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- PDB-2odj: Crystal structure of the outer membrane protein OprD from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 2odj
TitleCrystal structure of the outer membrane protein OprD from Pseudomonas aeruginosa
ComponentsPorin D
KeywordsMEMBRANE PROTEIN / outer membrane protein / beta-barrel / amino acid transport
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 / SAD / Resolution: 2.9 Å
AuthorsBiswas, S. / van den Berg, B.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structural insight into OprD substrate specificity.
Authors: Biswas, S. / Mohammad, M.M. / Patel, D.R. / Movileanu, L. / van den Berg, B.
History
DepositionDec 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Porin D
B: Porin D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,33910
Polymers94,8882
Non-polymers2,4528
Water00
1
A: Porin D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2837
Polymers47,4441
Non-polymers1,8396
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Porin D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0573
Polymers47,4441
Non-polymers6132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.370, 97.525, 95.788
Angle α, β, γ (deg.)90.00, 119.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 47443.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: oprD
Plasmid details: Oprd gene with Serratia marcescens ShlB signal sequence cloned into pB22 with C-terminal His8 tag. Protein expression under control of the arabinose promoter
Plasmid: pB22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43
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.: 8 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4
Details: 0.1 M LiSO4, 0.1 M NaCl, 0.1 M Na citrate, 28-32% PEG 400 (pH 3.5), pH 4.0, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2006 / Details: Platinum coated mirror
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 22385 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1872 / % possible all: 82.5

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Processing

Software
NameClassification
CBASSdata collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3154 1520 -RANDOM
Rwork0.2476 ---
all0.2476 19342 --
obs0.2476 19323 99.9 %-
Displacement parametersBiso mean: 42.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6031 0 168 0 6199
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
LS refinement shellResolution: 2.9→3.03 Å / Rfactor Rfree error: 0.032
RfactorNum. reflection% reflection
Rfree0.422 174 -
Rwork0.324 --
obs-2395 99.7 %

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