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- PDB-6k3m: Application of anti-helix antibodies in protein structure determi... -

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Basic information

Entry
Database: PDB / ID: 6k3m
TitleApplication of anti-helix antibodies in protein structure determination (8189-3LRH)
Components
  • 3LRH intrabody
  • SpA IgG-binding domain protein,Protein A
KeywordsSTRUCTURAL PROTEIN / antibody / protein design
Function / homology
Function and homology information


IgG binding / immunoglobulin 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
SpA IgG-binding domain protein / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLee, J.O. / Jin, M.S. / Kim, J.W. / Kim, S. / Lee, H. / Cho, G.Y.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2014R1A2A1A10050436 Korea, Republic Of
National Research Foundation (Korea)NRF-2017M3A9F6029753 Korea, Republic Of
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Application of antihelix antibodies in protein structure determination.
Authors: Kim, J.W. / Kim, S. / Lee, H. / Cho, G. / Kim, S.C. / Lee, H. / Jin, M.S. / Lee, J.O.
History
DepositionMay 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: SpA IgG-binding domain protein,Protein A
A: 3LRH intrabody


Theoretical massNumber of molelcules
Total (without water)23,5072
Polymers23,5072
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-13 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.345, 56.102, 96.096
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: Protein SpA IgG-binding domain protein,Protein A


Mass: 9303.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: protein A(1DEE) and n-terminal of huntingtin peptide (3LRH) fusion,protein A(1DEE) and n-terminal of huntingtin peptide (3LRH) fusion
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: D7RHB0, UniProt: P02976*PLUS
#2: Protein 3LRH intrabody


Mass: 14203.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 1.57 Å3/Da / Density % sol: 21.55 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 4000, 0.2M MgCl2, 0.1M MOPS pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 14114 / % possible obs: 98.4 % / Redundancy: 6 % / Rpim(I) all: 0.022 / Net I/σ(I): 39.1
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 14114 / Rpim(I) all: 0.037

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LRH, 1DEE

3lrh

1dee


Resolution: 1.8→28 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.896 / SU B: 2.45 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23123 717 5.1 %RANDOM
Rwork0.18964 ---
obs0.19179 13319 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.881 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0 Å20 Å2
2---0.19 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.8→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 0 149 1449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131323
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171180
X-RAY DIFFRACTIONr_angle_refined_deg1.711.6371793
X-RAY DIFFRACTIONr_angle_other_deg1.5161.5782758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9724.41268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87515219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.63156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02260
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1740.956678
X-RAY DIFFRACTIONr_mcbond_other1.1720.952677
X-RAY DIFFRACTIONr_mcangle_it1.9151.424844
X-RAY DIFFRACTIONr_mcangle_other1.9161.428845
X-RAY DIFFRACTIONr_scbond_it2.2251.201645
X-RAY DIFFRACTIONr_scbond_other2.2231.205646
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3651.709950
X-RAY DIFFRACTIONr_long_range_B_refined5.05412.2911492
X-RAY DIFFRACTIONr_long_range_B_other4.84911.9151461
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 49 -
Rwork0.18 971 -
obs--98.08 %

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