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- PDB-4ggm: Structure of LpxI -

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Basic information

Entry
Database: PDB / ID: 4ggm
TitleStructure of LpxI
ComponentsUDP-2,3-diacylglucosamine pyrophosphatase LpxI
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / 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 ...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-LP5 / UDP-2,3-diacylglucosamine pyrophosphatase LpxI / UDP-2,3-diacylglucosamine pyrophosphatase LpxI
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.897 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, L.E. / Lee, J.K. / Finer-Moore, J.S. / Raetz, C.R. / Stroud, R.M.
History
DepositionAug 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Nov 21, 2012Group: Database references
Revision 1.3Apr 17, 2013Group: Structure summary
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
X: UDP-2,3-diacylglucosamine pyrophosphatase LpxI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1133
Polymers30,3771
Non-polymers7362
Water1267
1
X: UDP-2,3-diacylglucosamine pyrophosphatase LpxI
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)62,2266
Polymers60,7542
Non-polymers1,4724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,-y-1/2,-z+1/41
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.286, 74.286, 364.644
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsBiochemical, analytical, and mass spec data suggests dimer, which is noted in the manuscript, but it can also be monomer based on crystallographic results.

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Components

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


Mass: 30376.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: NA1000 / CB15N / Gene: 7330127, CCNA_01987, 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.14 Å3/Da / Density % sol: 70.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 100 mM MES pH 5.7, 3-7% w/v PEG 6000, 2.5% 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: Oct 16, 2009 / Details: Double Crystals Si111
RadiationMonochromator: DoubleCrystalSi111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.9→45 Å / Num. all: 11975 / Num. obs: 11932 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.8971→3.1886 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX1.7.3_928refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.897→45.513 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 32.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2716 571 4.79 %
Rwork0.2159 --
obs0.2186 11932 99.64 %
all-11975 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.217 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.6372 Å20 Å2-0 Å2
2--15.6372 Å2-0 Å2
3----31.2744 Å2
Refinement stepCycle: LAST / Resolution: 2.897→45.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 49 7 2100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082167
X-RAY DIFFRACTIONf_angle_d1.3122915
X-RAY DIFFRACTIONf_dihedral_angle_d19.062854
X-RAY DIFFRACTIONf_chiral_restr0.079335
X-RAY DIFFRACTIONf_plane_restr0.005379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8971-3.18860.4481380.332760X-RAY DIFFRACTION100
3.1886-3.64980.31761490.25992771X-RAY DIFFRACTION100
3.6498-4.59760.2671460.18392822X-RAY DIFFRACTION100
4.5976-45.51870.22691380.19963008X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 19.5091 Å / Origin y: -34.0188 Å / Origin z: 22.8347 Å
111213212223313233
T0.5872 Å2-0.0947 Å20.0256 Å2-0.6146 Å20.0329 Å2--0.6129 Å2
L1.372 °2-0.3719 °21.2975 °2-0.3138 °20.3656 °2--3.5262 °2
S-0.0234 Å °0.0875 Å °-0.173 Å °0.0677 Å °-0.1084 Å °0.0847 Å °0.085 Å °-0.3108 Å °0.1508 Å °
Refinement TLS groupSelection details: all

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