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- PDB-5dl8: Crystal structure of Acinetobacter baumannii OccAB4 -

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Basic information

Entry
Database: PDB / ID: 5dl8
TitleCrystal structure of Acinetobacter baumannii OccAB4
ComponentsBenzoate transport porin BenP
KeywordsMEMBRANE PROTEIN / outer membrane protein / beta-barrel / antibiotic uptake / Acinetobacter baumannii
Function / homology
Function and homology information


membrane => GO:0016020 / metal ion binding
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
Benzoate transport porin BenP
Similarity search - Component
Biological speciesAcinetobacter baumannii AB307-0294 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Benzoate transport porin BenP
A: Benzoate transport porin BenP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,42214
Polymers93,8102
Non-polymers2,61212
Water5,729318
1
B: Benzoate transport porin BenP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2117
Polymers46,9051
Non-polymers1,3066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Benzoate transport porin BenP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2117
Polymers46,9051
Non-polymers1,3066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.303, 90.555, 101.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Benzoate transport porin BenP / Benzoate-specific porin


Mass: 46905.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii AB307-0294 (bacteria)
Gene: benP1, ABUW_1854 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D5YI36
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 4.18 Å3/Da / Density % sol: 70.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 4000 0.1 M potassium chloride 0.02 M Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→67.62 Å / Num. obs: 80260 / % possible obs: 99.8 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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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: 2.2→50.01 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.895 / SU B: 9.969 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24782 2055 2.6 %RANDOM
Rwork0.20665 ---
obs0.2077 78143 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2---0.52 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6372 0 112 318 6802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.026685
X-RAY DIFFRACTIONr_bond_other_d0.0020.026165
X-RAY DIFFRACTIONr_angle_refined_deg2.4191.9529024
X-RAY DIFFRACTIONr_angle_other_deg1.155314228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9935789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59325.087344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.198151090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3541516
X-RAY DIFFRACTIONr_chiral_restr0.1540.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027595
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021617
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_it1.4061.9213147
X-RAY DIFFRACTIONr_mcbond_other1.4061.9213146
X-RAY DIFFRACTIONr_mcangle_it2.1242.8753936
X-RAY DIFFRACTIONr_mcangle_other2.1242.8753937
X-RAY DIFFRACTIONr_scbond_it2.0252.2243538
X-RAY DIFFRACTIONr_scbond_other2.0252.2243539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1083.2115088
X-RAY DIFFRACTIONr_long_range_B_refined5.31116.097017
X-RAY DIFFRACTIONr_long_range_B_other5.31116.0967018
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 154 -
Rwork0.277 5695 -
obs--99.61 %
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)
12.487-1.09970.92371.5353-0.78650.56010.32390.7914-0.2648-0.0324-0.4269-0.27570.04530.23490.10310.12640.1227-0.06980.3524-0.12560.2381-24.715919.512-45.95
20.85710.16960.03272.34480.32840.27090.01820.0254-0.1270.2691-0.0075-0.27190.04810.0484-0.01070.12380.0104-0.05150.01250.00160.0738-27.81511.4571-37.9379
30.44240.2903-0.06032.2175-0.02780.5238-0.0156-0.0238-0.00830.0921-0.01540.07810.0201-0.04270.0310.10510.00440.00310.00780.00470.0282-46.128712.9611-44.368
43.71910.1165-0.26482.20080.06962.26670.12330.1462-0.2034-0.1682-0.1396-0.1968-0.12170.18460.01630.2056-0.0005-0.04180.03350.00780.0433-31.985223.5149-93.3782
50.71870.00020.1051.7439-0.06830.4690.02540.0991-0.10030.1207-0.0299-0.3385-0.00480.15440.00450.14820.0026-0.02990.0571-0.00810.1068-28.421510.5355-88.0534
60.71760.5216-0.06322.8656-0.41240.327-0.04120.04570.009-0.2112-0.01250.16390.0112-0.05460.05370.19540.0174-0.02820.0289-0.02280.05-47.388612.3786-96.1637
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 62
2X-RAY DIFFRACTION2A63 - 219
3X-RAY DIFFRACTION3A220 - 392
4X-RAY DIFFRACTION4B2 - 48
5X-RAY DIFFRACTION5B49 - 220
6X-RAY DIFFRACTION6B221 - 392

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