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- PDB-6k6b: Application of anti-helix antibodies in protein structure determi... -

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Basic information

Entry
Database: PDB / ID: 6k6b
TitleApplication of anti-helix antibodies in protein structure determination (8496-3LRH)
Components
  • 3LRH intrabody
  • Protein A
KeywordsSTRUCTURAL PROTEIN / antibody / protein design
Function / homology
Function and homology information


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: 2.06 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3LRH intrabody
B: Protein A


Theoretical massNumber of molelcules
Total (without water)22,7942
Polymers22,7942
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-14 kcal/mol
Surface area8870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.559, 51.351, 55.464
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 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)
#2: Protein Protein A


Mass: 8590.640 Da / Num. of mol.: 1
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.: 143 / 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: 1.64 Å3/Da / Density % sol: 25.08 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 35% PEG 4000, 0.1M MES pH 6.5

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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 315r / Detector: CCD / Date: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9479 / % possible obs: 99 % / Redundancy: 6.7 % / Rpim(I) all: 0.035 / Net I/σ(I): 25.2
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 1369 / Rpim(I) all: 0.19

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LRH, 1DEE

3lrh

1dee


Resolution: 2.06→26.279 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 24.4
RfactorNum. reflection% reflection
Rfree0.2484 734 7.75 %
Rwork0.2021 --
obs0.2057 9476 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.06→26.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 0 143 1391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021292
X-RAY DIFFRACTIONf_angle_d0.4121756
X-RAY DIFFRACTIONf_dihedral_angle_d11.861785
X-RAY DIFFRACTIONf_chiral_restr0.037197
X-RAY DIFFRACTIONf_plane_restr0.003234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0601-2.21910.26971340.2421571X-RAY DIFFRACTION90
2.2191-2.44230.27781400.21981771X-RAY DIFFRACTION100
2.4423-2.79540.21031390.2261777X-RAY DIFFRACTION100
2.7954-3.52050.25271640.19261780X-RAY DIFFRACTION100
3.5205-26.28160.2471570.1791843X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.454-3.15-1.73727.44633.89762.13360.01620.24560.1163-0.2667-0.06930.1039-0.35-0.18090.09770.18240.0176-0.02470.12930.03490.176965.366314.021-3.5242
21.75210.57260.34342.5349-0.0771.7273-0.06950.0794-0.0265-0.03490.0473-0.0538-0.06890.0671-0.00930.1366-0.0251-0.01970.14880.0190.096464.15921.0132-2.5229
38.26264.47640.75512.66430.14670.35140.0261-0.42760.50780.2916-0.10080.1844-0.2527-0.42090.08410.1495-0.0095-0.06370.22170.00060.137569.2217.64310.5673
40.44450.70080.75273.156-0.30332.38430.0759-0.1211-0.03450.1333-0.22860.2923-0.2398-0.35020.0520.112-0.0007-0.01420.18150.01210.140357.49554.83372.8525
52.6842-0.36880.11773.3922-0.87451.68750.0103-0.0730.19210.1473-0.1547-0.2572-0.17140.04060.16860.1285-0.0072-0.04230.1519-0.00280.075568.19126.11431.5919
65.84330.0907-0.86931.52560.24022.3594-0.1327-0.0985-0.49150.00590.0025-0.1540.1776-0.14070.08680.13470.04030.04530.16180.040.100569.8956-3.44139.0318
73.64241.38290.05156.0956-0.27873.6432-0.29520.4348-0.227-0.20850.2733-0.37760.1340.2143-0.04920.13460.03120.02010.1943-0.00880.188483.0109-6.93858.1131
88.07315.0875-1.9545.9797-1.34781.71670.3923-0.13660.01240.9616-0.0983-0.4171-0.3572-0.1596-0.20650.1620.0511-0.01390.1670.00910.173282.6967-2.382816.1422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 79 )
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 113 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 18 )
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 37 )
8X-RAY DIFFRACTION8chain 'B' and (resid 38 through 57 )

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