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- PDB-4y1k: PALMITOYLATED OPRM OUTER MEMBRANE FACTOR -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4y1k
TitlePALMITOYLATED OPRM OUTER MEMBRANE FACTOR
ComponentsOuter membrane protein OprM
KeywordsMEMBRANE PROTEIN / MEMBRANE / PALMITATE / OMF / RESISTANCE
Function / homology
Function and homology information


efflux transmembrane transporter activity / transmembrane transporter activity / cell outer membrane / transmembrane transport / response to antibiotic / membrane
Similarity search - Function
Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / RND efflux system, outer membrane lipoprotein, NodT / : / Outer membrane efflux protein / Outer membrane efflux protein / Single Sheet / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / RND efflux system, outer membrane lipoprotein, NodT / : / Outer membrane efflux protein / Outer membrane efflux protein / Single Sheet / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PALMITIC ACID / Outer membrane protein OprM
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsMonlezun, L. / Phan, G. / Broutin, I.
CitationJournal: Front Microbiol / Year: 2015
Title: New OprM structure highlighting the nature of the N-terminal anchor.
Authors: Monlezun, L. / Phan, G. / Benabdelhak, H. / Lascombe, M.B. / Enguene, V.Y. / Picard, M. / Broutin, I.
History
DepositionFeb 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein OprM
B: Outer membrane protein OprM
C: Outer membrane protein OprM
D: Outer membrane protein OprM
E: Outer membrane protein OprM
F: Outer membrane protein OprM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,1959
Polymers310,4266
Non-polymers7693
Water00
1
A: Outer membrane protein OprM
B: Outer membrane protein OprM
C: Outer membrane protein OprM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,9826
Polymers155,2133
Non-polymers7693
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17020 Å2
ΔGint-98 kcal/mol
Surface area61480 Å2
MethodPISA
2
D: Outer membrane protein OprM
E: Outer membrane protein OprM
F: Outer membrane protein OprM


Theoretical massNumber of molelcules
Total (without water)155,2133
Polymers155,2133
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16190 Å2
ΔGint-91 kcal/mol
Surface area61690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.642, 87.858, 355.942
Angle α, β, γ (deg.)90.00, 98.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Outer membrane protein OprM


Mass: 51737.605 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: oprM, oprK, PA0427 / Production host: Escherichia coli (E. coli) / References: UniProt: Q51487
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H32O2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.61 % / Description: RHOMBOHEDRAL CRYSTAL
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 MM SODIUM ACETATE (PH 4.5), 6% PEG 20 000 (W/V), 300 MM AMMONIUM CITRATE, 25-30% GLYCEROL (V/V) 0.9% BETAOG
PH range: 4.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.005
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 3.8→88 Å / Num. obs: 40566 / % possible obs: 87.7 % / Redundancy: 3.2 % / Rsym value: 0.122 / Net I/σ(I): 8.5
Reflection shellResolution: 3.8→4.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 3.3 / % possible all: 77.9

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Processing

Software
NameClassification
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
Cootphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D5K

3d5k


Resolution: 3.8→87.91 Å / SU ML: 0.64 / σ(F): 1.16 / Phase error: 40.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.346 1987 4.93 %
Rwork0.297 --
obs0.299 40322 86.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→87.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21005 0 51 0 21056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121392
X-RAY DIFFRACTIONf_angle_d1.40529085
X-RAY DIFFRACTIONf_dihedral_angle_d19.4287866
X-RAY DIFFRACTIONf_chiral_restr0.0873330
X-RAY DIFFRACTIONf_plane_restr0.0063874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.89510.49481180.36922428X-RAY DIFFRACTION79
3.8951-4.00040.42781320.35282441X-RAY DIFFRACTION76
4.0004-4.11810.39361220.31882450X-RAY DIFFRACTION80
4.1181-4.2510.38151300.29542411X-RAY DIFFRACTION77
4.251-4.40290.32561270.27992538X-RAY DIFFRACTION79
4.4029-4.57920.27481300.27522510X-RAY DIFFRACTION81
4.5792-4.78760.31551350.27472623X-RAY DIFFRACTION84
4.7876-5.040.31621340.27822711X-RAY DIFFRACTION86
5.04-5.35570.36441500.28232795X-RAY DIFFRACTION90
5.3557-5.76920.29571560.30692991X-RAY DIFFRACTION94
5.7692-6.34960.35411630.3073088X-RAY DIFFRACTION97
6.3496-7.2680.31521610.30233134X-RAY DIFFRACTION99
7.268-9.15540.31271650.2633134X-RAY DIFFRACTION99
9.1554-87.92820.38631640.31463081X-RAY DIFFRACTION93

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