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- PDB-4foz: Crystal Structure of OccD1 (OprD) Y282R/D307H -

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Basic information

Entry
Database: PDB / ID: 4foz
TitleCrystal Structure of OccD1 (OprD) Y282R/D307H
ComponentsPorin D
KeywordsPROTEIN TRANSPORT / beta-barrel / basic amino acid/imipenem transport / outer membrane
Function / homology
Function and homology information


basic amino acid transport / outer membrane / porin activity / pore complex / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / monoatomic ion transport / serine-type peptidase activity / cell outer membrane / proteolysis
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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsEren, E. / van den Berg, B.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Toward Understanding the Outer Membrane Uptake of Small Molecules by Pseudomonas aeruginosa.
Authors: Eren, E. / Parkin, J. / Adelanwa, A. / Cheneke, B. / Movileanu, L. / Khalid, S. / van den Berg, B.
History
DepositionJun 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Feb 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 D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,68710
Polymers46,9291
Non-polymers2,7589
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.458, 104.764, 47.355
Angle α, β, γ (deg.)90.000, 98.550, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Porin D / Imipenem/basic amino acid-specific outer membrane pore / Outer membrane protein D2


Mass: 46929.281 Da / Num. of mol.: 1 / Fragment: Porin D / Mutation: Y282R, D307H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: oprD, PA0958 / Production host: Escherichia coli (E. coli)
References: UniProt: P32722, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.0 M (NH4)2SO4 (Structure Screen 1/#44), pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 26471 / % possible obs: 94.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 46.19 Å2 / Rsym value: 0.084 / Net I/σ(I): 17.96
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1376 / Rsym value: 0.716 / % possible all: 97.2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→14.964 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8486 / SU ML: 0.36 / σ(F): 1.36 / Phase error: 22.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 1579 5 %
Rwork0.1971 --
obs0.1993 26345 94.29 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.78 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 107.78 Å2 / Biso mean: 48.6325 Å2 / Biso min: 23.02 Å2
Baniso -1Baniso -2Baniso -3
1-2.7839 Å2-0 Å23.2612 Å2
2--0.5615 Å20 Å2
3----3.3454 Å2
Refinement stepCycle: LAST / Resolution: 2.4→14.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 110 78 3137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083117
X-RAY DIFFRACTIONf_angle_d1.0994174
X-RAY DIFFRACTIONf_chiral_restr0.076427
X-RAY DIFFRACTIONf_plane_restr0.004537
X-RAY DIFFRACTIONf_dihedral_angle_d18.1461127
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4003-2.4960.32661510.26412869302097
2.496-2.6090.28661510.23522856300798
2.609-2.74570.27751490.2082858300798
2.7457-2.91660.25621520.18992882303498
2.9166-3.13990.26721530.18542903305698
3.1399-3.45230.22771510.18762869302098
3.4523-3.94390.21971010.18961918201965
3.9439-4.9390.22021530.18262889304299
4.939-14.96410.22581570.20782983314099
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)
13.66061.86452.34551.04691.7442.7069-0.0308-0.3735-0.2035-0.16870.0278-0.1106-0.2975-0.1944-0.06640.30410.05350.02060.33070.03260.2937-54.100110.233911.4647
21.86230.5627-0.39150.5893-0.55781.6036-0.0943-0.1902-0.16330.08370.1449-0.1392-0.05960.061-0.09140.2922-0.0068-0.02210.3739-0.00310.286-56.379814.0971-2.973
31.1314-0.30730.35750.2586-0.6321.9704-0.03590.0588-0.11630.02290.0714-0.0063-0.01810.1231-0.02880.242-0.02520.02980.2079-0.05070.2276-36.872515.9492-4.0706
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:108)A1 - 108
2X-RAY DIFFRACTION2chain 'A' and (resseq 109:182)A109 - 182
3X-RAY DIFFRACTION3chain 'A' and (resseq 183:420)A183 - 420

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