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- PDB-4g4w: Crystal structure of peptidoglycan-associated lipoprotein from Ac... -

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Basic information

Entry
Database: PDB / ID: 4g4w
TitleCrystal structure of peptidoglycan-associated lipoprotein from Acinetobacter baumannii
ComponentsPeptidoglycan-associated lipoprotein
KeywordsPEPTIDE BINDING PROTEIN / OmpA-like domain / MEMBRANE PROTEIN
Function / homologyOmpA-like domain / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / ALANINE / Peptidoglycan-associated lipoprotein / Peptidoglycan-associated lipoprotein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLee, W.C. / Song, J.H. / Park, J.S. / Kim, H.Y.
CitationJournal: to be published
Title: Enantiomer-dependent amino acid binding affinity of OmpA-like domains from Acinetobacter baumannii peptidoglycan-associated lipoprotein and OmpA
Authors: Lee, W.C. / Park, J.S. / Song, J.H. / Kim, S.I. / Lee, J.C. / Cheong, J. / Kim, H.Y.
History
DepositionJul 16, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Mar 20, 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

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Assembly

Deposited unit
A: Peptidoglycan-associated lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1875
Polymers12,8141
Non-polymers3734
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.140, 54.140, 114.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Peptidoglycan-associated lipoprotein


Mass: 12814.040 Da / Num. of mol.: 1 / Fragment: UNP residues 75-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: TCDC-AB0715 / Gene: ABTW07_3009, pal / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F0QP95, UniProt: A0A7U3YVT1*PLUS
#2: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.2
Details: 0.1M PHOSPHATE CITRATE, 1.4M NaH2PO4, 0.4M K2HPO4, pH 4.2, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 13980 / % possible obs: 98.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.083 / Χ2: 2.28 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.975.50.49713511.104198.1
1.97-2.055.80.40113501.191198.3
2.05-2.1460.29413611.421198.7
2.14-2.256.30.21513851.726198.5
2.25-2.396.40.17413701.864199
2.39-2.586.60.13413872.152199.1
2.58-2.846.80.10713862.438199.2
2.84-3.256.90.07814123.132199.3
3.25-4.096.90.05514403.584199.2
4.09-506.20.04415383.382197.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.229 699 5 %
Rwork0.2083 --
obs-13902 98.9 %
Solvent computationBsol: 41.9541 Å2
Displacement parametersBiso max: 63.11 Å2 / Biso mean: 27.7602 Å2 / Biso min: 11 Å2
Baniso -1Baniso -2Baniso -3
1-4.579 Å20 Å20 Å2
2--4.579 Å20 Å2
3----9.159 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms859 0 22 78 959
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.18
X-RAY DIFFRACTIONc_mcbond_it1.3191.5
X-RAY DIFFRACTIONc_scbond_it2.4112
X-RAY DIFFRACTIONc_mcangle_it2.0272
X-RAY DIFFRACTIONc_scangle_it3.7482.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.970.2796650.27741292135798.3
1.97-2.050.2492700.24241264133498.5
2.05-2.140.2576700.21911294136498.8
2.14-2.250.1818630.19091306136998.7
2.25-2.390.2554550.2111295135099.1
2.39-2.580.1852720.19221329140199.4
2.58-2.840.2516740.21851301137599.4
2.84-3.250.2676820.20921319140199.5
3.25-4.090.1997700.18691363143399.7
4.09-500.2241780.21151440151898
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6SO4.paramSO4.top
X-RAY DIFFRACTION7GOL.paramGOL.top

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