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- PDB-6ph9: Crystal Structure of the Klebsiella pneumoniae LpxH-lipid X complex -

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Basic information

Entry
Database: PDB / ID: 6ph9
TitleCrystal Structure of the Klebsiella pneumoniae LpxH-lipid X complex
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsBIOSYNTHETIC PROTEIN / lipid A / LpxH / lipid X
Function / homology
Function and homology information


UDP-2,3-diacylglucosamine diphosphatase / UDP-2,3-diacylglucosamine hydrolase activity / extrinsic component of plasma membrane / lipid A biosynthetic process / manganese ion binding / cytoplasm
Similarity search - Function
UDP-2,3-diacylglucosamine hydrolase / UDP-2,3-diacylglucosamine hydrolase LpxH-like / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
Chem-LP5 / : / UDP-2,3-diacylglucosamine hydrolase / UDP-2,3-diacylglucosamine hydrolase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsCho, J. / Zhou, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115355 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI139216 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics.
Authors: Cho, J. / Lee, M. / Cochrane, C.S. / Webster, C.G. / Fenton, B.A. / Zhao, J. / Hong, J. / Zhou, P.
History
DepositionJun 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-2,3-diacylglucosamine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,14910
Polymers29,7271
Non-polymers1,4229
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.990, 105.990, 52.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-304-

MN

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-2,3-diacylglucosamine hydrolase / UDP-2 / 3-diacylglucosamine diphosphatase


Mass: 29726.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: lpxH_1, lpxH, C3483_19950, NCTC9128_00880, SAMEA104305404_03891
Production host: Escherichia coli (E. coli)
References: UniProt: A0A1S0WIC1, UniProt: A6T5R0*PLUS, UDP-2,3-diacylglucosamine diphosphatase

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Non-polymers , 6 types, 214 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-LP5 / (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE


Mass: 711.861 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H66NO12P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 4 mg/mL protein, 10 mM MES, pH 6.0, 100 mM NaCl, 0.5 mM DTT, 2.5% glycerol, 100mM calcium chloride dihydrate, 50mM HEPES, pH 7.0, 16.5% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.92→45.895 Å / Num. obs: 26262 / % possible obs: 99.94 % / Redundancy: 19.7 % / Net I/σ(I): 33.03
Reflection shellResolution: 1.92→1.989 Å / Num. unique obs: 2588

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K8K

5k8k


Resolution: 1.92→45.895 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.91
RfactorNum. reflection% reflection
Rfree0.1994 1313 5 %
Rwork0.1783 --
obs0.1793 26251 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.92→45.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1903 0 83 205 2191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022093
X-RAY DIFFRACTIONf_angle_d0.5382840
X-RAY DIFFRACTIONf_dihedral_angle_d5.6171642
X-RAY DIFFRACTIONf_chiral_restr0.043308
X-RAY DIFFRACTIONf_plane_restr0.003369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.99690.37711440.31382739X-RAY DIFFRACTION100
1.9969-2.08780.27131430.23432734X-RAY DIFFRACTION100
2.0878-2.19780.25531450.20012753X-RAY DIFFRACTION100
2.1978-2.33550.20711440.19242730X-RAY DIFFRACTION100
2.3355-2.51590.24271460.18922772X-RAY DIFFRACTION100
2.5159-2.7690.19921450.18222758X-RAY DIFFRACTION100
2.769-3.16960.20881460.17942766X-RAY DIFFRACTION100
3.1696-3.9930.17741470.15522796X-RAY DIFFRACTION100
3.993-45.90810.17111530.16822890X-RAY DIFFRACTION100

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