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- PDB-1p42: Crystal structure of Aquifex aeolicus LpxC Deacetylase (Zinc-Inhi... -

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Basic information

Entry
Database: PDB / ID: 1p42
TitleCrystal structure of Aquifex aeolicus LpxC Deacetylase (Zinc-Inhibited Form)
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHYDROLASE / alpha+beta fold / hydrophobic tunnel
Function / homology
Function and homology information


UDP-3-O-acyl-N-acetylglucosamine deacetylase / : / 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
MYRISTIC ACID / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsWhittington, D.A. / Rusche, K.M. / Shin, H. / Fierke, C.A. / Christianson, D.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal Structure of LpxC, a Zinc-Dependent Deacetylase Essential for Endotoxin Biosynthesis
Authors: Whittington, D.A. / Rusche, K.M. / Shin, H. / Fierke, C.A. / Christianson, D.W.
History
DepositionApr 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_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 / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999sequence The residue numbering scheme for this structure follows that of the E. coli enzyme. This ...sequence The residue numbering scheme for this structure follows that of the E. coli enzyme. This treatment results in a break in the sequential numbering in a couple of places.

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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)62,63111
Polymers61,7172
Non-polymers9159
Water5,567309
1
A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3486
Polymers30,8581
Non-polymers4905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2835
Polymers30,8581
Non-polymers4254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules

B: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,63111
Polymers61,7172
Non-polymers9159
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z+1/31
Buried area2870 Å2
ΔGint-247 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.66, 101.66, 125.10
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsThe biological assembly is a monomer.

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Components

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


Mass: 30858.314 Da / Num. of mol.: 2 / Fragment: sequence database residue 2-271 / Mutation: C193A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: LPXC OR ENVA OR AQ_1772 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: O67648, 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.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.81 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: NaCl, HEPES, ZnSO4, magnesium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal
*PLUS
Density Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.2 mg/mlprotein1drop
225 mMHEPES1droppH7.0
350 mM1dropNaCl
410 mMmagnesium acetate1drop
50.5 mM1dropZnSO4
60.8 M1reservoirNaCl
70.1 MHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.2825, 1.2832, 1.2565
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2002
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28251
21.28321
31.25651
ReflectionResolution: 2→30 Å / Num. all: 97874 / Num. obs: 97852 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.059 / Net I/σ(I): 19
Reflection shellResolution: 2→2.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 5.8 / Num. unique all: 9760 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 100 % / Num. measured all: 497657 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.47 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2389966.37 / Data cutoff high rms absF: 2389966.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME, BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.211 4815 4.9 %RANDOM
Rwork0.199 ---
obs0.199 97852 99.9 %-
all-97874 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.9337 Å2 / ksol: 0.385119 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.26 Å2-0.69 Å20 Å2
2---5.26 Å20 Å2
3---10.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4314 0 39 309 4662
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.342.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 783 4.8 %
Rwork0.244 15503 -
obs-16312 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4MYR.PARMYR.TOP
Refinement
*PLUS
Num. reflection obs: 92811
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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