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- PDB-4ozb: Backbone Modifications in the Protein GB1 Helix: beta-ACPC24, bet... -

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Basic information

Entry
Database: PDB / ID: 4ozb
TitleBackbone Modifications in the Protein GB1 Helix: beta-ACPC24, beta-3-Lys28, beta-3-Lys31, beta-ACPC35
ComponentsStreptococcal Protein GB1 Backbone Modified Variant: beta-ACPC24, beta-3-Lys28, beta-3-Lys31, beta-ACPC35Streptococcus
KeywordsDE NOVO PROTEIN / unnatural backbone
Function / homology
Function and homology information


IgG binding / cell wall / extracellular region
Similarity search - Function
B domain / IgG-binding B / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...B domain / IgG-binding B / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / 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
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsReinert, Z.E. / Horne, W.S.
CitationJournal: Chem Sci / Year: 2014
Title: Folding Thermodynamics of Protein-Like Oligomers with Heterogeneous Backbones.
Authors: Reinert, Z.E. / Horne, W.S.
History
DepositionFeb 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_struct_oper_list / software
Item: _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptococcal Protein GB1 Backbone Modified Variant: beta-ACPC24, beta-3-Lys28, beta-3-Lys31, beta-ACPC35
B: Streptococcal Protein GB1 Backbone Modified Variant: beta-ACPC24, beta-3-Lys28, beta-3-Lys31, beta-ACPC35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6784
Polymers12,4942
Non-polymers1842
Water2,720151
1
A: Streptococcal Protein GB1 Backbone Modified Variant: beta-ACPC24, beta-3-Lys28, beta-3-Lys31, beta-ACPC35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3392
Polymers6,2471
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Streptococcal Protein GB1 Backbone Modified Variant: beta-ACPC24, beta-3-Lys28, beta-3-Lys31, beta-ACPC35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3392
Polymers6,2471
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)92.496, 22.622, 64.523
Angle α, β, γ (deg.)90.000, 120.930, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-219-

HOH

21A-235-

HOH

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Components

#1: Protein Streptococcal Protein GB1 Backbone Modified Variant: beta-ACPC24, beta-3-Lys28, beta-3-Lys31, beta-ACPC35 / Streptococcus


Mass: 6246.825 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptococcus sp. (bacteria) / References: UniProt: P19909*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate pH 5.6, 20% v/v isopropanol, 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 11, 2013
RadiationMonochromator: Rigaku VariMax Optics / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→22.75 Å / Num. obs: 10465 / % possible obs: 94.9 % / Redundancy: 4.41 % / Biso Wilson estimate: 19.41 Å2 / Rmerge(I) obs: 0.069 / Χ2: 1.16 / Net I/σ(I): 18 / Num. measured all: 46515 / Scaling rejects: 349
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.8-1.863.170.2423.330909750.56089.1
1.86-1.943.280.2063.932639930.6293.1
1.94-2.033.390.1865348910280.71794
2.03-2.133.580.1826361810080.891092.1
2.13-2.273.670.1626.9367810010.86490.9
2.27-2.443.980.1487.8403910110.91493.9
2.44-2.694.360.13410.4466810561.256397.3
2.69-3.084.810.10316537410961.5110798.8
3.08-3.876.180.0726.9703911301.395099.6
3.87-22.7570.04748.3825711671.5792100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CrystalClearphasing
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.14data extraction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QMT
Resolution: 1.8→22.753 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 26.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 506 4.84 %
Rwork0.1905 9947 -
obs0.1915 10453 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.35 Å2 / Biso mean: 24.2668 Å2 / Biso min: 8.88 Å2
Refinement stepCycle: final / Resolution: 1.8→22.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 22 151 1055
Biso mean--34.11 30.43 -
Num. residues----114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011908
X-RAY DIFFRACTIONf_angle_d1.4281232
X-RAY DIFFRACTIONf_chiral_restr0.088146
X-RAY DIFFRACTIONf_plane_restr0.005152
X-RAY DIFFRACTIONf_dihedral_angle_d13.954274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8001-1.98110.29851210.22962359248092
1.9811-2.26760.22121200.19392398251892
2.2676-2.85610.20951130.21022522263596
2.8561-22.75480.1931520.17352668282099

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