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- PDB-1k50: A V49A Mutation Induces 3D Domain Swapping in the B1 Domain of Pr... -

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Basic information

Entry
Database: PDB / ID: 1k50
TitleA V49A Mutation Induces 3D Domain Swapping in the B1 Domain of Protein L from Peptostreptococcus magnus
ComponentsProtein L
KeywordsPROTEIN BINDING / Protein L B1 domain / strained beta-hairpin turn / positive phi angles / domain swapping / amyloid formation
Function / homology
Function and homology information


molecular adaptor activity / extracellular region / metal ion binding
Similarity search - Function
Protein L, Ig light chain-binding / Protein L b1 domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Ubiquitin-like (UB roll) - #10 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Gram-positive cocci surface proteins LPxTG domain-containing protein
Similarity search - Component
Biological speciesFinegoldia magna (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsO'Neill, J.W. / Kim, D.E. / Johnsen, K. / Baker, D. / Zhang, K.Y.J.
CitationJournal: Structure / Year: 2001
Title: Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus.
Authors: O'Neill, J.W. / Kim, D.E. / Johnsen, K. / Baker, D. / Zhang, K.Y.
History
DepositionOct 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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 / _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: Protein L
B: Protein L
C: Protein L
D: Protein L


Theoretical massNumber of molelcules
Total (without water)27,4504
Polymers27,4504
Non-polymers00
Water3,279182
1
A: Protein L


Theoretical massNumber of molelcules
Total (without water)6,8631
Polymers6,8631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein L
D: Protein L


Theoretical massNumber of molelcules
Total (without water)13,7252
Polymers13,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-23 kcal/mol
Surface area7700 Å2
MethodPISA
3
C: Protein L


Theoretical massNumber of molelcules
Total (without water)6,8631
Polymers6,8631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-38 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.134, 53.134, 115.514
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Details2 monomers(Chain A,C)and 1 domain swapped dimer (Chain B,D)in asymmetric unit

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Components

#1: Protein
Protein L


Mass: 6862.503 Da / Num. of mol.: 4 / Fragment: B1 Domain (Residues 111-173) / Mutation: V49A, Y47W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna (bacteria) / Strain: ATCC 29328 / Gene: Protein L, B1 domain / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q51912
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 18% PEG3350, 0.2M (NH4)2SO4, 100mM Citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mMsodium phosphate1droppH7.0
218 %PEG33501reservoir
30.2 Mammonium sulfate1reservoir
4100 mMcitrate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 25, 1999 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 28770 / Num. obs: 28396 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.04 / Net I/σ(I): 30.9
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.418 / % possible all: 93.3
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 29286 / % possible obs: 98.7 % / Num. measured all: 134022 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Rmerge(I) obs: 0.435

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1hz6

1hz6


Resolution: 1.8→24.14 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 441418.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelyhood
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2821 9.9 %RANDOM
Rwork0.214 ---
all0.214 29622 --
obs0.214 28396 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.6397 Å2 / ksol: 0.378529 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.63 Å20 Å20 Å2
2--2.63 Å20 Å2
3----5.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 0 182 2122
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.552.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 418 10.1 %
Rwork0.297 3735 -
obs-3545 84.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3CARBOHYDRATE.PARAM
X-RAY DIFFRACTION4ION.PARAM
Refinement
*PLUS
% reflection Rfree: 9.5 % / Rfactor obs: 0.211 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0057
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shell
*PLUS
Rfactor Rfree: 0.303 / Rfactor Rwork: 0.297

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