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- PDB-5b4d: Crystal structure of H10N mutant of LpxH -

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Basic information

Entry
Database: PDB / ID: 5b4d
TitleCrystal structure of H10N mutant of LpxH
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 / 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
UDP-2,3-diacylglucosamine hydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)57,5705
Polymers57,2942
Non-polymers2763
Water10,665592
1
A: UDP-2,3-diacylglucosamine hydrolase


Theoretical massNumber of molelcules
Total (without water)28,6471
Polymers28,6471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11800 Å2
MethodPISA
2
B: UDP-2,3-diacylglucosamine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9234
Polymers28,6471
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-1 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.564, 87.888, 98.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 28646.891 Da / Num. of mol.: 2 / Mutation: H10N
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Proline, 0.1M HEPES pH 7.0, 10.0% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 59677 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rsym value: 0.078 / Net I/σ(I): 18.4
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.13 / Rsym value: 0.551 / % 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: 1.75→49.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.971 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 2991 5 %RANDOM
Rwork0.17831 ---
obs0.17949 56369 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.679 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å2-0 Å2
2---0.3 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.75→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 18 592 4362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193855
X-RAY DIFFRACTIONr_bond_other_d0.0030.023747
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9615211
X-RAY DIFFRACTIONr_angle_other_deg0.99138553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4395461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29321.546194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64215651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8171554
X-RAY DIFFRACTIONr_chiral_restr0.1110.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214301
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02953
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_it2.4062.061856
X-RAY DIFFRACTIONr_mcbond_other2.4062.0591855
X-RAY DIFFRACTIONr_mcangle_it3.1953.0642313
X-RAY DIFFRACTIONr_mcangle_other3.1953.0652314
X-RAY DIFFRACTIONr_scbond_it3.9972.6021999
X-RAY DIFFRACTIONr_scbond_other3.9922.6021999
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0593.6882899
X-RAY DIFFRACTIONr_long_range_B_refined7.85820.93617196
X-RAY DIFFRACTIONr_long_range_B_other7.68120.33216498
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 196 -
Rwork0.29 4136 -
obs--99.4 %
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)
10.5848-0.03530.09420.00410.0020.49890.0056-0.02330.0116-0.0041-0.0059-0.0037-0.0065-0.02790.00030.00810.00880.0020.0127-0.00170.0137-0.7895-17.110914.1585
20.6172-0.09790.10780.01790.01130.4809-0.0270.03810.00410.0042-0.01220.0037-0.01370.01370.03920.0045-0.00370.00280.0069-0.00080.0123-32.6408-18.503935.1733
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 241
2X-RAY DIFFRACTION2B2 - 303

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