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- PDB-1mvk: X-ray structure of the tetrameric mutant of the B1 domain of stre... -

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Basic information

Entry
Database: PDB / ID: 1mvk
TitleX-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G
ComponentsImmunoglobulin G binding protein G
KeywordsPROTEIN BINDING / strand-exchanged tetramer / channel
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. 'group G' (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.5 Å
AuthorsFrank, M.K. / Dyda, F. / Dobrodumov, A. / Gronenborn, A.M.
Citation
Journal: Nat.Struct.Biol. / Year: 2002
Title: Core mutations switch monomeric protein GB1 into an intertwined tetramer.
Authors: Kirsten Frank, M. / Dyda, F. / Dobrodumov, A. / Gronenborn, A.M.
#1: Journal: Science / Year: 1991
Title: A Novel, Highly Stable Fold of the Immunoglobulin Binding Domain of Streptococcal Protein G
Authors: Gronenborn, A.M. / Filpula, D.R. / Essig, N.Z. / Achari, A. / Whitlow, M. / Wingfield, P.T. / Clore, G.M.
#2: Journal: FEBS Lett. / Year: 1996
Title: Core Mutants of the Immunoglobulin Binding Domain of Streptococcal Protein G: Stability and Structural Integrity
Authors: Gronenborn, A.M. / Frank, M.K. / Clore, G.M.
History
DepositionSep 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
C: Immunoglobulin G binding protein G
D: Immunoglobulin G binding protein G
E: Immunoglobulin G binding protein G
F: Immunoglobulin G binding protein G
G: Immunoglobulin G binding protein G
H: Immunoglobulin G binding protein G
I: Immunoglobulin G binding protein G
J: Immunoglobulin G binding protein G
K: Immunoglobulin G binding protein G
L: Immunoglobulin G binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,92315
Polymers75,63512
Non-polymers2883
Water3,927218
1
A: Immunoglobulin G binding protein G
B: Immunoglobulin G binding protein G
C: Immunoglobulin G binding protein G
D: Immunoglobulin G binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3085
Polymers25,2124
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11190 Å2
ΔGint-97 kcal/mol
Surface area10120 Å2
MethodPISA
2
E: Immunoglobulin G binding protein G
F: Immunoglobulin G binding protein G
G: Immunoglobulin G binding protein G
H: Immunoglobulin G binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3085
Polymers25,2124
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-96 kcal/mol
Surface area10580 Å2
MethodPISA
3
I: Immunoglobulin G binding protein G
J: Immunoglobulin G binding protein G
K: Immunoglobulin G binding protein G
L: Immunoglobulin G binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3085
Polymers25,2124
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-97 kcal/mol
Surface area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.100, 210.400, 55.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe asymmetric unit contains three copies of the biological unit.

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Components

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


Mass: 6302.931 Da / Num. of mol.: 12 / Fragment: B1 domain, sequence database residues 228-282 / Mutation: T2Q, L5V, A26F, F30V, Y33F, A34F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Gene: SPG / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P06654
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 8000, ammonium sulfate, sodium acetate, sodium chloride, TrisHCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 mg/mlprotein1drop
220 %(w/v)PEG80001reservoir
3150 mMammonium sulfate1reservoir
4100 mMsodium acetate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 7, 2000 / Details: total-reflection mirror pair
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 31523 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.78 % / Biso Wilson estimate: 28.35 Å2 / Rsym value: 0.083 / Net I/σ(I): 11.1
Reflection shellResolution: 2.5→2.57 Å / % possible all: 93.4
Reflection
*PLUS
Num. measured all: 182446 / Rmerge(I) obs: 0.083

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Flexible region from residues 8-21 missing in electron density of most chains
RfactorNum. reflectionSelection details
Rfree0.283 1487 Random
Rwork0.237 --
all0.237 30039 -
obs0.237 30039 -
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4485 0 15 218 4718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.524
X-RAY DIFFRACTIONx_dihedral_angle_d23.381
X-RAY DIFFRACTIONx_improper_angle_d1.129
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.03088
RfactorNum. reflection
Rfree0.3882 158
Rwork0.3912 -
obs-3081
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor obs: 0.237 / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.52
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.381
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.129
LS refinement shell
*PLUS
Rfactor Rfree: 0.3882 / Rfactor Rwork: 0.3912

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