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- PDB-1k53: Monomeric Protein L B1 Domain with a G15A Mutation -

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Basic information

Entry
Database: PDB / ID: 1k53
TitleMonomeric Protein L B1 Domain with a G15A Mutation
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: 2.1 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: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / software / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,65710
Polymers16,1342
Non-polymers5238
Water2,450136
1
A: Protein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4597
Polymers8,0671
Non-polymers3926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Protein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1983
Polymers8,0671
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.511, 66.511, 109.192
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protein L


Mass: 8066.934 Da / Num. of mol.: 2 / Fragment: B1 Domain (Residues 111-173) / Mutation: G15A, Y47W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna (bacteria) / Strain: ATCC 29328 / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q51912
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 4.32 Å3/Da / Density % sol: 71.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 225mM ZnOAC, 50mM Cacadylate pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mM1droppH4.5NaOAc
2150 mM1dropNaCl
32 mMEDTA1drop
4225 mM1reservoirZnOAc
550 mMcacodylate1reservoirpH6.5

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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: Apr 21, 2000 / 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: 2.1→30 Å / Num. all: 16917 / Num. obs: 16901 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.079 / Net I/σ(I): 14.6
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1118 / Rsym value: 0.386 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 109046 / Rmerge(I) obs: 0.109
Reflection shell
*PLUS
Rmerge(I) obs: 0.428

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1HZ5

1hz5


Resolution: 2.1→24.55 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1267659.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.233 851 5 %RANDOM
Rwork0.2129 ---
all0.23 16871 --
obs0.23 16869 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.9449 Å2 / ksol: 0.358714 e/Å3
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å21.56 Å20 Å2
2--1.38 Å20 Å2
3----2.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 8 136 1282
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it2.462
X-RAY DIFFRACTIONc_scangle_it3.532.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.241 150 5.4 %
Rwork0.213 2616 -
obs-2539 100 %
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
Highest resolution: 2.1 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor all: 0.23 / Rfactor obs: 0.213 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.2129
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0056
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.63
LS refinement shell
*PLUS
Rfactor Rfree: 0.241 / Rfactor Rwork: 0.213

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