, -0.399327)44.164661, -1.18404, 46.417831
13given(1), (1), (1)
14given(-0.676108, -0.335311, 0.656082), (-0.7348, 0.241252, -0.63393), (0.054283, -0.910694, -0.409499)29.14039, 4.92227, 17.33918
15given(1), (1), (1)
16given(-0.167376, 0.302312, 0.938399), (-0.703081, -0.70385, 0.101346), (0.691131, -0.642808, 0.330358)9.55897, 18.311119, -29.318649
17given(1), (1), (1)
18given(-0.061685, -0.997621, 0.030771), (0.998017, -0.062039, -0.010679), (0.012562, 0.030051, 0.999469)17.88102, -19.31036, -55.360081
19given(1), (1), (1)
20given(-0.215813, -0.300513, -0.929041), (-0.708249, 0.703153, -0.062922), (0.672167, 0.644413, -0.364588)-9.21596, 20.430691, 24.661909
21given(1), (1), (1)
22given(0.031459, -0.997863, -0.057272), (-0.998323, -0.034155, 0.046731), (-0.048587, 0.055706, -0.997264)-23.142719, 56.718399, 59.664398
23given(1), (1), (1)
24given(0.703614, 0.337764, 0.625174), (0.708478, -0.265797, -0.653767), (-0.05465, 0.902922, -0.426317)-68.26857, 47.892929, 66.522247
25given(1), (1), (1)
26given(0.667054, 0.277757, -0.691296), (-0.743187, 0.312947, -0.591386), (0.052078, 0.908248, 0.415178)0.87564, 52.280861, -2.17175
27given(1), (1), (1)
28given(-0.690491, 0.722134, 0.041779), (0.25136, 0.293703, -0.922256), (-0.678263, -0.626308, -0.384315)21.418751, 64.034088, 37.873051
29given(1), (1), (1)
30given(-0.682573, 0.231741, 0.693102), (-0.729292, -0.277231, -0.62552), (0.047191, -0.932437, 0.358238)7.0537, 45.7314, -4.62112

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Components

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


Mass: 28048.730 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain PA7) (bacteria)
Strain: PA7 / Gene: lpxA, PSPA7_1495 / Production host: Escherichia coli (E. coli)
References: UniProt: A6V1E4, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Chemical
ChemComp-U21 / uridine-5'-diphosphate-3-O-(R-3-hydroxydecanoyl)-N-acetyl-D-glucosamine / (2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydrox ytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H- pyran-4-yl (3R)-3-hydroxydecanoate


Mass: 777.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C27H45N3O19P2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M calcium acetate, 0.1M imidazole pH8.0, 20% PEG 1000, 10mM UDP-3-O-(R-3-hydroxydecanoyl)-GlcNAc

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→110.18 Å / Num. obs: 65433 / % possible obs: 98.5 % / Redundancy: 6.4 % / Net I/σ(I): 26.27

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data scaling
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→110.18 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R: 0.533 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24505 3038 5 %RANDOM
Rwork0.19316 ---
obs0.1958 57656 91.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.049 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.3→110.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11663 0 209 231 12103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01912128
X-RAY DIFFRACTIONr_bond_other_d00.0211485
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.94716475
X-RAY DIFFRACTIONr_angle_other_deg3.743326289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3451524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90622.741540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.233151862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.10315104
X-RAY DIFFRACTIONr_chiral_restr0.1110.21857
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213775
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022881
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5274.16117
X-RAY DIFFRACTIONr_mcbond_other2.5274.16116
X-RAY DIFFRACTIONr_mcangle_it3.5986.9047634
X-RAY DIFFRACTIONr_mcangle_other3.5976.9047635
X-RAY DIFFRACTIONr_scbond_it2.5784.4746011
X-RAY DIFFRACTIONr_scbond_other2.5764.4746011
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8187.3818841
X-RAY DIFFRACTIONr_long_range_B_refined5.19.24813981
X-RAY DIFFRACTIONr_long_range_B_other5.1019.24913976
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2183TIGHT POSITIONAL0.410.11
1A2254TIGHT POSITIONAL0.350.11
1A2246TIGHT POSITIONAL0.40.11
1A2183TIGHT POSITIONAL0.440.11
1A2185TIGHT POSITIONAL0.40.11
1A2241TIGHT POSITIONAL0.430.11
1A2242TIGHT THERMAL4.381.12
2A2255TIGHT THERMAL3.631.12
3A2188TIGHT THERMAL2.991.12
4A2250TIGHT THERMAL5.151.12
5A2242TIGHT THERMAL3.471.12
6B2246TIGHT THERMAL3.211.12
7B2185TIGHT THERMAL3.921.12
8B2241TIGHT THERMAL3.211.12
9B2285TIGHT THERMAL3.911.12
10C2183TIGHT THERMAL3.321.12
11C2254TIGHT THERMAL3.741.12
12C2246TIGHT THERMAL3.871.12
13D2183TIGHT THERMAL3.831.12
14D2185TIGHT THERMAL2.61.12
15E2241TIGHT THERMAL3.921.12
LS refinement shellResolution: 2.296→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 161 -
Rwork0.224 2729 -
obs--59.32 %

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