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- PDB-4fw6: Crystal Structure of the LpxC in complex with N-[(2S,3R)-3-HYDROX... -

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Basic information

Entry
Database: PDB / ID: 4fw6
TitleCrystal Structure of the LpxC in complex with N-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOBUTAN-2-YL]-4-(PHENYLETHYNYL)BENZAMIDE inhibitor
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHydrolase/Hydrolase Inhibitor / Hydrolase / 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
ACETATE ION / Chem-L59 / DI(HYDROXYETHYL)ETHER / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsKang, Y.N. / Stuckey, J.A.
CitationJournal: to be published
Title: Crystal Structure of the LpxC
Authors: Kang, Y.N. / Stuckey, J.A.
History
DepositionJun 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 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_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_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_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
C: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
D: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,20436
Polymers133,6764
Non-polymers3,52932
Water12,214678
1
A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,39610
Polymers33,4191
Non-polymers9779
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,44310
Polymers33,4191
Non-polymers1,0249
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2178
Polymers33,4191
Non-polymers7987
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1488
Polymers33,4191
Non-polymers7297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.477, 89.630, 169.997
Angle α, β, γ (deg.)90.000, 90.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 33418.875 Da / Num. of mol.: 4 / Mutation: C43S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: envA, lpxC, PA4406 / Plasmid: pMOCR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 AI
References: UniProt: P47205, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 7 types, 710 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-L59 / N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]-4-(phenylethynyl)benzamide


Mass: 338.357 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H18N2O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 678 / 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: 2.02 Å3/Da / Density % sol: 39.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: 24-30% PEG8000, 0.2M Sodium Acetate, 0.1M Sodium acetate pH 4.9, vapor diffusion, sitting drop, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2011
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 90449 / % possible obs: 96.7 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.075 / Χ2: 1.387 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.83-1.8650.39643940.748192.7
1.86-1.950.33742570.811193.4
1.9-1.9350.29643420.867193.1
1.93-1.974.90.25144360.949193.7
1.97-2.0150.22642920.995194.5
2.01-2.0650.18944221.104194.6
2.06-2.1150.17244281.123194.4
2.11-2.1750.15844391.155195.5
2.17-2.2350.14545081.204195.9
2.23-2.315.10.13644421.263197.1
2.31-2.3950.12245811.372197.2
2.39-2.485.10.12245401.5197.4
2.48-2.65.10.11746081.646198.5
2.6-2.735.20.11346611.944198.9
2.73-2.95.20.10545941.869199.3
2.9-3.135.20.09446641.956199.9
3.13-3.445.40.07946821.923199.5
3.44-3.945.50.05847301.696199.8
3.94-4.975.70.04346491.697199.1
4.97-505.60.03847801.448199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.11data extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→39.64 Å / Cor.coef. Fo:Fc: 0.9608 / Cor.coef. Fo:Fc free: 0.9437 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1971 4543 5.02 %RANDOM
Rwork0.1629 ---
obs0.1646 90426 96.44 %-
Displacement parametersBiso max: 101.92 Å2 / Biso mean: 28.8515 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-2.1974 Å20 Å2-0.005 Å2
2--0.5021 Å20 Å2
3----2.6995 Å2
Refine analyzeLuzzati coordinate error obs: 0.185 Å
Refinement stepCycle: LAST / Resolution: 1.83→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9254 0 226 678 10158
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4756SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes258HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1607HARMONIC5
X-RAY DIFFRACTIONt_it10015HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1308SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance16HARMONIC1
X-RAY DIFFRACTIONt_utility_angle24HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12442SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10015HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13668HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.71
X-RAY DIFFRACTIONt_other_torsion2.65
LS refinement shellResolution: 1.83→1.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 297 4.82 %
Rwork0.1847 5870 -
all0.1859 6167 -
obs--96.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.693-0.0170.20740.7299-0.02770.68960.04120.0022-0.0676-0.00380.0120.02080.08120.0196-0.0532-0.0409-0.001-0.0025-0.0453-0.007-0.031616.527715.49227.3013
20.72380.0452-0.20070.7165-0.05350.63150.04440.0070.06720.00710.01110.0142-0.06720.0135-0.0555-0.04480.0060.0042-0.0505-0.0088-0.021916.622759.690757.7803
30.9356-0.0539-0.15980.5931-0.53822.07890.0431-0.03060.08650.0309-0.0381-0.0485-0.07310.0488-0.005-0.0763-0.0289-0.0112-0.0505-0.013-0.072432.037463.259313.2472
40.96370.05380.12820.5866-0.52492.11540.03370.0278-0.0901-0.0312-0.0397-0.04870.08270.02890.006-0.07230.03190.012-0.0635-0.0148-0.068532.056311.818171.7499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 302
2X-RAY DIFFRACTION2{ B|* }B0 - 302
3X-RAY DIFFRACTION3{ C|* }C-2 - 302
4X-RAY DIFFRACTION4{ D|* }D-2 - 302

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