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- PDB-5dl7: Crystal structure of Acinetobacter baumannii OccAB3 -

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Basic information

Entry
Database: PDB / ID: 5dl7
TitleCrystal structure of Acinetobacter baumannii OccAB3
ComponentsPorin
KeywordsMEMBRANE PROTEIN / outer membrane protein / beta-barrel / antibiotic uptake / Acinetobacter baumannii
Function / homology
Function and homology information


porin activity / metal ion binding / 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
Biological speciesAcinetobacter baumannii AB307-0294 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,61612
Polymers48,3111
Non-polymers2,30511
Water3,891216
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-40 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.563, 125.717, 137.459
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-681-

HOH

21A-711-

HOH

31A-808-

HOH

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Components

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


Mass: 48310.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii AB307-0294 (bacteria)
Gene: ABUW_2771 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D5YKR4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.65 Å3/Da / Density % sol: 66.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% 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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→70.14 Å / Num. obs: 71286 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 20
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.9 / % 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: 1.75→70.14 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.167 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19144 1831 2.6 %RANDOM
Rwork0.16815 ---
obs0.16875 69454 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.383 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2---1.64 Å20 Å2
3---0.8 Å2
Refinement stepCycle: 1 / Resolution: 1.75→70.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 110 216 3586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0193436
X-RAY DIFFRACTIONr_bond_other_d0.0020.023218
X-RAY DIFFRACTIONr_angle_refined_deg2.9491.974589
X-RAY DIFFRACTIONr_angle_other_deg1.31237397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4295401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42823.552183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2615559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8181527
X-RAY DIFFRACTIONr_chiral_restr0.1880.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.023871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02864
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_it1.8911.9621607
X-RAY DIFFRACTIONr_mcbond_other1.8881.961606
X-RAY DIFFRACTIONr_mcangle_it2.4432.9312007
X-RAY DIFFRACTIONr_mcangle_other2.4442.9322008
X-RAY DIFFRACTIONr_scbond_it3.7182.521829
X-RAY DIFFRACTIONr_scbond_other3.7192.5221830
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2023.5642583
X-RAY DIFFRACTIONr_long_range_B_refined7.14517.5393775
X-RAY DIFFRACTIONr_long_range_B_other7.14517.5473776
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 137 -
Rwork0.218 5069 -
obs--99.83 %
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)
14.58062.16462.81124.38162.85274.228-0.0759-0.14110.05520.0991-0.01120.0771-0.1002-0.08890.08710.06420.06290.04550.10080.05610.0454-12.0637-36.8483-13.4176
21.34890.03220.06440.87970.21781.36820.0251-0.15970.13610.09330.00690.0407-0.1560.0298-0.0320.0368-0.00480.01560.0218-0.01440.02062.9256-38.3452-22.8205
31.3919-2.6028-0.41767.15210.84810.41070.0194-0.00030.1676-0.0428-0.0341-0.1614-0.119-0.06930.01470.05180.0177-0.03870.03140.00760.0853-14.6311-34.2997-32.2633
41.4693-0.50860.25993.01460.84382.3742-0.1101-0.19450.21830.06960.04230.0629-0.4375-0.08170.06780.10090.0299-0.00280.06340.01030.1108-15.0201-35.3195-21.0712
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 43
2X-RAY DIFFRACTION2A44 - 307
3X-RAY DIFFRACTION3A308 - 362
4X-RAY DIFFRACTION4A363 - 404

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