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- PDB-3fil: Structural and energetic determinants for hyperstable variants of... -

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Basic information

Entry
Database: PDB / ID: 3fil
TitleStructural and energetic determinants for hyperstable variants of GB1 obtained from in-vitro evolution
Components(Immunoglobulin G-binding protein G) x 2
KeywordsPROTEIN BINDING / dimerization / beta sheet / alpha helix / improved hydrophobic packing of core residues / Cell wall / IgG-binding protein / Peptidoglycan-anchor / Secreted
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
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. 'group G' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.88 Å
AuthorsMax, K.E.A. / Heinemann, U.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Dimer Formation of a Stabilized Gbeta1 Variant: A Structural and Energetic Analysis
Authors: Thoms, S. / Max, K.E.A. / Wunderlich, M. / Jacso, T. / Lilie, H. / Reif, B. / Heinemann, U. / Schmid, F.X.
History
DepositionDec 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 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

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G
B: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5123
Polymers12,4722
Non-polymers401
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-13 kcal/mol
Surface area6310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.694, 38.930, 83.326
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: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 6249.999 Da / Num. of mol.: 1
Fragment: immunoglobulin binding domain, UNP residues 303-357
Mutation: T2Q, E15V, T16L, T18I, N37L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Strain: G148 / Gene: spg / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: P19909
#2: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 6221.989 Da / Num. of mol.: 1
Fragment: immunoglobulin binding domain, UNP residues 303-357
Mutation: T2Q, E15V, T16L, T18I, N37L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Strain: G148 / Gene: spg / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: P19909
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFME IS INITIATING N-FORMYLMETHIONINE THAT IS THE BIOLOGICAL STARTING RESIDUE IN E. COLI WHICH HAS ...FME IS INITIATING N-FORMYLMETHIONINE THAT IS THE BIOLOGICAL STARTING RESIDUE IN E. COLI WHICH HAS BEEN USED FOR BACTERIAL EXPRESSION. THE OTHER WAY, IN CASE OF THE STARTING METHIONINE OF CHAIN B, THE DEPOSITORS DID NOT SEE THESE ADDITIONAL GROUPS, WHICH IS PROBABLY DUE TO THE FACT THAT THE SIDECHAIN OF THIS RESIDUE IS IN A DIFFERENT CRYSTAL PACKING ENVIRONMENT.

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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: 1.93 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: protein solution: 50mM sodium acetate pH 5.6, 50mg/ml protein. reservoir solution: 25% PEG 3350, 0.1M citric acids pH 3.5. Drop 400nl protein solution & 400nl reservoir solution, 80 micro-l ...Details: protein solution: 50mM sodium acetate pH 5.6, 50mg/ml protein. reservoir solution: 25% PEG 3350, 0.1M citric acids pH 3.5. Drop 400nl protein solution & 400nl reservoir solution, 80 micro-l reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.88561 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 6, 2006
Details: Mirror 1: Silicon, active surface 50nm Rh-coated. Mirror 2: Glas, active surface 50 nm Rh-coated.
RadiationMonochromator: silicon-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88561 Å / Relative weight: 1
ReflectionResolution: 0.842→19.466 Å / Num. all: 87156 / Num. obs: 86548 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Redundancy: 7.08 % / Biso Wilson estimate: 11.564 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.063 / Net I/σ(I): 13.26
Reflection shellResolution: 0.84→0.98 Å / Redundancy: 5.82 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.56 / Num. unique all: 9687 / Rsym value: 0.775 / % possible all: 84.8

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Processing

Software
NameClassification
MAR345data collection
AMoREphasing
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PGA

1pga


Resolution: 0.88→19.466 Å / Num. parameters: 10668 / Num. restraintsaints: 13229 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: According to PROCHECK and WHATCHECK, no backbone outliers were reported. The ASN A8 backbone and sidechain groups are centered in their 2FOFC density
RfactorNum. reflection% reflectionSelection details
Rfree0.1493 -5 %RANDOM
Rwork0.1239 ---
obs0.125 76999 99.3 %-
all-77514 --
Refine analyzeNum. disordered residues: 17 / Occupancy sum hydrogen: 853 / Occupancy sum non hydrogen: 1102.25
Refinement stepCycle: LAST / Resolution: 0.88→19.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms939 0 1 245 1185
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0302
X-RAY DIFFRACTIONs_zero_chiral_vol0.075
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.086
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.071
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.037
X-RAY DIFFRACTIONs_approx_iso_adps0.083

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