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- PDB-1wp1: Crystal structure of the drug-discharge outer membrane protein, OprM -

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Basic information

Entry
Database: PDB / ID: 1wp1
TitleCrystal structure of the drug-discharge outer membrane protein, OprM
ComponentsOuter membrane protein oprM
KeywordsMEMBRANE PROTEIN / BETA BARREL
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. / Up-down Bundle ...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
Outer membrane protein OprM
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.56 Å
AuthorsAkama, H. / Kanemaki, M. / Yoshimura, M. / Tsukihara, T. / Kashiwagi, T. / Narita, S. / Nakagawa, A. / Nakae, T.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of the drug discharge outer membrane protein, OprM, of Pseudomonas aeruginosa: dual modes of membrane anchoring and occluded cavity end
Authors: Akama, H. / Kanemaki, M. / Yoshimura, M. / Tsukihara, T. / Kashiwagi, T. / Yoneyama, H. / Narita, S. / Nakagawa, A. / Nakae, T.
History
DepositionAug 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)103,4752
Polymers103,4752
Non-polymers00
Water43224
1
A: Outer membrane protein oprM

A: Outer membrane protein oprM

A: Outer membrane protein oprM


Theoretical massNumber of molelcules
Total (without water)155,2133
Polymers155,2133
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area15730 Å2
ΔGint-103 kcal/mol
Surface area59050 Å2
MethodPISA, PQS
2
B: Outer membrane protein oprM

B: Outer membrane protein oprM

B: Outer membrane protein oprM


Theoretical massNumber of molelcules
Total (without water)155,2133
Polymers155,2133
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12420 Å2
ΔGint-77 kcal/mol
Surface area55700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.43, 85.43, 1044.3
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a trimer by the operation -Y,X-Y,Z and Y-X,-X,Z.

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Components

#1: Protein Outer membrane protein oprM / drug-discharge outer membrane protein OprM


Mass: 51737.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: oprM / Plasmid: pMMB67EH / Production host: Pseudomonas aeruginosa (bacteria) / Strain (production host): TNP072 / References: UniProt: Q51487
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.5 Å3/Da / Density % sol: 65.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: sodium acetate, imidazole, octyl-POE, CYMAL-3, MPD, tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: May 30, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.56→40 Å / Num. all: 48709 / Num. obs: 48709 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 11.4 % / Biso Wilson estimate: 79.2 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 6.4
Reflection shellResolution: 2.56→2.7 Å / % possible obs: 94.5 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2 / Num. unique all: 47683 / Rsym value: 0.362 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.56→38.63 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 25.59 / SU ML: 0.251 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30772 2438 5.1 %RANDOM
Rwork0.25235 ---
all0.25503 48677 --
obs0.25503 48677 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.123 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.36 Å20 Å2
2--0.73 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.56→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6647 0 0 24 6671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226752
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9639182
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9895856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30724.458332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0381557
X-RAY DIFFRACTIONr_chiral_restr0.0850.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025202
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.23033
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24680
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.2155
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5931.54402
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04426814
X-RAY DIFFRACTIONr_scbond_it1.59132664
X-RAY DIFFRACTIONr_scangle_it2.64.52368
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.564→2.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 161 -
Rwork0.349 2993 -
obs--90.14 %
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)
10.29711.067-0.95276.76880.65268.70880.06260.12370.6061-0.1987-0.26160.0049-1.9353-0.06370.19910.0010.00070.00110.00070.0001-0.00087.10275.00838.963
22.1157-1.0792.82471.7899-2.39114.5002-0.2719-0.0390.33010.09520.3356-0.749-1.21311.4318-0.06370.0957-0.29560.13250.4793-0.02530.030523.73660.05854.643
30.39780.13690.20530.4012-0.23265.042-0.00220.0736-0.0016-0.001-0.0183-0.0906-0.40771.03780.0206-0.1477-0.05250.0134-0.0397-0.0132-0.041611.58953.27359.358
40.1662-0.0371-1.39070.00830.310811.63590.3562-0.0873-0.2462-0.3979-0.2512-0.1734-0.45880.1187-0.1050.00030.01010.0118-0.0057-0.0125-0.00447.07151.135-5.796
51.97260.3087-1.75083.246-2.228719.0608-1.0136-0.71010.00510.5138-0.4726-0.31311.2414-0.93921.48620.0004-0.00050.0019-0.00030.0005-0.0002-7.101-25.75136.675
61.4328-1.45411.02774.1992-2.56061.5828-0.2277-0.4219-0.61410.6601-0.0292-0.62441.04680.56240.25690.03450.1030.12860.03530.0722-0.017514.471-20.97120.086
71.75160.4037-0.28012.00560.21411.833-0.0086-0.2874-0.43910.2436-0.234-0.44380.40020.24410.2427-0.10620.0436-0.017-0.02030.157-0.13087.934-9.352116.203
85.38155.22.24796.2927-2.741719.97870.48911.1470.74160.2039-0.4698-1.90811.3489-0.4678-0.0193-0.00010.0008-0.00030.00040.0003-0.0003-4.511-14.904170.369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 60
3X-RAY DIFFRACTION2A239 - 273
4X-RAY DIFFRACTION2A449 - 456
5X-RAY DIFFRACTION3A61 - 85
6X-RAY DIFFRACTION3A131 - 238
7X-RAY DIFFRACTION3A274 - 295
8X-RAY DIFFRACTION3A340 - 446
9X-RAY DIFFRACTION4A86 - 130
10X-RAY DIFFRACTION4A296 - 339
11X-RAY DIFFRACTION5B1 - 23
12X-RAY DIFFRACTION6B24 - 60
13X-RAY DIFFRACTION6B239 - 273
14X-RAY DIFFRACTION7B61 - 85
15X-RAY DIFFRACTION7B131 - 238
16X-RAY DIFFRACTION7B274 - 295
17X-RAY DIFFRACTION7B340 - 446
18X-RAY DIFFRACTION8B86 - 89
19X-RAY DIFFRACTION8B123 - 130
20X-RAY DIFFRACTION8B296 - 303
21X-RAY DIFFRACTION8B329 - 339

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