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- PDB-1hz6: CRYSTAL STRUCTURES OF THE B1 DOMAIN OF PROTEIN L FROM PEPTOSTREPT... -

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Basic information

Entry
Database: PDB / ID: 1hz6
TitleCRYSTAL STRUCTURES OF THE B1 DOMAIN OF PROTEIN L FROM PEPTOSTREPTOCOCCUS MAGNUS WITH A TYROSINE TO TRYPTOPHAN SUBSTITUTION
ComponentsPROTEIN L
KeywordsPROTEIN BINDING / Four stranded beta-sheet with central alpha helix / binds kappa light chain of immunoglobulins
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: 1.7 Å
AuthorsO'Neill, J.W. / Kim, D.E. / Baker, D. / Zhang, K.Y.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution.
Authors: O'Neill, J.W. / Kim, D.E. / Baker, D. / Zhang, K.Y.
History
DepositionJan 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: 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


Theoretical massNumber of molelcules
Total (without water)24,1593
Polymers24,1593
Non-polymers00
Water5,386299
1
A: PROTEIN L


Theoretical massNumber of molelcules
Total (without water)8,0531
Polymers8,0531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN L


Theoretical massNumber of molelcules
Total (without water)8,0531
Polymers8,0531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN L


Theoretical massNumber of molelcules
Total (without water)8,0531
Polymers8,0531
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 area2020 Å2
ΔGint-14 kcal/mol
Surface area10440 Å2
MethodPISA
5
B: PROTEIN L
C: PROTEIN L


Theoretical massNumber of molelcules
Total (without water)16,1062
Polymers16,1062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-7 kcal/mol
Surface area7040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.611, 54.020, 95.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN L / IG KAPPA LIGHT CHAIN-BINDING PROTEIN


Mass: 8052.908 Da / Num. of mol.: 3 / Fragment: B1 DOMAIN / Mutation: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.75 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30%PEG 8000, 0.2M Ammonium Sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDUnitCommon nameCrystal-IDSol-IDDetails
1%PEG80001reservoir
2Mammonium sulfate1reservoir
3%PEG4001reservoircryoprotectant

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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: Oct 5, 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: 1.7→25 Å / Num. all: 120968 / Num. obs: 28825 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.94 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 1.69→1.71 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 6.8 / Num. unique all: 1031 / Rsym value: 0.252 / % possible all: 95.1
Reflection shell
*PLUS
% possible obs: 95.1 %

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: C3 DOMAIN OF PROTEIN L (UNPUBLISHED: T. WAN AND B. SUTTON)

Resolution: 1.7→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 923930.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1471 5.1 %RANDOM
Rwork0.193 ---
obs0.193 28825 96.3 %-
all-29936 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.29 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--1.1 Å20 Å2
3----1.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 0 299 1787
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0056
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.671.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.872
X-RAY DIFFRACTIONc_scangle_it4.282.5
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 141 5.2 %
Rwork0.293 4360 -
obs-2618 94.5 %
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
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68

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