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- PDB-5b4a: Crystal structure of LpxH with lipid X in spacegroup P21 -

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Basic information

Entry
Database: PDB / ID: 5b4a
TitleCrystal structure of LpxH with lipid X in spacegroup P21
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsHYDROLASE / LpxH / Lipid A / Lipid X / UDP-2 / 3-diacylglucosamine
Function / homology
Function and homology information


UDP-2,3-diacylglucosamine diphosphatase / UDP-2,3-diacylglucosamine hydrolase activity / glycolipid binding / lipid A biosynthetic process / extrinsic component of plasma membrane / 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
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsOkada, C. / Wakabayashi, H. / Yao, M. / Tanaka, I.
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structures of the UDP-diacylglucosamine pyrophosphohydrase LpxH from Pseudomonas aeruginosa
Authors: Okada, C. / Wakabayashi, H. / Kobayashi, M. / Shinoda, A. / Tanaka, I. / Yao, M.
History
DepositionApr 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,9506
Polymers57,3422
Non-polymers1,6084
Water10,413578
1
A: UDP-2,3-diacylglucosamine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4753
Polymers28,6711
Non-polymers8042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-3 kcal/mol
Surface area11940 Å2
MethodPISA
2
B: UDP-2,3-diacylglucosamine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4753
Polymers28,6711
Non-polymers8042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-5 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.016, 108.805, 51.685
Angle α, β, γ (deg.)90.00, 92.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28670.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: lpxH, PA1792 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I2V0, UDP-2,3-diacylglucosamine diphosphatase
#2: 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.: 2 / Source method: obtained synthetically / Formula: C34H66NO12P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.2M L-Proline, 0.1M HEPES pH 7.4, 9.0% PEG 3350, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 57104 / % possible obs: 99.9 % / Redundancy: 5 % / Rsym value: 0.064 / Net I/σ(I): 18.2
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.01 / Rsym value: 0.542 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B49

5b49


Resolution: 1.72→25.64 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.115 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18824 2919 5.1 %RANDOM
Rwork0.15968 ---
obs0.1611 54092 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.72→25.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 108 578 4636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194154
X-RAY DIFFRACTIONr_bond_other_d0.0030.024038
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9735608
X-RAY DIFFRACTIONr_angle_other_deg0.96839243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5995485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91421.388209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77615686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3591558
X-RAY DIFFRACTIONr_chiral_restr0.0520.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214575
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021029
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9681.5531946
X-RAY DIFFRACTIONr_mcbond_other1.9671.551945
X-RAY DIFFRACTIONr_mcangle_it2.762.3172429
X-RAY DIFFRACTIONr_mcangle_other2.7592.3212430
X-RAY DIFFRACTIONr_scbond_it3.5372.0592208
X-RAY DIFFRACTIONr_scbond_other3.5362.0592208
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4142.9083180
X-RAY DIFFRACTIONr_long_range_B_refined6.7116.04318209
X-RAY DIFFRACTIONr_long_range_B_other6.50415.52517586
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.722→1.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 207 -
Rwork0.261 3942 -
obs--98.67 %
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)
10.1165-0.0820.07380.5016-0.30330.2983-0.02890.024-0.03230.06590.04530.0398-0.0792-0.0271-0.01630.02390.00370.00490.0151-0.00510.011526.634124.986-3.7676
20.3595-0.23010.03230.25620.08780.1621-0.0152-0.0048-0.00720.00050.00330.01880.0050.02140.01190.00870.0060.00380.0088-0.00090.010740.27470.918420.5523
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 241
2X-RAY DIFFRACTION2B2 - 248

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