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- PDB-4j6e: Structure of LPXI D225A Mutant -

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Basic information

Entry
Database: PDB / ID: 4j6e
TitleStructure of LPXI D225A Mutant
ComponentsUDP-2,3-diacylglucosamine pyrophosphatase LpxI
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Center for Structures of Membrane Proteins / CSMP / lipid binding
Function / homology
Function and homology information


identical protein binding
Similarity search - Function
LpxI C-terminal catalytic domain / LpxI, C-terminal / LpxI N-terminal domain / LpxI, C-terminal domain superfamily / LpxI C-terminal domain / LpxI N-terminal domain / Cytidine Deaminase; domain 2 / Rossmann fold - #20 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-UDG / UDP-2,3-diacylglucosamine pyrophosphatase LpxI / UDP-2,3-diacylglucosamine pyrophosphatase LpxI
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.52 Å
AuthorsMetzger IV, L.E. / Lee, J.K. / Finer-Moore, J.S. / Raetz, C.R.H. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: LpxI structures reveal how a lipid A precursor is synthesized.
Authors: Metzger IV, L.E. / Lee, J.K. / Finer-Moore, J.S. / Raetz, C.R.H. / Stroud, R.M.
History
DepositionFeb 11, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionMay 8, 2013ID: 4GGI
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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-2,3-diacylglucosamine pyrophosphatase LpxI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9762
Polymers29,9581
Non-polymers1,0181
Water34219
1
A: UDP-2,3-diacylglucosamine pyrophosphatase LpxI
hetero molecules

A: UDP-2,3-diacylglucosamine pyrophosphatase LpxI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9524
Polymers59,9152
Non-polymers2,0362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area2270 Å2
ΔGint-15 kcal/mol
Surface area22840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.297, 107.297, 81.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein UDP-2,3-diacylglucosamine pyrophosphatase LpxI


Mass: 29957.740 Da / Num. of mol.: 1 / Mutation: D225A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: CB15N / Gene: 77330127, CCNA_01987, CC_1910, lpxI / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: B8GWR0, UniProt: A0A0H3C8Q1*PLUS, UDP-2,3-diacylglucosamine diphosphatase
#2: Chemical ChemComp-UDG / (2R,3R,4R,5S,6R)-2-{[(S)-{[(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)-3-{[(3R)-3-hydroxytetradecanoyl]amino}tetrahydro-2H-pyran-4-yl (3R)-3-hydroxytetradecanoate


Mass: 1018.027 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H77N3O20P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM TRIS pH 7.5-9.0,180-200 mM NaCl, 1.3-1.6 M (NH4)2SO4 and 6% V/V glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2011 / Details: monochromator
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.52→61.2 Å / Num. obs: 9602 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 32
Reflection shellResolution: 2.52→2.65 Å / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
PHENIXmodel building
ELVESrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.52→61.182 Å / SU ML: 0.29 / Isotropic thermal model: isotropic / σ(F): 0.3 / Phase error: 27.14 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2857 962 10.02 %
Rwork0.2207 --
obs0.2271 9602 98.1 %
all-9602 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→61.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 68 19 2064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092073
X-RAY DIFFRACTIONf_angle_d1.3572802
X-RAY DIFFRACTIONf_dihedral_angle_d20.778786
X-RAY DIFFRACTIONf_chiral_restr0.081327
X-RAY DIFFRACTIONf_plane_restr0.006365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.65290.33491280.28761152X-RAY DIFFRACTION95
2.6529-2.81910.33451330.27241191X-RAY DIFFRACTION96
2.8191-3.03670.3091320.24051188X-RAY DIFFRACTION98
3.0367-3.34230.25991370.21811229X-RAY DIFFRACTION99
3.3423-3.82590.27481380.20421246X-RAY DIFFRACTION100
3.8259-4.81990.31371420.20161270X-RAY DIFFRACTION100
4.8199-61.20040.25891520.22061364X-RAY DIFFRACTION100
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)
18.0588-4.1308-3.05892.96470.82644.5680.32550.1802-0.555-0.68180.2758-0.46190.66640.8418-0.63970.95240.1412-0.16691.3048-0.1970.9154-1.580127.55882.3643
20.66870.35590.20222.8077-1.27423.9119-0.3427-0.0043-0.755-1.3040.3715-1.10530.661.48080.60430.7561-0.37830.39341.5848-0.0111.0067-3.614242.3285-13.9144
33.98331.3743-1.84984.57851.25663.9589-0.3580.2644-0.1922-0.38480.1913-0.3637-0.26980.58040.20040.5581-0.26810.02020.82150.12690.4089-14.312851.4962-6.2245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 118 )
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 145 )
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 276 )

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