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- PDB-1kh0: Accurate Computer Base Design of a New Backbone Conformation in t... -

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Basic information

Entry
Database: PDB / ID: 1kh0
TitleAccurate Computer Base Design of a New Backbone Conformation in the Second Turn of Protein L
Componentsprotein L
KeywordsPROTEIN BINDING / Protein L B1 domain / computational based protein design / Type 1' beta turn / extensive amino acid mutations.
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: 1.9 Å
AuthorsO'Neill, J.W. / Kuhlman, B. / Kim, D.E. / Zhang, K.Y. / Baker, D.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Accurate computer-based design of a new backbone conformation in the second turn of protein L.
Authors: Kuhlman, B. / O'Neill, J.W. / Kim, D.E. / Zhang, K.Y. / Baker, D.
History
DepositionNov 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: 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 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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 1.5Aug 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

Downloads & links

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Assembly

Deposited unit
A: protein L
B: protein L


Theoretical massNumber of molelcules
Total (without water)14,2482
Polymers14,2482
Non-polymers00
Water1,44180
1
A: protein L


Theoretical massNumber of molelcules
Total (without water)7,1241
Polymers7,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: protein L


Theoretical massNumber of molelcules
Total (without water)7,1241
Polymers7,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.622, 55.542, 67.382
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


Mass: 7124.085 Da / Num. of mol.: 2 / Fragment: B1 DOMAIN (RESIDUES 111-173)
Mutation: F26K, T30L, A33V, Y34L, Y47W, V49I, A54T, D55N, K56G, G57B, Y58I, T59I
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.: 80 / 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: 2.2 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M Sodium Citrate, 100mM Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1100 mM1dropNaCl
22 mMEDTA1drop
325 mg/mlprotein1drop
41.0 Msodium citrate1reservoir
5100 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: Oct 22, 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: 1.9→25 Å / Num. all: 11610 / Num. obs: 11610 / % possible obs: 96.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.043 / Net I/σ(I): 36.4
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 6.9 / Num. unique all: 923 / Rsym value: 0.252 / % possible all: 95.1
Reflection
*PLUS
Lowest resolution: 25 Å

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HZ6

1hz6


Resolution: 1.9→23.09 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1027037.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1134 9.8 %RANDOM
Rwork0.197 ---
obs0.197 11579 97 %-
all-11579 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.2031 Å2 / ksol: 0.341182 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.22 Å20 Å20 Å2
2---3.83 Å20 Å2
3----2.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.9→23.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 0 80 1074
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.741.5
X-RAY DIFFRACTIONc_mcangle_it2.722
X-RAY DIFFRACTIONc_scbond_it3.82
X-RAY DIFFRACTIONc_scangle_it5.192.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 171 9.2 %
Rwork0.208 1683 -
obs-1630 95.1 %
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
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
X-RAY DIFFRACTIONc_mcbond_it1.741.5
X-RAY DIFFRACTIONc_scbond_it3.82
X-RAY DIFFRACTIONc_mcangle_it2.722
X-RAY DIFFRACTIONc_scangle_it5.192.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.265 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.208

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