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- PDB-3td5: Crystal structure of OmpA-like domain from Acinetobacter baumanni... -

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Basic information

Entry
Database: PDB / ID: 3td5
TitleCrystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala
Components
  • Outer membrane protein omp38
  • peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
KeywordsMEMBRANE PROTEIN/PEPTIDE BINDING PROTEIN / OmpA-like fold / cell-wall attachment / peptidoglycan-binding / MEMBRANE PROTEIN-PEPTIDE BINDING PROTEIN complex
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 profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain ...: / Outer membrane protein beta-barrel domain / Outer membrane protein beta-barrel domain / OmpA-like domain / Outer membrane protein, bacterial / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein Omp38
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPark, J.S. / Lee, W.C. / Song, J.H. / Kim, H.Y.
CitationJournal: Faseb J. / Year: 2012
Title: Mechanism of anchoring of OmpA protein to the cell wall peptidoglycan of the gram-negative bacterial outer membrane
Authors: Park, J.S. / Lee, W.C. / Yeo, K.J. / Ryu, K.S. / Kumarasiri, M. / Hesek, D. / Lee, M. / Mobashery, S. / Song, J.H. / Kim, S.I. / Lee, J.C. / Cheong, C. / Jeon, Y.H. / Kim, H.Y.
History
DepositionAug 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 1, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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 / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
I: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
J: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
K: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
L: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
M: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
N: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
O: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
P: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,50922
Polymers115,29616
Non-polymers2136
Water15,943885
1
A: Outer membrane protein omp38
B: Outer membrane protein omp38
I: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
J: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8956
Polymers28,8244
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Outer membrane protein omp38
D: Outer membrane protein omp38
K: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
L: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8595
Polymers28,8244
Non-polymers351
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Outer membrane protein omp38
F: Outer membrane protein omp38
M: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
N: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8956
Polymers28,8244
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Outer membrane protein omp38
H: Outer membrane protein omp38
O: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
P: peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8595
Polymers28,8244
Non-polymers351
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.090, 162.610, 66.228
Angle α, β, γ (deg.)90.00, 112.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Outer membrane protein omp38 / AbOmpA / Outer membrane protein ompA / Outer membrane protein ompAb


Mass: 13879.479 Da / Num. of mol.: 8 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: omp38 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RYW5
#2: Protein/peptide
peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala)


Mass: 532.544 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: synthetic peptide
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 885 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PEPTIDOGLYCAN IN CHAINS I, J, K, L, M, N, O, P CORRESPONDS TO MURAMYL PENTAPEPTIDE. HOWEVER, ...THE PEPTIDOGLYCAN IN CHAINS I, J, K, L, M, N, O, P CORRESPONDS TO MURAMYL PENTAPEPTIDE. HOWEVER, THE SUGAR 1-O-METHYL-N-ACETYL-MURAMIC ACID (AMV) IS DISORDERED IN THE STRUCTURE.

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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: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 62.5%(v/v) 2-methyl-2,4-pentanediol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2011
RadiationMonochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→81.3 Å / Num. obs: 78672 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.11 Å / % possible all: 92.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TD3

3td3


Resolution: 2→81.3 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 --RANDOM
Rwork0.2197 ---
obs-78672 92.2 %-
Refinement stepCycle: LAST / Resolution: 2→81.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7950 0 6 885 8841
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005479
X-RAY DIFFRACTIONc_angle_deg1.17514
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.3439 --
Rwork0.3348 --
obs-7640 94.2 %

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