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- PDB-4mdt: Structure of LpxC bound to the reaction product UDP-(3-O-(R-3-hyd... -

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Basic information

Entry
Database: PDB / ID: 4mdt
TitleStructure of LpxC bound to the reaction product UDP-(3-O-(R-3-hydroxymyristoyl))-glucosamine
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHYDROLASE / Deacetylase
Function / homologylpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / Ribosomal Protein S5; domain 2 / 2-Layer Sandwich / Alpha Beta / Chem-24G / PHOSPHATE ION / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsClayton, G.M. / Klein, D.J. / Rickert, K.W. / Patel, S.B. / Kornienko, M. / Zugay-Murphy, J. / Reid, J.C. / Tummala, S. / Sharma, S. / Singh, S.B. ...Clayton, G.M. / Klein, D.J. / Rickert, K.W. / Patel, S.B. / Kornienko, M. / Zugay-Murphy, J. / Reid, J.C. / Tummala, S. / Sharma, S. / Singh, S.B. / Miesel, L. / Lumb, K.J. / Soisson, S.M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure of the Bacterial Deacetylase LpxC Bound to the Nucleotide Reaction Product Reveals Mechanisms of Oxyanion Stabilization and Proton Transfer.
Authors: Clayton, G.M. / Klein, D.J. / Rickert, K.W. / Patel, S.B. / Kornienko, M. / Zugay-Murphy, J. / Reid, J.C. / Tummala, S. / Sharma, S. / Singh, S.B. / Miesel, L. / Lumb, K.J. / Soisson, S.M.
History
DepositionAug 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Sep 20, 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 / 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)139,72716
Polymers135,9194
Non-polymers3,80812
Water2,756153
1
A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9324
Polymers33,9801
Non-polymers9523
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)34,9324
Polymers33,9801
Non-polymers9523
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)34,9324
Polymers33,9801
Non-polymers9523
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)34,9324
Polymers33,9801
Non-polymers9523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)168.973, 103.520, 103.968
Angle α, β, γ (deg.)90.000, 103.960, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 33979.805 Da / Num. of mol.: 4 / Mutation: C125S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lpxC, O3O_04310 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: K0BGQ2, 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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-24G / uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-glucosamine / (2R,3R,4R,5S,6R)-3-amino-2-{[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl (3R)-3-hydroxytetradecanoate


Mass: 791.672 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H51N3O18P2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 0.4 M sodium phosphate monobasic, 0.8 M potassium phosphate dibasic, 0.2 M CAPS, pH 10.5, 50 mM lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 25, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→100 Å / Num. obs: 51839 / % possible obs: 96 % / Redundancy: 3.6 % / Biso Wilson estimate: 66.57 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 17.2
Reflection shellResolution: 2.59→2.73 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.3 / % possible all: 79.3

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.9.7refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
BUSTER2.9.7refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P3G

3p3g


Resolution: 2.59→50.45 Å / Cor.coef. Fo:Fc: 0.9316 / Cor.coef. Fo:Fc free: 0.9056 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.449 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.417 / SU Rfree Blow DPI: 0.264 / SU Rfree Cruickshank DPI: 0.273 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 2646 5.11 %RANDOM
Rwork0.1966 ---
obs0.1989 51830 95.66 %-
Displacement parametersBiso max: 177.31 Å2 / Biso mean: 64.8643 Å2 / Biso min: 24.05 Å2
Baniso -1Baniso -2Baniso -3
1-3.8769 Å20 Å22.4831 Å2
2---10.1569 Å20 Å2
3---6.28 Å2
Refine analyzeLuzzati coordinate error obs: 0.332 Å
Refinement stepCycle: LAST / Resolution: 2.59→50.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9361 0 232 153 9746
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3423SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes255HARMONIC8
X-RAY DIFFRACTIONt_gen_planes1418HARMONIC8
X-RAY DIFFRACTIONt_it9785HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion1291SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact11355SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9785HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13265HARMONIC21.28
X-RAY DIFFRACTIONt_omega_torsion2.15
X-RAY DIFFRACTIONt_other_torsion19.24
LS refinement shellResolution: 2.59→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2722 149 5.22 %
Rwork0.2307 2703 -
all0.2331 2852 -
obs--95.66 %

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