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- PDB-5dl6: Crystal structure of Acinetobacter baumannii OccAB2 -

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Basic information

Entry
Database: PDB / ID: 5dl6
TitleCrystal structure of Acinetobacter baumannii OccAB2
ComponentsPutative porin for vanillate trafficking (VanP)
KeywordsMEMBRANE PROTEIN / outer membrane protein / beta-barrel / antibiotic uptake Acinetobacter
Function / homology
Function and homology information


membrane => GO:0016020 / membrane
Similarity search - Function
Outer membrane porin, bacterial / outer membrane porin, OprD family / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
OprD family porin / Outer membrane porin, OprD family
Similarity search - Component
Biological speciesAcinetobacter baumannii AB307-0294 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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

Downloads & links

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Assembly

Deposited unit
A: Putative porin for vanillate trafficking (VanP)


Theoretical massNumber of molelcules
Total (without water)47,0261
Polymers47,0261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.169, 150.169, 105.224
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Putative porin for vanillate trafficking (VanP)


Mass: 47026.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii AB307-0294 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E4HLL9, UniProt: A0A5P9QVH7*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22% PEG 400 0.2 M calcium chloride 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.9→55.32 Å / Num. obs: 15640 / % possible obs: 98.4 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 10.6
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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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: 2.9→55.32 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.889 / SU B: 45.275 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R: 0.845 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28424 746 4.8 %RANDOM
Rwork0.23703 ---
obs0.23951 14888 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.913 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20.58 Å20 Å2
2--1.17 Å2-0 Å2
3----3.79 Å2
Refinement stepCycle: 1 / Resolution: 2.9→55.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 0 0 3170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193250
X-RAY DIFFRACTIONr_bond_other_d0.0020.022958
X-RAY DIFFRACTIONr_angle_refined_deg2.1771.9434402
X-RAY DIFFRACTIONr_angle_other_deg1.14536794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5735393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26524.083169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.34915524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.081518
X-RAY DIFFRACTIONr_chiral_restr0.1220.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023763
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02815
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_it2.0324.1371578
X-RAY DIFFRACTIONr_mcbond_other2.0324.1361577
X-RAY DIFFRACTIONr_mcangle_it3.2756.2041969
X-RAY DIFFRACTIONr_mcangle_other3.2756.2041970
X-RAY DIFFRACTIONr_scbond_it2.1454.3711672
X-RAY DIFFRACTIONr_scbond_other2.1454.3711672
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4816.4832433
X-RAY DIFFRACTIONr_long_range_B_refined5.29733.1063397
X-RAY DIFFRACTIONr_long_range_B_other5.29733.1093398
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 54 -
Rwork0.299 1085 -
obs--99.56 %
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)
12.07580.59280.16496.0531-4.34045.55230.03930.0191-0.0074-0.1769-0.00510.03710.3594-0.0335-0.03430.10590.0443-0.02190.1216-0.08850.068913.521445.2225.8263
21.10550.07410.28981.4033-0.38490.19540.08720.080.0172-0.2059-0.117-0.08710.08740.07820.02980.1876-0.0035-0.01110.22960.0230.010730.303847.042925.9947
30.065-0.2336-0.40521.91342.85384.35190.00560.13130.0686-0.0478-0.2610.2798-0.0156-0.52950.25550.46560.08740.00060.37770.22040.340432.827931.334930.9429
41.9206-0.74590.69441.32-0.63540.40750.16760.3972-0.0623-0.1767-0.12330.1770.11410.1112-0.04420.23240.0753-0.03960.2594-0.06020.068720.884631.41627.0502
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 33
2X-RAY DIFFRACTION2A34 - 285
3X-RAY DIFFRACTION3A286 - 308
4X-RAY DIFFRACTION4A309 - 398

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