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- PDB-1eq7: CORE STRUCTURE OF THE OUTER MEMBRANE LIPOPROTEIN FROM ESCHERICHIA... -

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Basic information

Entry
Database: PDB / ID: 1eq7
TitleCORE STRUCTURE OF THE OUTER MEMBRANE LIPOPROTEIN FROM ESCHERICHIA COLI AT 1.9 ANGSTROM RESOLUTION
ComponentsOUTER MEMBRANE LIPOPROTEIN
KeywordsMEMBRANE PROTEIN / lipoprotein / outer membrane / protein folding / helix capping
Function / homology
Function and homology information


periplasmic space organization / lipid modification / peptidoglycan binding / cell outer membrane / outer membrane-bounded periplasmic space / lipid binding / extracellular region / identical protein binding / membrane
Similarity search - Function
Lipoprotein leucine-zipper / Major outer membrane lipoprotein Lpp / Lipoprotein leucine-zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #190 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Major outer membrane lipoprotein Lpp
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsShu, W. / Liu, J. / Ji, H. / Lu, M.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Core structure of the outer membrane lipoprotein from Escherichia coli at 1.9 A resolution.
Authors: Shu, W. / Liu, J. / Ji, H. / Lu, M.
History
DepositionApr 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OUTER MEMBRANE LIPOPROTEIN


Theoretical massNumber of molelcules
Total (without water)6,1621
Polymers6,1621
Non-polymers00
Water1,09961
1
A: OUTER MEMBRANE LIPOPROTEIN

A: OUTER MEMBRANE LIPOPROTEIN

A: OUTER MEMBRANE LIPOPROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4853
Polymers18,4853
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area5980 Å2
ΔGint-58 kcal/mol
Surface area9050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)34.363, 34.363, 194.135
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 constructed from chain A and its two symmetry partners generated by the three-fold.

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Components

#1: Protein OUTER MEMBRANE LIPOPROTEIN


Mass: 6161.724 Da / Num. of mol.: 1 / Fragment: PROTEIN MOIETY
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PLPP-56 / Production host: Escherichia coli (E. coli) / References: UniProt: P69776
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.79 Å3/Da / Density % sol: 31.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Details: drop was eluted 1:1 with a reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.2 Mammonium sulfate1reservoir
30.1 Msodium acetate1reservoir
430 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. all: 3749 / Num. obs: 3749 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→15 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 567 15.1 %RANDOM
Rwork0.214 ---
obs0.214 3749 99.8 %-
all-3749 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 82.36 Å2 / ksol: 0.444 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20.15 Å20 Å2
2---0.57 Å20 Å2
3---1.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms408 0 0 61 469
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.61
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.81.5
X-RAY DIFFRACTIONc_mcangle_it1.222
X-RAY DIFFRACTIONc_scbond_it1.562
X-RAY DIFFRACTIONc_scangle_it2.242.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 94 15.5 %
Rwork0.269 511 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.61

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