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- PDB-1lp1: Protein Z in complex with an in vitro selected affibody -

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Basic information

Entry
Database: PDB / ID: 1lp1
TitleProtein Z in complex with an in vitro selected affibody
Components
  • Affibody binding protein Z
  • Immunoglobulin G binding protein A
KeywordsIMMUNE SYSTEM / in vitro evolved / protein-protein complex / three-helix bundle / affibody
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHogbom, M. / Eklund, M. / Nygren, P.A. / Nordlund, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structural basis for recognition by an in vitro evolved affibody.
Authors: Hogbom, M. / Eklund, M. / Nygren, P.A. / Nordlund, P.
History
DepositionMay 7, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_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 1.5Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: Affibody binding protein Z
B: Immunoglobulin G binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5047
Polymers13,0962
Non-polymers4095
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-55 kcal/mol
Surface area6280 Å2
MethodPISA
2
A: Affibody binding protein Z
B: Immunoglobulin G binding protein A
hetero molecules

A: Affibody binding protein Z
B: Immunoglobulin G binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,00814
Polymers26,1914
Non-polymers81710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6360 Å2
ΔGint-128 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.546, 55.546, 155.749
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Affibody binding protein Z


Mass: 6447.263 Da / Num. of mol.: 1 / Fragment: In vitro selected binding protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Antibody Immunoglobulin G binding protein A


Mass: 6648.316 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-58 / Mutation: A1V, G29A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P38507
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.32 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MgSO4, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
172 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
31.6 M1reservoirMgSO4
4100 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.098 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 1, 2001
RadiationMonochromator: asymmetrically cut Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.098 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 6899 / Num. obs: 6899 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 51.3 Å2 / Rmerge(I) obs: 0.05
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.296 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 6847 / % possible obs: 99.7 % / Num. measured all: 57198 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.29

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Polyserine model of PDB entry 1DEE, chain G

1dee


Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.256 327 RANDOM
Rwork0.224 --
all0.225 6865 -
obs0.225 6865 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 0 21 182 1071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.165
X-RAY DIFFRACTIONc_bond_d0.006
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.255
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.17

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