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- PDB-3ps2: Crystal structure of the Escherichia Coli LPXC/LPC-012 complex -

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Basic information

Entry
Database: PDB / ID: 3ps2
TitleCrystal structure of the Escherichia Coli LPXC/LPC-012 complex
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHYDROLASE/ANTIBIOTIC / LPXC / HYDROLASE / DEACETYLATION / ANTIBIOTIC / ACYL UDP-GLCNAC / HYDROXAMATE / LPC-012 / BAAB SANDWICH / LIPID A BIOSYNTHESIS / LIPID A SYNTHESIS / HYDROLASE-ANTIBIOTIC complex
Function / homologylpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / Ribosomal Protein S5; domain 2 / 2-Layer Sandwich / Alpha Beta / Chem-UKW / Chem-ZH4 / :
Function and homology information
Biological speciesEscherichia coli IHE3034 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsLee, C.-J. / Zhou, P.
CitationJournal: Bioorg.Med.Chem. / Year: 2011
Title: Syntheses, structures and antibiotic activities of LpxC inhibitors based on the diacetylene scaffold.
Authors: Liang, X. / Lee, C.J. / Chen, X. / Chung, H.S. / Zeng, D. / Raetz, C.R. / Li, Y. / Zhou, P. / Toone, E.J.
History
DepositionNov 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 21, 2024Group: 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 / struct_conn / 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_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_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.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_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)34,77810
Polymers33,5541
Non-polymers1,2249
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.449, 107.449, 53.422
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 33554.352 Da / Num. of mol.: 1 / Fragment: UNP residues 1-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli IHE3034 (bacteria) / Strain: IHE3034 / ExPEC / Gene: ECOK1_0097, ENVA, lpxC / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D5CV28, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 6 types, 114 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ZH4 / 4-[4-(3-aminophenyl)buta-1,3-diyn-1-yl]-N-[(2S,3R)-3-hydroxy-1-nitroso-1-oxobutan-2-yl]benzamide


Mass: 375.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17N3O4
#4: Chemical ChemComp-UKW / 4-ethynyl-N-[(1S,2R)-2-hydroxy-1-(oxocarbamoyl)propyl]benzamide


Mass: 260.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N2O4
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES PH 7.5, 1.5-1.7 M LISO4 AND 10 MM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 15727 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.118 / Χ2: 2.162 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.346.30.8727641.476100
2.34-2.386.40.6787821.557100
2.38-2.436.50.6137941.438100
2.43-2.486.40.5877671.602100
2.48-2.536.50.5157841.58100
2.53-2.596.60.4747791.552100
2.59-2.666.70.4037941.639100
2.66-2.736.80.3387722.06100
2.73-2.816.90.2627991.593100
2.81-2.97.10.257581.609100
2.9-37.30.1927991.6100
3-3.127.40.1587781.582100
3.12-3.267.60.1337961.70799.9
3.26-3.447.60.1147842.434100
3.44-3.656.90.1197843.76199.9
3.65-3.936.50.1327817.2299.7
3.93-4.337.40.0688002.19199.5
4.33-4.957.90.067932.38999.7
4.95-6.247.90.0638041.87199.8
6.24-507.70.0678152.49897.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.69 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.86 Å
Translation2.5 Å26.86 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→26.862 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7985 / SU ML: 0.38 / σ(F): 0.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2611 785 5.03 %
Rwork0.2071 --
obs0.2099 15618 99.17 %
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.444 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 197.58 Å2 / Biso mean: 50.1128 Å2 / Biso min: 13.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.7151 Å20 Å20 Å2
2---0.7151 Å20 Å2
3---1.4302 Å2
Refinement stepCycle: LAST / Resolution: 2.3→26.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 75 105 2536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072480
X-RAY DIFFRACTIONf_angle_d0.7973362
X-RAY DIFFRACTIONf_chiral_restr0.046371
X-RAY DIFFRACTIONf_plane_restr0.006435
X-RAY DIFFRACTIONf_dihedral_angle_d13.512915
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.44670.33791150.26072458257399
2.4467-2.63550.33171300.257424482578100
2.6355-2.90040.3331510.236624472598100
2.9004-3.31950.29211370.22362471260899
3.3195-4.17960.26751210.20382465258698
4.1796-26.86410.18531310.17172544267599
Refinement TLS params.Method: refined / Origin x: 31.62 Å / Origin y: -21.0965 Å / Origin z: -3.5572 Å
111213212223313233
T0.1623 Å20.0206 Å20.0269 Å2-0.1802 Å2-0.0176 Å2--0.1599 Å2
L1.1294 °2-0.6432 °20.1935 °2-1.6626 °2-0.4226 °2--0.7204 °2
S-0.097 Å °-0.2158 Å °-0.1302 Å °0.2053 Å °0.141 Å °0.2727 Å °-0.0516 Å °0.0339 Å °-0.038 Å °
Refinement TLS groupSelection details: ALL

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