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- PDB-2on8: Gbeta1 stabilization by in vitro evolution and computational design -

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Basic information

Entry
Database: PDB / ID: 2on8
TitleGbeta1 stabilization by in vitro evolution and computational design
ComponentsImmunoglobulin G-binding protein G
KeywordsPROTEIN BINDING / beta sheet / alpha helix / improved hydrophobic packing of core residues
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / 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 / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsMax, K.E.A. / Heinemann, U.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Optimization of the gbeta1 domain by computational design and by in vitro evolution: structural and energetic basis of stabilization.
Authors: Wunderlich, M. / Max, K.E. / Roske, Y. / Mueller, U. / Heinemann, U. / Schmid, F.X.
History
DepositionJan 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT the biological unit information is unknown for this isolated domain.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,3091
Polymers6,3091
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.104, 52.104, 22.765
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4

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Components

#1: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 6309.003 Da / Num. of mol.: 1 / Mutation: T1M, T2Q, Y3F, V6I, T16I, T18L, T25E, V29K, V39I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. (bacteria) / Strain: G148 / Gene: spg / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19909
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 50mM Na acetate, pH 5.0, 17 mg/ml protein mixed with equal volume of 2.3M ammonium suphate, 0.1M sodium acetate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2006 / Details: mirrors
RadiationMonochromator: double crystal monochromator (Si-111 crystal)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. all: 14227 / Num. obs: 13293 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.053 / Χ2: 0.789 / Net I/σ(I): 18
Reflection shellResolution: 1.34→1.39 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.365 / Num. unique all: 770 / Rsym value: 0.365 / Χ2: 0.737 / % possible all: 56.4

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Phasing

Phasing MRRfactor: 0.377 / Cor.coef. Fo:Fc: 0.514 / Cor.coef. Io to Ic: 0.161
Highest resolutionLowest resolution
Rotation3 Å52.129 Å
Translation3 Å52.129 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PGA

1pga


Resolution: 1.35→19 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.927 / SU ML: 0.035 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.058 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE FACTORS ARE TWINNED. TWIN TYPE: PARTIAL MEROHEDRAL TWIN TWIN FRACTION: 0.235 TWINNING RELATIONSHIP RELATES REFLECTIONS WITH ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE FACTORS ARE TWINNED. TWIN TYPE: PARTIAL MEROHEDRAL TWIN TWIN FRACTION: 0.235 TWINNING RELATIONSHIP RELATES REFLECTIONS WITH INDICES h,k,l to h,k,-l. Authors also state that the structure was refined using a combination of isotropic (atomic) and TLS refinement. The whole molecule was defined as one TLS group. The atomic B-values are reported as anisotropic B-values which were calculated by combining the isotropic B-values and TLS parameters using TLSANL program from the CCP4 suite.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 635 5 %RANDOM
Rwork0.158 ---
all0.162 12697 --
obs0.16 12044 92.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.35→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms444 0 0 54 498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022454
X-RAY DIFFRACTIONr_bond_other_d0.0060.02395
X-RAY DIFFRACTIONr_angle_refined_deg2.4341.951611
X-RAY DIFFRACTIONr_angle_other_deg2.4623932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.646555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.02427.39123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2731586
X-RAY DIFFRACTIONr_chiral_restr0.1220.268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02504
X-RAY DIFFRACTIONr_gen_planes_other00.0283
X-RAY DIFFRACTIONr_nbd_refined0.2240.266
X-RAY DIFFRACTIONr_nbd_other0.1660.2365
X-RAY DIFFRACTIONr_nbtor_refined0.1940.2207
X-RAY DIFFRACTIONr_nbtor_other0.1060.2300
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.570.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1320.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.210
X-RAY DIFFRACTIONr_mcbond_it4.3392363
X-RAY DIFFRACTIONr_mcbond_other1.9992118
X-RAY DIFFRACTIONr_mcangle_it4.9373443
X-RAY DIFFRACTIONr_scbond_it6.5464.5211
X-RAY DIFFRACTIONr_scangle_it8.736168
X-RAY DIFFRACTIONr_rigid_bond_restr3.27431037
X-RAY DIFFRACTIONr_sphericity_free13.886354
X-RAY DIFFRACTIONr_sphericity_bonded6.9533843
LS refinement shellResolution: 1.35→1.397 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.189 35 -
Rwork0.225 758 -
obs-793 60.53 %

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