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

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Basic information

Entry
Database: PDB / ID: 1kfm
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: 2 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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)6,0741
Polymers6,0741
Non-polymers00
Water34219
1
A: MAJOR OUTER MEMBRANE LIPOPROTEIN

A: MAJOR OUTER MEMBRANE LIPOPROTEIN

A: MAJOR OUTER MEMBRANE LIPOPROTEIN


Theoretical massNumber of molelcules
Total (without water)18,2213
Polymers18,2213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area5690 Å2
ΔGint-43 kcal/mol
Surface area8040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)37.057, 37.057, 81.912
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: 6073.553 Da / Num. of mol.: 1 / Mutation: 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.: 19 / 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: 1.78 Å3/Da / Density % sol: 30.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 4000, sodium cacodylate, ammonium acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP at 293K, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
20.1 Msodium cacodylate1droppH7.0
30.2 Mammonium acetate1drop
433 %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: 2→50 Å / Num. all: 2761 / Num. obs: 2761 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 12.3 / Num. unique all: 267 / % possible all: 97
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / Num. measured all: 20868 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.097

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MADNESSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EQ7

1eq7


Resolution: 2→25.26 Å / Rfactor Rfree error: 0.018 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 254 9.2 %RANDOM
Rwork0.26 ---
obs0.26 2761 97.8 %-
all-2761 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.1498 Å2 / ksol: 0.425897 e/Å3
Displacement parametersBiso mean: 43.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å24.24 Å20 Å2
2--1.61 Å20 Å2
3----3.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→25.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms363 0 0 19 382
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_deg0.9
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_d0.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.662
X-RAY DIFFRACTIONc_scangle_it4.172.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.074 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.356 25 9 %
Rwork0.353 267 -
obs-267 97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor obs: 0.26 / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.26
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_deg0.63
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.356 / Rfactor Rwork: 0.353

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