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- PDB-4g4v: Crystal structure of peptidoglycan-associated lipoprotein from Ac... -

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Basic information

Entry
Database: PDB / ID: 4g4v
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 / 2,6-DIAMINOPIMELIC ACID / Peptidoglycan-associated lipoprotein / Peptidoglycan-associated lipoprotein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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)13,0042
Polymers12,8141
Non-polymers1901
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.040, 45.130, 50.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-API / 2,6-DIAMINOPIMELIC ACID


Type: L-peptide linking / Mass: 190.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.85 Å3/Da / Density % sol: 33.63 % / Mosaicity: 1.278 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.2
Details: 0.1M PHOSPHATE CITRATE, 30% PEG 3350, 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-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: 1.9→50 Å / Num. obs: 7884 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.071 / Χ2: 3.123 / Net I/σ(I): 16.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.976.90.3277671.941100
1.97-2.056.90.267752.2461100
2.05-2.146.90.1897692.506199.9
2.14-2.256.70.1617792.7921100
2.25-2.396.70.1367753.086199.9
2.39-2.586.70.1077743.435199.9
2.58-2.846.50.0927873.532199.7
2.84-3.256.30.0667933.649199.9
3.25-4.095.90.0578094.116199.8
4.09-505.50.0548564.264198.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TD4

3td4


Resolution: 1.9→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2618 415 5.2 %
Rwork0.2258 --
obs-7850 99.1 %
Solvent computationBsol: 39.427 Å2
Displacement parametersBiso max: 62.46 Å2 / Biso mean: 33.1362 Å2 / Biso min: 17.66 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 13 50 943
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.209
X-RAY DIFFRACTIONc_mcbond_it1.4281.5
X-RAY DIFFRACTIONc_scbond_it2.2592
X-RAY DIFFRACTIONc_mcangle_it2.1132
X-RAY DIFFRACTIONc_scangle_it3.2932.5
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 (%)
1.9-1.970.3675380.257468071893.5
1.97-2.050.2375340.2499749783100
2.05-2.140.2723360.236573477099.9
2.14-2.250.2829500.2346731781100
2.25-2.390.2771300.244575378399.9
2.39-2.580.2549410.228673677799.9
2.58-2.840.3519370.237375579299.7
2.84-3.250.2544450.242574879399.9
3.25-4.090.2773550.217575380899.8
4.09-500.2154490.204879684598.5
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 DIFFRACTION6API.paramAPI.top

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