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- PDB-3p3g: Crystal Structure of the Escherichia coli LpxC/LPC-009 complex -

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Basic information

Entry
Database: PDB / ID: 3p3g
TitleCrystal Structure of the Escherichia coli 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 / homologylpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / Ribosomal Protein S5; domain 2 / 2-Layer Sandwich / Alpha Beta / Chem-3P3 / Chem-UKW / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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: 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)34,80110
Polymers33,5541
Non-polymers1,2469
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.725, 106.725, 52.684
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


Mass: 33554.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / 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, 317 molecules

#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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.5 M LiSO4 and 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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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: 1.65→50 Å / Num. obs: 41012 / % possible obs: 99.6 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.074 / Χ2: 1.1 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.65-1.686.90.49719050.70894.4
1.68-1.717.30.46720350.64898.8
1.71-1.747.80.42120490.67299.9
1.74-1.788.20.35720440.659100
1.78-1.828.40.29620410.693100
1.82-1.868.60.2520360.688100
1.86-1.98.60.2120550.705100
1.9-1.968.70.16520440.744100
1.96-2.018.70.13620470.77100
2.01-2.088.80.11320700.828100
2.08-2.158.80.10520440.86100
2.15-2.248.90.09420530.891100
2.24-2.348.90.08520430.929100
2.34-2.468.90.07920531.031100
2.46-2.628.90.07820701.145100
2.62-2.828.90.08220761.549100
2.82-3.118.90.09220632.464100
3.11-3.558.90.07420762.095100
3.55-4.488.80.0620841.813100
4.48-508.40.05221241.69298.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.26 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.6 Å
Translation2.5 Å26.6 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: 1.65→26.595 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.9071 / SU ML: 0.16 / σ(F): 0.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1771 1995 4.88 %
Rwork0.1551 --
obs0.1562 40920 99.4 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.145 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso max: 224.62 Å2 / Biso mean: 41.769 Å2 / Biso min: 15.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.1353 Å20 Å2-0 Å2
2--0.1353 Å2-0 Å2
3----0.2706 Å2
Refinement stepCycle: LAST / Resolution: 1.65→26.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 76 308 2741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112506
X-RAY DIFFRACTIONf_angle_d1.1043401
X-RAY DIFFRACTIONf_chiral_restr0.067372
X-RAY DIFFRACTIONf_plane_restr0.008441
X-RAY DIFFRACTIONf_dihedral_angle_d13.445927
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.7110.23381960.22553720391696
1.711-1.77950.24661930.203638954088100
1.7795-1.86050.22822010.175538594060100
1.8605-1.95850.19071970.161638904087100
1.9585-2.08120.17362030.149138914094100
2.0812-2.24180.17272050.152639194124100
2.2418-2.46730.17631970.144338794076100
2.4673-2.8240.1692050.145739344139100
2.824-3.55660.1851960.160939464142100
3.5566-26.59860.1612020.14813992419499
Refinement TLS params.Method: refined / Origin x: 31.193 Å / Origin y: -21.3967 Å / Origin z: -8.0805 Å
111213212223313233
T0.1488 Å20.0307 Å20.0435 Å2-0.1645 Å2-0.0025 Å2--0.1439 Å2
L1.429 °2-0.7718 °20.208 °2-1.9305 °2-0.1827 °2--0.9318 °2
S-0.1211 Å °-0.2573 Å °-0.0332 Å °0.25 Å °0.1464 Å °0.2189 Å °-0.0012 Å °0.0928 Å °-0.0225 Å °
Refinement TLS groupSelection details: (chain A and resid 1:300)

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