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- PDB-4g4x: Crystal structure of peptidoglycan-associated lipoprotein from Ac... -

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Basic information

Entry
Database: PDB / ID: 4g4x
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 / D-ALANINE / Peptidoglycan-associated lipoprotein / Peptidoglycan-associated lipoprotein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.1Mar 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)13,1835
Polymers12,8141
Non-polymers3694
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.420, 53.840, 140.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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: pal / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F0QP95, UniProt: A0A7U3YVT1*PLUS
#2: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES NaOH, 2% PEG 400, 2.0M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / 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: 1.5→50 Å / Num. obs: 32078

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2124 842 4.7 %
Rwork0.1969 --
obs-17394 97.4 %
Solvent computationBsol: 53.6947 Å2
Displacement parametersBiso max: 44.36 Å2 / Biso mean: 13.6107 Å2 / Biso min: 2.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.319 Å20 Å20 Å2
2--2.155 Å20 Å2
3----1.836 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms855 0 23 111 989
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d1.22
X-RAY DIFFRACTIONc_mcbond_it0.9731.5
X-RAY DIFFRACTIONc_scbond_it2.0992
X-RAY DIFFRACTIONc_mcangle_it1.4962
X-RAY DIFFRACTIONc_scangle_it2.972.5
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 (%)
1.5-1.550.2627800.231630171099.3
1.55-1.620.2266790.20911703178299.9
1.62-1.690.2262850.20351681176699.9
1.69-1.780.2171710.19261690176199.8
1.78-1.890.218910.19231650174199.7
1.89-2.040.2097920.20011671176398.8
2.04-2.240.2064820.19671625170797.2
2.24-2.560.2169810.19491652173396.1
2.56-3.230.2144840.18571603168793.8
3.23-500.1976970.19741647174490.7
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 DIFFRACTION6DAL.paramDAL.top
X-RAY DIFFRACTION7GOL.paramGOL.top

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