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- PDB-4g88: Crystal structure of OmpA peptidoglycan-binding domain from Acine... -

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Basic information

Entry
Database: PDB / ID: 4g88
TitleCrystal structure of OmpA peptidoglycan-binding domain from Acinetobacter baumannii
ComponentsOuter membrane protein Omp38
KeywordsPEPTIDE BINDING PROTEIN / OmpA-like domain
Function / homology
Function and homology information


porin activity / pore complex / host cell mitochondrion / monoatomic ion transport / cell outer membrane
Similarity search - Function
Outer membrane protein beta-barrel domain / Outer membrane protein beta-barrel domain / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / 60s Ribosomal Protein L30; Chain: A; ...Outer membrane protein beta-barrel domain / Outer membrane protein beta-barrel domain / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,6-DIAMINOPIMELIC ACID / S,R MESO-TARTARIC ACID / Outer membrane protein Omp38
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 22, 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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: Outer membrane protein Omp38
B: Outer membrane protein Omp38
C: Outer membrane protein Omp38
D: Outer membrane protein Omp38
E: Outer membrane protein Omp38
F: Outer membrane protein Omp38
G: Outer membrane protein Omp38
H: Outer membrane protein Omp38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,85818
Polymers111,0368
Non-polymers1,82210
Water12,683704
1
A: Outer membrane protein Omp38
C: Outer membrane protein Omp38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1394
Polymers27,7592
Non-polymers3802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-4 kcal/mol
Surface area12800 Å2
MethodPISA
2
B: Outer membrane protein Omp38
D: Outer membrane protein Omp38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2895
Polymers27,7592
Non-polymers5303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-2 kcal/mol
Surface area12540 Å2
MethodPISA
3
E: Outer membrane protein Omp38
H: Outer membrane protein Omp38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1394
Polymers27,7592
Non-polymers3802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-1 kcal/mol
Surface area13150 Å2
MethodPISA
4
F: Outer membrane protein Omp38
G: Outer membrane protein Omp38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2895
Polymers27,7592
Non-polymers5303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-2 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.520, 99.300, 98.120
Angle α, β, γ (deg.)90.000, 105.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Outer membrane protein Omp38 / Outer membrane protein OmpA / Outer membrane protein OmpAb


Mass: 13879.479 Da / Num. of mol.: 8
Fragment: peptidoglycan-binding domain, UNP residues 221-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: omp38, ompA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6RYW5
#2: Chemical
ChemComp-API / 2,6-DIAMINOPIMELIC ACID / Diaminopimelic acid


Type: L-peptide linking / Mass: 190.197 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H14N2O4
#3: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.47 Å3/Da / Density % sol: 50.18 % / Mosaicity: 0.157 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.1M AMMONIUM TARTRATE, 15%-20% PEG 3350, pH 8, 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 315r / Detector: CCD / Date: May 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 118342 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Χ2: 1.56 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.763.80.441117981.019199.9
1.76-1.833.80.334118091.0811100
1.83-1.913.80.252117781.1571100
1.91-2.023.80.182118021.2661100
2.02-2.143.80.128117651.3691100
2.14-2.313.80.102118541.4411100
2.31-2.543.80.082118121.5571100
2.54-2.913.80.073118591.9991100
2.91-3.663.70.057118842.6361100
3.66-503.70.039119812.082199.8

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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: 1.7→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2338 5974 5 %
Rwork0.2103 --
obs-118291 99.9 %
Solvent computationBsol: 40.9985 Å2
Displacement parametersBiso max: 54.65 Å2 / Biso mean: 17.7575 Å2 / Biso min: 4.69 Å2
Baniso -1Baniso -2Baniso -3
1--2.359 Å20 Å2-0.273 Å2
2--2.007 Å20 Å2
3---0.352 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7730 0 124 704 8558
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.277
X-RAY DIFFRACTIONc_mcbond_it1.0561.5
X-RAY DIFFRACTIONc_scbond_it2.1292
X-RAY DIFFRACTIONc_mcangle_it1.512
X-RAY DIFFRACTIONc_scangle_it3.1982.5
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 (%)
1.7-1.760.28975820.2588111891177199.8
1.76-1.830.2716160.23921120111817100
1.83-1.910.25865860.22411118511771100
1.91-2.020.25375620.21711124711809100
2.02-2.140.24655640.20771119311757100
2.14-2.310.25236150.211123711852100
2.31-2.540.24276060.21021120811814100
2.54-2.910.24526340.2221121911853100
2.91-3.660.21885830.20971129911882100
3.66-500.19726260.1858113391196599.8
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
X-RAY DIFFRACTION7TAR2.paramTAR.top

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