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- PDB-2ves: Crystal Structure of LpxC from Pseudomonas aeruginosa complexed w... -

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Basic information

Entry
Database: PDB / ID: 2ves
TitleCrystal Structure of LpxC from Pseudomonas aeruginosa complexed with the potent BB-78485 inhibitor
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsHYDROLASE / LPXC / BB-78485 / ANTIBIOTICS / DEACETYLASE / LIPID SYNTHESIS / METALLOPROTEASE / HYDROXAMIC ACID / GRAM-NEGATIVE BACTERIA / LIPOPOLYSACCHARIDE / LIPID A BIOSYNTHESIS
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
Chem-GVR / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMochalkin, I. / Knafels, J.D.
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal structure of LpxC from Pseudomonas aeruginosa complexed with the potent BB-78485 inhibitor.
Authors: Mochalkin, I. / Knafels, J.D. / Lightle, S.
History
DepositionOct 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 19, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_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_asym_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_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-3-O-acyl-N-acetylglucosamine deacetylase
B: UDP-3-O-acyl-N-acetylglucosamine deacetylase
C: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,35115
Polymers99,4403
Non-polymers1,91112
Water22,0321223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-1.9 kcal/mol
Surface area43700 Å2
MethodPQS
Unit cell
Length a, b, c (Å)90.542, 103.331, 105.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33146.617 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-299 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: 287 / Gene: lpxC, envA, PA4406 / Production host: Escherichia coli (E. coli)
References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GVR / (2R)-N-hydroxy-3-naphthalen-2-yl-2-[(naphthalen-2-ylsulfonyl)amino]propanamide


Mass: 420.481 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H20N2O4S
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1223 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 40 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 40 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 40 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 40 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 40 TO SER
Nonpolymer details3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE (GVR): BB-78485 FROM BRITISH BIOTECH ...3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE (GVR): BB-78485 FROM BRITISH BIOTECH PHARMACEUTICAL. REPORTED IN CLEMENTS ET AL., 2002, ANTIMICROB. CHEMOTHER. 46, 1793-1799.
Sequence detailsRESIDUES 1-299, C40S MUTATION.

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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: 2.13 Å3/Da / Density % sol: 50.32 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: PALPXC, 10 MG/ML IN 25 MM HEPES PH 7.0, 2 MM TCEP, 0.3 M NACL, 1MM ZNCL2. BB-78485 ADDED TO 1 MM. HANGING DROP, 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M AMMONIUM SULFATE AND 10 % PEG 8000, 10 MM ZNCL2.

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 1, 2004 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→34.15 Å / Num. obs: 78112 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.61
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P42

1p42


Resolution: 1.9→73.72 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.672 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE ARE THREE MOLECULES IN ASYMMETRIC UNIT - CHAINS A, B AND C. C-TERMINAL ENDS IN CHAIN A AND B ARE DISORDERED. CHAIN C IS COMPLETE.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3927 5 %RANDOM
Rwork0.177 ---
obs0.179 74089 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2---0.83 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→73.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6863 0 107 1223 8193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227142
X-RAY DIFFRACTIONr_bond_other_d0.0010.026617
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.989665
X-RAY DIFFRACTIONr_angle_other_deg1.024315339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8225888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12423.976332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.611151245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2591556
X-RAY DIFFRACTIONr_chiral_restr0.1010.21098
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027957
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021504
X-RAY DIFFRACTIONr_nbd_refined0.1960.21294
X-RAY DIFFRACTIONr_nbd_other0.1680.26906
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23534
X-RAY DIFFRACTIONr_nbtor_other0.0790.24326
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2797
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.274
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.671.55684
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.76827080
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.28933228
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8564.52580
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.257 278
Rwork0.217 5170

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