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- PDB-4oza: Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, be... -

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Basic information

Entry
Database: PDB / ID: 4oza
TitleBackbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Gln32, beta-3-Asp36
ComponentsStreptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Gln32, beta-3-Asp36Streptococcus
KeywordsDE NOVO PROTEIN / unnatural backbone
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / 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. ...IgG-binding B / B domain / 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
ISOPROPYL ALCOHOL / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.201 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
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_torsion
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega

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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-3-Ala24, beta-3-Lys28, beta-3-Gln32, beta-3-Asp36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2992
Polymers6,2391
Non-polymers601
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint3 kcal/mol
Surface area3620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.944, 65.944, 21.896
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Gln32, beta-3-Asp36 / Streptococcus


Mass: 6238.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus sp. (bacteria) / References: UniProt: P19909*PLUS
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.91 Å3/Da / Density % sol: 35.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M calcium chloride, 0.1 M sodium acetate pH 4.6, 30% v/v isopropanol

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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: Aug 30, 2012
RadiationMonochromator: Rigaku VariMax Optics / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→23.31 Å / Num. obs: 2418 / % possible obs: 96.6 % / Redundancy: 5.46 % / Biso Wilson estimate: 23.01 Å2 / Rmerge(I) obs: 0.102 / Χ2: 0.95 / Net I/σ(I): 11 / Num. measured all: 13303 / Scaling rejects: 100
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
2.2-2.285.420.2963.212952390.56098.8
2.28-2.375.360.2583.312862390.54697.2
2.37-2.485.420.2064.812792360.64095.9
2.48-2.615.580.2144.712792290.66297.4
2.61-2.775.290.1745.713312510.67496.5
2.77-2.995.610.1557.313262360.86395.2
2.99-3.295.590.1469.413762451.04798.8
3.29-3.765.040.09716.911872321.441891.7
3.76-4.735.190.08322.212892431.462794.2
4.73-23.316.050.07229.216552681.5733100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CrystalClearphasing
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
PDB_EXTRACT3.14data extraction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QMT

2qmt


Resolution: 2.201→23.315 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 32.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 104 4.31 %
Rwork0.2334 2307 -
obs0.2345 2411 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.24 Å2 / Biso mean: 38.0906 Å2 / Biso min: 28.37 Å2
Refinement stepCycle: final / Resolution: 2.201→23.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms440 0 8 37 485
Biso mean--41.89 42.25 -
Num. residues----57
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007457
X-RAY DIFFRACTIONf_angle_d1.139620
X-RAY DIFFRACTIONf_chiral_restr0.08973
X-RAY DIFFRACTIONf_plane_restr0.00378
X-RAY DIFFRACTIONf_dihedral_angle_d15.327140
LS refinement shellHighest resolution: 2.201 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.26 104 -
Rwork0.2334 2307 -
all-2411 -
obs--96 %

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