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- PDB-4fuv: Crystal Structure of Acinetobacter baumannii CarO -

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Basic information

Entry
Database: PDB / ID: 4fuv
TitleCrystal Structure of Acinetobacter baumannii CarO
Componentsporin protein associated with imipenem resistance
KeywordsTRANSPORT PROTEIN / 8-stranded b-barrel / ornithine/imipenem transport / outer membrane
Function / homologyPorin - #170 / Porin / Beta Barrel / Mainly Beta / Putative porin protein associated with imipenem resistance / Putative porin protein associated with imipenem resistance
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.151 Å
AuthorsEren, E. / van den Berg, B.
CitationJournal: To be Published
Title: Outer membrane transport of amino acids and antibiotics by an 8-stranded b-barrel protein
Authors: Eren, E. / Ohneswere, S. / Adelanwa, A. / van den Berg, B.
History
DepositionJun 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: porin protein associated with imipenem resistance
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,23811
Polymers25,3841
Non-polymers2,85410
Water2,270126
1
A: porin protein associated with imipenem resistance
hetero molecules

A: porin protein associated with imipenem resistance
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,47622
Polymers50,7682
Non-polymers5,70820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7240 Å2
ΔGint-34 kcal/mol
Surface area23470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.526, 120.867, 112.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein porin protein associated with imipenem resistance


Mass: 25383.787 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 22-246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: TCDC-AB0715 / Gene: ABTW07_2987 / Production host: Escherichia coli (E. coli) / References: UniProt: F0QP73, UniProt: A0A7U4DTK0*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.11 Å3/Da / Density % sol: 70.06 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 1000, 0.1M lithium sulfate, 0.1M sodium sulfate, 0.05M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X6A10.9784, 0.9788, 0.9184
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDFeb 1, 2012
ADSC QUANTUM 3152CCDApr 1, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97841
20.97881
30.91841
41.11
ReflectionResolution: 2.15→50 Å / Num. obs: 22958 / % possible obs: 99.1 % / Redundancy: 6 % / Rsym value: 4.4 / Net I/σ(I): 39.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.14 / Num. unique all: 1041 / Rsym value: 53.2 / % possible all: 91.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
AutoSolphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.151→41.11 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 2245 9.88 %
Rwork0.2018 --
obs0.2057 22727 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.151→41.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 112 126 1842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081759
X-RAY DIFFRACTIONf_angle_d1.1922359
X-RAY DIFFRACTIONf_dihedral_angle_d24.92634
X-RAY DIFFRACTIONf_chiral_restr0.083240
X-RAY DIFFRACTIONf_plane_restr0.005306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1509-2.19750.39841430.35461188X-RAY DIFFRACTION92
2.1975-2.24850.59221230.47151141X-RAY DIFFRACTION91
2.2485-2.30450.38081400.28431253X-RAY DIFFRACTION99
2.3045-2.36660.28941330.20461298X-RAY DIFFRACTION99
2.3666-2.43590.21671320.19871280X-RAY DIFFRACTION100
2.4359-2.51420.27441310.1951306X-RAY DIFFRACTION100
2.5142-2.60360.23071450.19351272X-RAY DIFFRACTION100
2.6036-2.70730.23741360.19231299X-RAY DIFFRACTION100
2.7073-2.82970.28041390.1941286X-RAY DIFFRACTION100
2.8297-2.97780.22541470.20411292X-RAY DIFFRACTION100
2.9778-3.16270.25621450.19251266X-RAY DIFFRACTION100
3.1627-3.40430.20631390.18621313X-RAY DIFFRACTION100
3.4043-3.7420.23251460.18821282X-RAY DIFFRACTION98
3.742-4.27250.2341450.20111307X-RAY DIFFRACTION100
4.2725-5.34210.19491480.17431317X-RAY DIFFRACTION99
5.3421-14.99040.25161530.20751382X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.1343 Å / Origin y: 73.6753 Å / Origin z: 40.1813 Å
111213212223313233
T0.261 Å2-0.0518 Å2-0.0382 Å2-0.2616 Å20.0211 Å2--0.1972 Å2
L1.3302 °20.9945 °2-0.3915 °2-1.7158 °2-0.2922 °2--0.2534 °2
S0.1002 Å °-0.1381 Å °0.0878 Å °0.1259 Å °-0.1734 Å °-0.0338 Å °-0.0612 Å °0.0266 Å °0.0832 Å °
Refinement TLS groupSelection details: all

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