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- PDB-3p76: X-ray crystal structure of Aquifex aeolicus LpxC complexed SCH1379777 -

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Basic information

Entry
Database: PDB / ID: 3p76
TitleX-ray crystal structure of Aquifex aeolicus LpxC complexed SCH1379777
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHYDROLASE / Amidohydrolases / Amino Acid Motifs / Binding Sites / Drug Design / Enzyme Inhibitors / Escherichia coli Proteins / Hydrophobicity / Lipid A / Protein Conformation / Protein Folding / Recombinant Fusion Proteins / Structure-Activity Relationship
Function / homology
Function and homology information


UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / 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
IMIDAZOLE / Chem-P76 / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsOrth, P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Design and synthesis of potent Gram-negative specific LpxC inhibitors.
Authors: Faruk Mansoor, U. / Vitharana, D. / Reddy, P.A. / Daubaras, D.L. / McNicholas, P. / Orth, P. / Black, T. / Arshad Siddiqui, M.
History
DepositionOct 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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)31,6115
Polymers30,9901
Non-polymers6214
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.592, 65.592, 133.588
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: 30989.510 Da / Num. of mol.: 1 / Fragment: UNP residues 1-271 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (bacteria)
References: UniProt: O67648, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-P76 / N-[(1S,2R)-2-hydroxy-1-(hydroxycarbamoyl)propyl]-4-[4-(phenylethynyl)phenyl]piperidine-1-carboxamide


Mass: 421.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27N3O4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG MME 5K, 1M NaCl, 100mM Imidazol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 2006
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 24460 / Num. obs: 24215 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.115 / Χ2: 1.044 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.93-23.10.314.822581.00293.6
2-2.083.20.2557.524071.03199.2
2.08-2.173.20.2187.224461.02999.4
2.17-2.293.20.19115.724171.06199.5
2.29-2.433.20.16221.524561.07499.6
2.43-2.623.20.15311.624171.06699.8
2.62-2.883.30.13816.924381.04299.8
2.88-3.33.30.1216.924461.06799.8
3.3-4.163.30.10228.824471.04499.8
4.16-503.30.08327.424831.02399.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
AMoREphasing
BUSTER2.9.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1P42

1p42


Resolution: 1.93→29.44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1197 4.95 %RANDOM
Rwork0.168 ---
all0.169 24460 --
obs0.169 24215 99.1 %-
Displacement parametersBiso max: 108.85 Å2 / Biso mean: 26.745 Å2 / Biso min: 12.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.223 Å20 Å20 Å2
2---0.223 Å20 Å2
3---0.446 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.93→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 38 208 2387
LS refinement shellResolution: 1.93→2.02 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.196 140 5.03 %
Rwork0.185 2641 -
all0.185 2781 -
obs--99.1 %
Refinement TLS params.Method: refined / Origin x: -2.7308 Å / Origin y: 29.7424 Å / Origin z: -0.0018 Å
111213212223313233
T-0.0364 Å20.0013 Å20.0066 Å2--0.0415 Å2-0.0059 Å2---0.0426 Å2
L0.8487 °20.0564 °2-0.3296 °2-0.7281 °20.3967 °2--0.7962 °2
S-0.0068 Å °-0.0196 Å °-0.008 Å °0.0313 Å °-0.0042 Å °0.0108 Å °0.0436 Å °0.036 Å °0.0111 Å °

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