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- PDB-5dem: Structure of Pseudomonas aeruginosa LpxA -

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Basic information

Entry
Database: PDB / ID: 5dem
TitleStructure of Pseudomonas aeruginosa LpxA
ComponentsAcyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
KeywordsTRANSFERASE / Acyltransferase Catalytic Domain / 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 / 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 proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...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 proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Other
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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)168,3877
Polymers168,2926
Non-polymers951
Water14,700816
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)84,2414
Polymers84,1463
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-46 kcal/mol
Surface area29110 Å2
MethodPISA
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


Theoretical massNumber of molelcules
Total (without water)84,1463
Polymers84,1463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-39 kcal/mol
Surface area29100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.031, 82.176, 220.515
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: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERARGARGAA2 - 2582 - 258
21SERSERARGARGBB2 - 2582 - 258
12LEULEUTHRTHRAA3 - 2573 - 257
22LEULEUTHRTHRCC3 - 2573 - 257
13SERSERARGARGAA2 - 2582 - 258
23SERSERARGARGDD2 - 2582 - 258
14SERSERARGARGAA2 - 2582 - 258
24SERSERARGARGEE2 - 2582 - 258
15SERSERARGARGAA2 - 2582 - 258
25SERSERARGARGFF2 - 2582 - 258
16LEULEUTHRTHRBB3 - 2573 - 257
26LEULEUTHRTHRCC3 - 2573 - 257
17SERSERARGARGBB2 - 2582 - 258
27SERSERARGARGDD2 - 2582 - 258
18SERSERARGARGBB2 - 2582 - 258
28SERSERARGARGEE2 - 2582 - 258
19SERSERARGARGBB2 - 2582 - 258
29SERSERARGARGFF2 - 2582 - 258
110LEULEUTHRTHRCC3 - 2573 - 257
210LEULEUTHRTHRDD3 - 2573 - 257
111LEULEUTHRTHRCC3 - 2573 - 257
211LEULEUTHRTHREE3 - 2573 - 257
112LEULEUTHRTHRCC3 - 2573 - 257
212LEULEUTHRTHRFF3 - 2573 - 257
113SERSERARGARGDD2 - 2582 - 258
213SERSERARGARGEE2 - 2582 - 258
114SERSERARGARGDD2 - 2582 - 258
214SERSERARGARGFF2 - 2582 - 258
115SERSERARGARGEE2 - 2582 - 258
215SERSERARGARGFF2 - 2582 - 258

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

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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-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 816 / 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: 2.13 Å3/Da / Density % sol: 42.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M calcium acetate, 0.1M imidazole pH8.0, 20% PEG 1000

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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: Jan 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.809→110.26 Å / Num. obs: 130011 / % possible obs: 98.8 % / Redundancy: 7.5 % / Net I/σ(I): 38.54

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data scaling
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→110.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21135 6531 5.1 %RANDOM
Rwork0.1844 ---
obs0.18578 122365 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.365 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.81→110.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11790 0 5 816 12611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01912094
X-RAY DIFFRACTIONr_bond_other_d00.0211504
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.92716414
X-RAY DIFFRACTIONr_angle_other_deg3.657326315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06251545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90822.739555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.845151908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.44115108
X-RAY DIFFRACTIONr_chiral_restr0.0890.21836
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213915
X-RAY DIFFRACTIONr_gen_planes_other0.0310.022915
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_it2.0962.8456183
X-RAY DIFFRACTIONr_mcbond_other2.0952.8456182
X-RAY DIFFRACTIONr_mcangle_it2.9064.7777727
X-RAY DIFFRACTIONr_mcangle_other2.9064.7777728
X-RAY DIFFRACTIONr_scbond_it3.1713.4895911
X-RAY DIFFRACTIONr_scbond_other3.1713.4895911
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7935.6248687
X-RAY DIFFRACTIONr_long_range_B_refined6.0336.84814247
X-RAY DIFFRACTIONr_long_range_B_other6.0236.84114195
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A301180.13
12B301180.13
21A298600.12
22C298600.12
31A309760.1
32D309760.1
41A299120.13
42E299120.13
51A299500.13
52F299500.13
61B299960.12
62C299960.12
71B300520.13
72D300520.13
81B303160.13
82E303160.13
91B309060.1
92F309060.1
101C299880.11
102D299880.11
111C305780.11
112E305780.11
121C296840.13
122F296840.13
131D302400.12
132E302400.12
141D299960.13
142F299960.13
151E299320.14
152F299320.14
LS refinement shellResolution: 1.809→1.856 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 431 -
Rwork0.244 7958 -
obs--87.56 %

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