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

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Basic information

Entry
Database: PDB / ID: 4kgr
TitleBackbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35
ComponentsStreptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35
KeywordsDE NOVO PROTEIN / unnatural backbone
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
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsReinert, Z.E. / Lengyel, G.A. / Horne, W.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Protein-like Tertiary Folding Behavior from Heterogeneous Backbones.
Authors: Reinert, Z.E. / Lengyel, G.A. / Horne, W.S.
History
DepositionApr 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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-Lys31, beta-3-Asn35
B: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35
C: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35
D: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35
E: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35
F: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35
G: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35
H: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9949
Polymers49,9028
Non-polymers921
Water3,549197
1
A: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35


Theoretical massNumber of molelcules
Total (without water)6,2381
Polymers6,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35


Theoretical massNumber of molelcules
Total (without water)6,2381
Polymers6,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35


Theoretical massNumber of molelcules
Total (without water)6,2381
Polymers6,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35


Theoretical massNumber of molelcules
Total (without water)6,2381
Polymers6,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35


Theoretical massNumber of molelcules
Total (without water)6,2381
Polymers6,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35


Theoretical massNumber of molelcules
Total (without water)6,2381
Polymers6,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35


Theoretical massNumber of molelcules
Total (without water)6,2381
Polymers6,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3302
Polymers6,2381
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.162, 81.168, 52.063
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35


Mass: 6237.775 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: chemically synthesized protein / References: UniProt: P06654*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.15 M sodium acetate pH 4.6, 20% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 12, 2012 / Details: Rigaku VariMax Optics
RadiationMonochromator: Rigaku VariMax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→32.031 Å / Num. obs: 27508 / % possible obs: 93.7 % / Redundancy: 3.55 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 23.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2QMT

2qmt


Resolution: 2→32.031 Å / σ(F): 1.4 / Phase error: 20.95 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.192 2092 7.61 %
Rwork0.1584 --
obs0.1619 27506 93.71 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.723 Å2 / ksol: 0.5 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7944 Å20 Å21.1791 Å2
2--5.3096 Å20 Å2
3----2.5152 Å2
Refinement stepCycle: LAST / Resolution: 2→32.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 6 197 3723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113583
X-RAY DIFFRACTIONf_angle_d1.5444863
X-RAY DIFFRACTIONf_dihedral_angle_d16.2611088
X-RAY DIFFRACTIONf_chiral_restr0.092572
X-RAY DIFFRACTIONf_plane_restr0.005618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0005-2.05050.26921090.21931590X-RAY DIFFRACTION77
2.0505-2.10590.26141390.19381628X-RAY DIFFRACTION77
2.1059-2.16790.18711200.16411642X-RAY DIFFRACTION79
2.1679-2.23780.21651280.15881720X-RAY DIFFRACTION82
2.2378-2.31770.22651430.17881718X-RAY DIFFRACTION83
2.3177-2.41050.21381420.17051794X-RAY DIFFRACTION85
2.4105-2.52010.25651330.16811806X-RAY DIFFRACTION88
2.5201-2.65290.21321430.16881901X-RAY DIFFRACTION90
2.6529-2.81890.18431310.14911929X-RAY DIFFRACTION93
2.8189-3.03630.19251590.15351955X-RAY DIFFRACTION92
3.0363-3.34140.17991650.13331930X-RAY DIFFRACTION92
3.3414-3.82380.18431420.13621948X-RAY DIFFRACTION93
3.8238-4.81320.1321590.12921960X-RAY DIFFRACTION92
4.8132-27.28030.21921660.21621977X-RAY DIFFRACTION92

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