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- PDB-3p3c: Crystal Structure of the Aquifex aeolicus LpxC/LPC-009 complex -

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Basic information

Entry
Database: PDB / ID: 3p3c
TitleCrystal Structure of the Aquifex aeolicus LpxC/LPC-009 complex
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHYDROLASE / LIPID A BIOSYNTHESIS / LIPID A SYNTHESIS / LPXC / baab sandwich / Deacetylation / ANTIBIOTIC / Acyl UDP-GlcNac / HYDROXAMATE / LPC-009
Function / homology
Function and homology information


UDP-3-O-acyl-N-acetylglucosamine deacetylase / : / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding
Similarity search - Function
lpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / UDP-3-O-acyl N-acetylglucosamine deacetylase / UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal / UDP-3-O-acyl N-acetylglycosamine deacetylase / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3P3 / PHOSPHATE ION / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsLee, C.-J. / Zhou, P.
CitationJournal: Chem.Biol. / Year: 2011
Title: Species-specific and inhibitor-dependent conformations of LpxC: implications for antibiotic design.
Authors: Lee, C.J. / Liang, X. / Chen, X. / Zeng, D. / Joo, S.H. / Chung, H.S. / Barb, A.W. / Swanson, S.M. / Nicholas, R.A. / Li, Y. / Toone, E.J. / Raetz, C.R. / Zhou, P.
History
DepositionOct 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8454
Polymers31,3221
Non-polymers5233
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.604, 65.604, 132.263
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase / UDP-3-O-acyl-GlcNAc deacetylase


Mass: 31321.814 Da / Num. of mol.: 1 / Fragment: UNP residues 2-275 / Mutation: C181A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_1772, envA, lpxC / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O67648, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-3P3 / N-[(1S,2R)-2-hydroxy-1-(hydroxycarbamoyl)propyl]-4-(4-phenylbuta-1,3-diyn-1-yl)benzamide


Mass: 362.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18N2O4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, and 2.5 M ammonium phosphate dibasic, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.0001 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 88659 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.121 / Χ2: 1.287 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.25-1.276.80.47143910.681100
1.27-1.297.30.42644320.682100
1.29-1.327.30.38244200.678100
1.32-1.357.30.33844170.705100
1.35-1.387.40.30144310.736100
1.38-1.417.40.26544160.752100
1.41-1.447.40.2444370.794100
1.44-1.487.40.21244080.834100
1.48-1.537.40.18344620.921100
1.53-1.577.50.16844010.989100
1.57-1.637.50.15344591.089100
1.63-1.77.50.14243991.08100
1.7-1.777.60.13444721.226100
1.77-1.877.60.12544291.438100
1.87-1.987.60.12444161.642100
1.98-2.147.60.1344312.263100
2.14-2.357.70.13344352.759100
2.35-2.697.70.11444501.959100
2.69-3.397.70.10544502.096100
3.39-507.60.10445032.10499.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 26.27 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.1 Å
Translation2.5 Å26.1 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→26.101 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9211 / SU ML: 0.11 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1606 4438 5.01 %RANDOM
Rwork0.1521 ---
obs0.1526 88540 99.93 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.597 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso max: 110.31 Å2 / Biso mean: 17.8763 Å2 / Biso min: 5.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.3996 Å20 Å2-0 Å2
2--0.3996 Å2-0 Å2
3----0.7992 Å2
Refinement stepCycle: LAST / Resolution: 1.25→26.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 33 452 2684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042326
X-RAY DIFFRACTIONf_angle_d0.9383138
X-RAY DIFFRACTIONf_chiral_restr0.057340
X-RAY DIFFRACTIONf_plane_restr0.005404
X-RAY DIFFRACTIONf_dihedral_angle_d11.965883
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.25-1.29520.23134310.206383698800
1.2952-1.3470.17554290.180784098838
1.347-1.40840.17644460.164483808826
1.4084-1.48260.16664300.158584188848
1.4826-1.57550.15524350.150284218856
1.5755-1.69710.15354340.145284158849
1.6971-1.86780.16814820.148483998881
1.8678-2.1380.16644360.144384128848
2.138-2.69320.14424150.143784588873
2.6932-26.10680.15625000.151584218921
Refinement TLS params.Method: refined / Origin x: -24.8242 Å / Origin y: 17.4259 Å / Origin z: -23.3026 Å
111213212223313233
T0.0331 Å20.0014 Å20.0003 Å2-0.0389 Å20.0059 Å2--0.0426 Å2
L0.6137 °2-0.0628 °20.0982 °2-0.4824 °2-0.1578 °2--0.4985 °2
S0.0072 Å °0.0295 Å °-0.0108 Å °-0.0225 Å °-0.0215 Å °-0.0005 Å °0.0497 Å °0.0253 Å °0.0156 Å °
Refinement TLS groupSelection details: chain A and resid all

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