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- PDB-5azc: Crystal structure of Escherichia coli Lgt in complex with phospha... -

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Basic information

Entry
Database: PDB / ID: 5azc
TitleCrystal structure of Escherichia coli Lgt in complex with phosphatidylglycerol
ComponentsProlipoprotein diacylglyceryl transferase
KeywordsTRANSFERASE / Inhibitor / Complex
Function / homology
Function and homology information


phosphatidylglycerol-prolipoprotein diacylglyceryl transferase / phosphatidylglycerol-prolipoprotein diacylglyceryl transferase activity / lipoprotein biosynthetic process / cytoplasmic side of plasma membrane / plasma membrane
Similarity search - Function
Phosphatidylglycerol--prolipoprotein diacylglyceryl transferase Lgt / Prolipoprotein diacylglyceryl transferase / Prolipoprotein diacylglyceryl transferase signature.
Similarity search - Domain/homology
Chem-PGT / Phosphatidylglycerol--prolipoprotein diacylglyceryl transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsZhang, X.C. / Mao, G. / Zhao, Y.
CitationJournal: Nat Commun / Year: 2016
Title: Crystal structure of E. coli lipoprotein diacylglyceryl transferase
Authors: Mao, G. / Zhao, Y. / Kang, X. / Li, Z. / Zhang, Y. / Wang, X. / Sun, F. / Sankaran, K. / Zhang, X.C.
History
DepositionSep 30, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prolipoprotein diacylglyceryl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,81411
Polymers34,3041
Non-polymers7,51010
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-16 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.117, 60.885, 117.448
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 Prolipoprotein diacylglyceryl transferase


Mass: 34304.070 Da / Num. of mol.: 1 / Fragment: UNP residues 20291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lgt, umpA, b2828, JW2796 / Production host: Escherichia coli (E. coli) / References: UniProt: P60955, EC: 2.4.99.-
#2: Chemical
ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris, CaCl2, PEG2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 28535 / % possible obs: 98.3 % / Redundancy: 9 % / Net I/σ(I): 19.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.902→27.52 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 1426 5.06 %Random selection
Rwork0.2117 ---
obs0.2137 28163 97.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.902→27.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 223 130 2646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072672
X-RAY DIFFRACTIONf_angle_d1.1083590
X-RAY DIFFRACTIONf_dihedral_angle_d17.0771081
X-RAY DIFFRACTIONf_chiral_restr0.079362
X-RAY DIFFRACTIONf_plane_restr0.006425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9016-1.96960.50461140.5532385X-RAY DIFFRACTION87
1.9696-2.04840.25431600.24712668X-RAY DIFFRACTION100
2.0484-2.14160.27641300.19992722X-RAY DIFFRACTION100
2.1416-2.25440.31441470.24562632X-RAY DIFFRACTION96
2.2544-2.39560.2531400.18842696X-RAY DIFFRACTION99
2.3956-2.58050.25531510.17222705X-RAY DIFFRACTION100
2.5805-2.83990.21921490.17552740X-RAY DIFFRACTION100
2.8399-3.25030.23471460.19162769X-RAY DIFFRACTION100
3.2503-4.09290.23851590.19452614X-RAY DIFFRACTION94
4.0929-27.52330.22061300.20862806X-RAY DIFFRACTION95

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