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- PDB-5drp: Structure of the AaLpxC/LPC-023 Complex -

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Basic information

Entry
Database: PDB / ID: 5drp
TitleStructure of the AaLpxC/LPC-023 Complex
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
Keywordshydrolase/hydrolase inhibitor / LpxC / Inhibitor / Lipid A / Gram-negative bacteria / 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-5EP / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.889 Å
AuthorsNajeeb, J. / Lee, C.-J. / Zhou, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI055588 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094475 United States
CitationJournal: Nat Commun / Year: 2016
Title: Drug design from the cryptic inhibitor envelope.
Authors: Lee, C.J. / Liang, X. / Wu, Q. / Najeeb, J. / Zhao, J. / Gopalaswamy, R. / Titecat, M. / Sebbane, F. / Lemaitre, N. / Toone, E.J. / Zhou, P.
History
DepositionSep 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)63,6538
Polymers62,6302
Non-polymers1,0236
Water4,666259
1
A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7703
Polymers31,3151
Non-polymers4552
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)31,8835
Polymers31,3151
Non-polymers5684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.657, 50.419, 61.730
Angle α, β, γ (deg.)80.260, 71.710, 88.900
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 31314.865 Da / Num. of mol.: 2 / Mutation: C181A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: lpxC, envA, aq_1772 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O67648, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 5 types, 265 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-5EP / N~2~-{4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]benzoyl}-N-hydroxy-L-isoleucinamide


Mass: 389.447 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H23N3O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.18 M ammonium chloride, 11.8% PEG3350, 10% 1,3-propanediol.
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 43313 / % possible obs: 97.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 27.18 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.028 / Rrim(I) all: 0.06 / Χ2: 0.983 / Net I/av σ(I): 24.488 / Net I/σ(I): 8.7 / Num. measured all: 191641
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.4 % / Rejects: 0

Resolution (Å)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.84-1.870.31121240.9260.1680.3540.43595.9
1.87-1.910.26121650.9440.1410.2970.46796.5
1.91-1.940.22621350.9580.1220.2570.53996.5
1.94-1.980.19421870.9670.1040.220.54796.3
1.98-2.030.16420890.9790.0880.1860.60496.7
2.03-2.070.14221820.9820.0770.1610.64397.1
2.07-2.120.12621270.9840.0680.1430.67897
2.12-2.180.11321850.9850.0610.1290.7297.3
2.18-2.250.10121130.9890.0550.1150.80496.8
2.25-2.320.0921810.9910.0490.1020.85897.6
2.32-2.40.08121820.9920.0440.0930.86497.5
2.4-2.50.07221530.9940.0390.0820.8697.8
2.5-2.610.06721560.9950.0360.0760.95298
2.61-2.750.06221600.9950.0330.071.02998
2.75-2.920.05622200.9960.030.0630.99998.3
2.92-3.150.04921590.9970.0260.0551.06398.2
3.15-3.460.04221890.9980.0230.0481.12698.4
3.46-3.960.03822050.9970.0210.0432.11398.9
3.96-4.990.03721990.9970.020.0421.57899.1
4.99-500.05322020.9910.0280.062.70299.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P3C

3p3c


Resolution: 1.889→34.808 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 19.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1915 2008 4.98 %
Rwork0.1561 38325 -
obs0.1578 40333 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.07 Å2 / Biso mean: 34.9078 Å2 / Biso min: 13.13 Å2
Refinement stepCycle: final / Resolution: 1.889→34.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 0 64 259 4611
Biso mean--37.28 40.87 -
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064451
X-RAY DIFFRACTIONf_angle_d0.9915996
X-RAY DIFFRACTIONf_chiral_restr0.04653
X-RAY DIFFRACTIONf_plane_restr0.004767
X-RAY DIFFRACTIONf_dihedral_angle_d12.6681643
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8889-1.93620.21951410.18812730287197
1.9362-1.98850.22051510.17742719287096
1.9885-2.0470.23711300.17422654278497
2.047-2.11310.21751450.16932737288297
2.1131-2.18860.20981510.16662747289897
2.1886-2.27620.22651330.16392729286297
2.2762-2.37980.19931390.16152722286198
2.3798-2.50520.21161490.16582749289898
2.5052-2.66210.20431430.17052749289298
2.6621-2.86760.19711460.17192711285798
2.8676-3.1560.25181430.17572756289998
3.156-3.61220.17211500.15632778292899
3.6122-4.54940.17041420.13162786292899
4.5494-34.81420.15481450.14032758290399
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)
12.2722-0.5929-0.08712.86490.04382.1286-0.02970.15930.2579-0.05760.00640.2482-0.2001-0.39990.00770.22180.0815-0.00990.36720.01840.231535.704338.373-11.1298
24.3039-1.34323.99363.3551-2.09478.547-0.5667-0.12640.74870.3888-0.013-0.5238-0.61270.08160.5630.34560.05420.01230.3691-0.08430.407551.239446.557-1.5294
32.7049-0.86610.98224.53212.80573.20180.0728-0.07530.10390.24140.1946-0.41980.20540.4029-0.18480.22030.032-0.05480.3905-0.04410.258557.999631.803-3.4003
43.06940.4649-0.72663.1727-0.73633.144-0.18370.12660.0480.20790.21080.09330.2296-0.4043-0.00620.24750.04520.02570.3603-0.02460.163946.968823.6544-6.9818
56.4068-0.2610.16323.5305-2.71783.30140.02260.0125-0.4690.10210.15650.41170.3433-0.2581-0.2020.2718-0.05910.03960.284-0.01510.258239.486918.5042-7.2794
65.78053.4384-0.70934.8412-0.03916.7419-0.236-0.1486-0.27210.09840.3606-0.3110.65630.0947-0.03890.27090.07180.00880.2507-0.05270.266251.912415.7803-11.588
72.9927-0.3023-0.38813.4487-0.08912.7884-0.0322-0.24110.32210.34920.207-0.1402-0.16860.0055-0.14950.19790.0533-0.03590.2839-0.03410.187949.644938.4879-1.2258
82.2638-0.2371-0.37450.7745-0.29152.54170.0190.2018-0.0722-0.09940.05080.113-0.0221-0.4562-0.11320.1991-0.0412-0.01930.3765-0.02420.226718.626425.252221.3965
94.73970.9275-2.08417.03520.64636.0179-0.0108-0.3281-0.04080.22480.0061-0.13440.09410.10790.01340.1922-0.0067-0.0030.2599-0.00750.142225.909928.203833.963
102.8132-0.6683-0.18712.3271-0.37551.53980.12630.3634-0.1386-0.0738-0.1240.0960.0179-0.1684-0.02190.1542-0.0209-0.01330.2844-0.04380.154925.565524.50917.2795
115.90510.50972.03241.41710.83284.2216-0.1268-0.09841.238-0.0042-0.1251-0.1264-0.55470.11160.24480.3762-0.02910.02870.2308-0.02630.400536.78241.539122.2312
124.53380.6071-0.28163.6264-1.02181.90210.0506-0.2236-0.36650.2102-0.1264-0.1120.04280.15890.05260.22880.00420.00990.2326-0.03280.191842.459319.119324.0674
132.3203-0.92631.17967.5216-2.50437.60040.10020.3309-0.7683-0.4905-0.344-0.52140.73180.4810.25790.29450.03450.08680.3036-0.03040.502246.43311.256519.3613
143.1374-0.6777-0.82642.75940.62662.37420.0342-0.11690.24180.02780.0426-0.0541-0.2450.163-0.02270.1652-0.0310.00080.1792-0.00810.1738.857531.234622.7883
154.9876-2.88530.23932.3816-1.92865.25540.0886-0.2970.52690.627-0.0229-0.0201-0.76460.0308-0.04230.3384-0.10820.05130.3567-0.12420.284835.636639.052931.9441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 116 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 137 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 167 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 168 through 191 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 192 through 206 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 207 through 221 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 222 through 268 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 47 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 48 through 72 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 73 through 116 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 147 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 148 through 206 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 207 through 221 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 222 through 252 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 253 through 268 )B0

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