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- PDB-5dl5: Crystal structure of Acinetobacter baumannii OccAB1 -

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Basic information

Entry
Database: PDB / ID: 5dl5
TitleCrystal structure of Acinetobacter baumannii OccAB1
ComponentsMembrane protein
KeywordsMEMBRANE PROTEIN / outer membrane protein / beta-barrel / antibiotic uptake
Function / homologyPorin / Porin / Beta Barrel / Mainly Beta / PHOSPHATE ION / :
Function and homology information
Biological speciesAcinetobacter baumannii AB307-0294 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZahn, M. / Basle, A. / van den Berg, B.
CitationJournal: Structure / Year: 2016
Title: Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii.
Authors: Zahn, M. / Bhamidimarri, S.P. / Basle, A. / Winterhalter, M. / van den Berg, B.
History
DepositionSep 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4905
Polymers47,4761
Non-polymers1,0144
Water1,36976
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-2 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.073, 134.073, 54.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Membrane protein


Mass: 47476.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii AB307-0294 (bacteria)
Gene: VM83_01045 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F5EN03
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32% PEG 400, 0.2 M ammonium phosphate, 0.1 M ammonium sulphate, 0.1 M sodium citrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→116.11 Å / Num. obs: 35036 / % possible obs: 99.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 19.1
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.1 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SYS

3sys


Resolution: 2.05→116.11 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.63 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 1705 4.9 %RANDOM
Rwork0.19035 ---
obs0.19181 33329 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.05→116.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 42 76 3350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0193345
X-RAY DIFFRACTIONr_bond_other_d0.0020.023034
X-RAY DIFFRACTIONr_angle_refined_deg2.2671.934520
X-RAY DIFFRACTIONr_angle_other_deg1.10936958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2625415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.61924.675169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24115510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0431515
X-RAY DIFFRACTIONr_chiral_restr0.1510.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02836
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9852.6331663
X-RAY DIFFRACTIONr_mcbond_other1.9822.6321662
X-RAY DIFFRACTIONr_mcangle_it2.6683.9352077
X-RAY DIFFRACTIONr_mcangle_other2.6683.9362078
X-RAY DIFFRACTIONr_scbond_it3.3363.0961682
X-RAY DIFFRACTIONr_scbond_other3.2913.0911679
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8944.4632438
X-RAY DIFFRACTIONr_long_range_B_refined6.53322.2313606
X-RAY DIFFRACTIONr_long_range_B_other6.53322.2373607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 108 -
Rwork0.237 2375 -
obs--95.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1352-0.1910.0722.6154-0.89020.61-0.0107-0.01160.03560.05780.00580.1083-0.0585-0.06080.00490.0137-0.01550.00820.0831-0.04570.0709-17.0763-54.78842.6498
23.2221.46052.37272.69760.4634.3456-0.0051-0.40480.0350.284-0.1558-0.054-0.2706-0.08840.16090.0697-0.02460.02070.1129-0.01660.10734.0586-55.901211.328
32.38120.0763-0.29021.7141-0.07241.0952-0.09350.02560.1684-0.03380.0525-0.0753-0.1232-0.11330.0410.0421-0.0252-0.01110.0803-0.01260.0684-0.0644-43.8566-1.7062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 179
2X-RAY DIFFRACTION2A180 - 222
3X-RAY DIFFRACTION3A223 - 415

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