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- PDB-1kfn: Core side-chain packing and backbone conformation in Lpp-56 coile... -

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Basic information

Entry
Database: PDB / ID: 1kfn
TitleCore side-chain packing and backbone conformation in Lpp-56 coiled-coil mutants
ComponentsMAJOR OUTER MEMBRANE LIPOPROTEIN
KeywordsMEMBRANE PROTEIN / LIPOPROTEIN / PROTEIN FOLDING / HELIX CAPPING / ALANINE-ZIPPER
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLiu, J. / Cao, W. / Lu, M.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Core side-chain packing and backbone conformation in Lpp-56 coiled-coil mutants.
Authors: Liu, J. / Cao, W. / Lu, M.
History
DepositionNov 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Refinement description / Category: database_2 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAJOR OUTER MEMBRANE LIPOPROTEIN


Theoretical massNumber of molelcules
Total (without water)6,0031
Polymers6,0031
Non-polymers00
Water73941
1
A: MAJOR OUTER MEMBRANE LIPOPROTEIN

A: MAJOR OUTER MEMBRANE LIPOPROTEIN

A: MAJOR OUTER MEMBRANE LIPOPROTEIN


Theoretical massNumber of molelcules
Total (without water)18,0103
Polymers18,0103
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 area5670 Å2
ΔGint-41 kcal/mol
Surface area8640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)36.290, 36.290, 83.473
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingtrigonal
Space group name H-MH3
DetailsThe biological assembly is a trimer generated from the monomer by the three fold axis.

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Components

#1: Protein MAJOR OUTER MEMBRANE LIPOPROTEIN / murein-lipoprotein lpp / murein-lipoprotein lpp


Mass: 6003.420 Da / Num. of mol.: 1 / Mutation: L23A, V27A, M30A, V34A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P69776
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.76 Å3/Da / Density % sol: 30.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 4000, sodium acetate, ammonium acetate, L-cystein, pH 4.0, VAPOR DIFFUSION, HANGING DROP at 293K, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 Msodium acetate1droppH4.0
30.2 Mammonium acetate1drop
420 mML-cysteine1drop
527 %(w/v)PEG40001drop

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Oct 12, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 4921 / Num. obs: 4921 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.7
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 6.5 / Num. unique all: 232 / % possible all: 97.9
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 33447 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Rmerge(I) obs: 0.203

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MADNESSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→29.41 Å / Rfactor Rfree error: 0.012 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 517 10.5 %RANDOM
Rwork0.244 ---
obs0.244 4921 99.7 %-
all-4921 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.6494 Å2 / ksol: 0.456794 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1--3 Å2-0.21 Å20 Å2
2---3 Å20 Å2
3---6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.65→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms386 0 0 41 427
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it2.742
X-RAY DIFFRACTIONc_scangle_it4.12.5
LS refinement shellResolution: 1.65→1.71 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.331 57 12.1 %
Rwork0.342 413 -
obs-413 98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor obs: 0.244 / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
LS refinement shell
*PLUS
Lowest resolution: 1.68 Å / Rfactor Rfree: 0.331 / Rfactor Rwork: 0.342

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