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- PDB-6k6a: Application of anti-helix antibodies in protein structure determi... -

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Basic information

Entry
Database: PDB / ID: 6k6a
TitleApplication of anti-helix antibodies in protein structure determination (8188cys-3LRHcys)
Components
  • 3LRH intrabody
  • Engineered Protein A
KeywordsSTRUCTURAL PROTEIN / antibody / protein design
Function / homology
Function and homology information


symbiont-mediated suppression of host signal transduction pathway via antagonism of host cell surface receptor / IgG binding / extracellular region
Similarity search - Function
Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / 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 speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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
DepositionJun 2, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 3LRH intrabody
A: 3LRH intrabody
C: Engineered Protein A
D: Engineered Protein A


Theoretical massNumber of molelcules
Total (without water)46,0634
Polymers46,0634
Non-polymers00
Water4,432246
1
B: 3LRH intrabody
C: Engineered Protein A


Theoretical massNumber of molelcules
Total (without water)23,0312
Polymers23,0312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-15 kcal/mol
Surface area8710 Å2
MethodPISA
2
A: 3LRH intrabody
D: Engineered Protein A


Theoretical massNumber of molelcules
Total (without water)23,0312
Polymers23,0312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-16 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.227, 40.603, 61.691
Angle α, β, γ (deg.)87.16, 75.20, 65.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 3LRH intrabody


Mass: 14143.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Engineered Protein A


Mass: 8887.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P02976*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.78 Å3/Da / Density % sol: 30.79 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 45% PEG 4000, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 21978 / % possible obs: 94.8 % / Redundancy: 2.8 % / Rpim(I) all: 0.035 / Net I/σ(I): 27.2
Reflection shellResolution: 1.9→2 Å / Num. unique obs: 1985 / Rpim(I) all: 0.091

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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: 6K64

6k64


Resolution: 1.94→25.99 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.271 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.192 / ESU R Free: 0.163 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21525 2023 9.2 %RANDOM
Rwork0.16938 ---
obs0.17366 19954 94.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.649 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.33 Å20.03 Å2
2---0.05 Å2-0.19 Å2
3---0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.94→25.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 0 246 2741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132538
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172259
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.6343442
X-RAY DIFFRACTIONr_angle_other_deg1.4421.5775283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8695327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74624.409127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99915417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2491512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02488
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_it2.7312.7441320
X-RAY DIFFRACTIONr_mcbond_other2.7292.7421319
X-RAY DIFFRACTIONr_mcangle_it3.8554.0891643
X-RAY DIFFRACTIONr_mcangle_other3.8554.091644
X-RAY DIFFRACTIONr_scbond_it3.6733.2511218
X-RAY DIFFRACTIONr_scbond_other3.6713.2521219
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7134.681800
X-RAY DIFFRACTIONr_long_range_B_refined7.62933.5382809
X-RAY DIFFRACTIONr_long_range_B_other7.5233.0622758
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.945→1.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 126 -
Rwork0.187 1200 -
obs--77.32 %

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