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- PDB-4okg: LpxC from P.aeruginosa with the inhibitor 6-(benzimidazol-1-yl)-5... -

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Basic information

Entry
Database: PDB / ID: 4okg
TitleLpxC from P.aeruginosa with the inhibitor 6-(benzimidazol-1-yl)-5-[4-[2-[6-[(4-methylpiperazin-1-yl)methyl]-3-pyridyl]ethynyl]phenyl]pyridine-3-carbohydroxamic acid
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / hydroxamate / beta-alpha-alpha-beta sandwich / deacetylase / intracellular / cytoplasm / HYDROLASE-HYDROLASE INHIBITOR complex
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-2SZ / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsOlivier, N.B. / Lahiri, S.D. / Prince, D.B.
CitationJournal: Protein Express.Purif. / Year: 2014
Title: Overexpression of Pseudomonas aeruginosa LpxC in the Presence of an Inhibitor in an acrB Deletion Escherichia coli strain for Structural Studies
Authors: Gao, N. / McLeod, S.M. / Hajec, H. / Lahiri, S.D. / Prince, D.B. / Thresher, J. / Whiteaker, J. / Ross, P. / Olivier, N.B. / Doig, P.
History
DepositionJan 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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_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.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_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
B: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5116
Polymers66,2932
Non-polymers1,2184
Water6,792377
1
A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7563
Polymers33,1471
Non-polymers6092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7563
Polymers33,1471
Non-polymers6092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.770, 157.115, 48.946
Angle α, β, γ (deg.)90.000, 101.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33146.617 Da / Num. of mol.: 2 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: envA, lpxC, PA4406 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)delta-acrB
References: UniProt: P47205, 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-2SZ / 6-(1H-benzimidazol-1-yl)-N-hydroxy-5-[4-({6-[(4-methylpiperazin-1-yl)methyl]pyridin-3-yl}ethynyl)phenyl]pyridine-3-carboxamide


Mass: 543.618 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H29N7O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.03 Å3/Da / Density % sol: 39.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Cocrystallization; protein in the following buffer: 20mM HEPES pH7.3, 150 mM NaCl, 2mM DTT, 10% Glycerol and concentrated to 11.3 mg/ml. Well solution contained: 2.2M ammonium sulfate, 0.1 M ...Details: Cocrystallization; protein in the following buffer: 20mM HEPES pH7.3, 150 mM NaCl, 2mM DTT, 10% Glycerol and concentrated to 11.3 mg/ml. Well solution contained: 2.2M ammonium sulfate, 0.1 M Tris pH 8.3, 4.1% PEG 400, 29 mM NaPO4 di-basic. Protein coexpressed with compound and well solution were combined 1:1 as a sitting drop. Crystals harvested approximately 21 days later., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 25, 2010 / Details: Vari Max HR
RadiationMonochromator: Rigaku VariMax; graded, multilayer confocal optic
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 31059 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 23.04 Å2 / Rmerge(I) obs: 0.064 / Χ2: 4.724 / Net I/σ(I): 28.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.06-2.120.10913322.847181.4
2.1-2.132.20.10814613.086191
2.13-2.172.40.1115163.17195.5
2.17-2.222.60.10815403.456193.5
2.22-2.272.60.10715143.412194.4
2.27-2.322.60.115073.649195.1
2.32-2.382.60.09615773.86194.7
2.38-2.442.60.08715353.871195.4
2.44-2.512.60.08315583.912197.9
2.51-2.62.60.08115913.825197.6
2.6-2.692.60.0815964.59198.8
2.69-2.82.70.07215824.284198.8
2.8-2.922.70.06816204.112199.7
2.92-3.082.80.06516244.485199.7
3.08-3.272.90.0616375.0751100
3.27-3.5230.05816065.757199.9
3.52-3.8830.05416216.024199.6
3.88-4.443.10.05415926.626197.6
4.44-5.593.30.05515146.51193.6
5.59-503.50.0615367.024192.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.14data extraction
StructureStudiodata collection
PHASESphasing
BUSTER2.11.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→26.55 Å / Cor.coef. Fo:Fc: 0.9437 / Cor.coef. Fo:Fc free: 0.9155 / SU R Cruickshank DPI: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1567 5.05 %RANDOM
Rwork0.1668 ---
obs0.1694 31031 95.29 %-
Displacement parametersBiso max: 107.77 Å2 / Biso mean: 24.81 Å2 / Biso min: 4.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.6276 Å20 Å20.1936 Å2
2--1.0817 Å20 Å2
3----1.7093 Å2
Refine analyzeLuzzati coordinate error obs: 0.203 Å
Refinement stepCycle: LAST / Resolution: 2.06→26.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4597 0 84 377 5058
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1672SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes123HARMONIC2
X-RAY DIFFRACTIONt_gen_planes693HARMONIC5
X-RAY DIFFRACTIONt_it4765HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion613SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5768SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4765HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6440HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion17.9
LS refinement shellResolution: 2.06→2.13 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2201 129 5.4 %
Rwork0.176 2261 -
all0.1784 2390 -
obs--95.29 %

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