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- PDB-4dm5: Putative Osmotically inducible lipoprotein OsmE characterization ... -

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Basic information

Entry
Database: PDB / ID: 4dm5
TitlePutative Osmotically inducible lipoprotein OsmE characterization by Xray crystallography
ComponentsOsmotically inducible lipoprotein OsmE
KeywordsUNKNOWN FUNCTION / lipoprotein
Function / homology
Function and homology information


Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / Lipoprotein SmpA/OmlA / Outer membrane protein assembly factor BamE domain / BamE-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Osmotically inducible lipoprotein OsmE
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMamelli, L. / Spinelli, S. / Goemaere, E. / Vuillard, L.
CitationJournal: TO BE PUBLISHED
Title: Putative Osmotically inducible lipoprotein OsmE characterization by Xray crystallography
Authors: Mamelli, L. / Spinelli, S. / Goemaere, E. / Vuillard, L.
History
DepositionFeb 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Osmotically inducible lipoprotein OsmE
B: Osmotically inducible lipoprotein OsmE
C: Osmotically inducible lipoprotein OsmE
D: Osmotically inducible lipoprotein OsmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0435
Polymers46,9514
Non-polymers921
Water6,305350
1
A: Osmotically inducible lipoprotein OsmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8302
Polymers11,7381
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Osmotically inducible lipoprotein OsmE


Theoretical massNumber of molelcules
Total (without water)11,7381
Polymers11,7381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Osmotically inducible lipoprotein OsmE


Theoretical massNumber of molelcules
Total (without water)11,7381
Polymers11,7381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Osmotically inducible lipoprotein OsmE


Theoretical massNumber of molelcules
Total (without water)11,7381
Polymers11,7381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.130, 44.260, 59.280
Angle α, β, γ (deg.)94.20, 93.92, 116.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Osmotically inducible lipoprotein OsmE


Mass: 11737.640 Da / Num. of mol.: 4 / Fragment: UNP residues 19-114
Source method: isolated from a genetically manipulated source
Details: Protein without leader peptide / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: osmE, PA4876 / Plasmid: pET28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] pLysS / References: UniProt: Q9HUT7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
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: 1.95 Å3/Da / Density % sol: 36.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.01M Na-Borate, 1.7M Na-Citrate, Glycerol 2.5%, 0.01M Tris, 0.125M NaCl, 0.001M DTT , pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97926 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2011
RadiationMonochromator: YALE MIRRORS / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.5→39.49 Å / Num. obs: 104647 / % possible obs: 92.2 % / Observed criterion σ(I): 3.56
Reflection shellResolution: 1.5→1.54 Å / Num. unique all: 7813 / % possible all: 92.7

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Processing

Software
NameVersionClassification
XDSdata scaling
SHELXSphasing
REFMAC5.6.0117refinement
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→39.49 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.993 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(I): 3.56 / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20854 1616 3 %RANDOM
Rwork0.1791 ---
all0.1796 53849 --
obs0.18002 52232 94.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20.05 Å20.28 Å2
2--0.04 Å2-0.07 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 6 350 3135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192918
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4671.9733927
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1225368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70424.467150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5415492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4011523
X-RAY DIFFRACTIONr_chiral_restr0.1820.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212277
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 119 -
Rwork0.254 3832 -
obs-3832 93.98 %
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)
12.54410.3853-0.26460.75990.64261.49940.0023-0.14170.1325-0.04790.02060.14160.02850.1589-0.02290.0827-0.0363-0.01060.08920.00530.06753.6996-0.7603-40.8426
21.3282-0.01180.33570.89630.90611.4013-0.01590.1881-0.05990.03030.06450.1083-0.00960.2194-0.04870.08580.03640.0230.12950.00290.09040.95092.1789-13.5439
33.97110.7808-0.28821.4014-0.06480.85390.0282-0.1409-0.46380.0394-0.0744-0.0029-0.0546-0.01340.04620.0518-0.047-0.00420.06160.00690.1369-8.0759-18.2017-42.7466
43.4845-0.78920.34751.28520.03921.020.02810.06570.3888-0.0259-0.06920.01420.04170.01660.04110.05840.02870.00810.03340.01630.13317.5365-20.4463-9.9356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 95
2X-RAY DIFFRACTION2B8 - 102
3X-RAY DIFFRACTION3C9 - 95
4X-RAY DIFFRACTION4D8 - 94

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