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- PDB-6k68: Application of anti-helix antibodies in protein structure determi... -

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Basic information

Entry
Database: PDB / ID: 6k68
TitleApplication of anti-helix antibodies in protein structure determination (8420-3MNZ)
Components
  • 3MNZ Variable heavy chain
  • 3MNZ Variable light chain
  • Protein A
KeywordsSTRUCTURAL PROTEIN / antibody / protein design
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 speciesMus musculus (house mouse)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 1, 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 20, 2019Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Nov 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: 3MNZ Variable heavy chain
B: 3MNZ Variable light chain
C: 3MNZ Variable heavy chain
D: 3MNZ Variable light chain
E: Protein A
F: 3MNZ Variable heavy chain
G: 3MNZ Variable light chain
H: Protein A
I: Protein A
J: 3MNZ Variable heavy chain
K: 3MNZ Variable light chain
L: Protein A


Theoretical massNumber of molelcules
Total (without water)135,51112
Polymers135,51112
Non-polymers00
Water0
1
A: 3MNZ Variable heavy chain
B: 3MNZ Variable light chain
H: Protein A


Theoretical massNumber of molelcules
Total (without water)33,8783
Polymers33,8783
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-18 kcal/mol
Surface area13210 Å2
MethodPISA
2
C: 3MNZ Variable heavy chain
D: 3MNZ Variable light chain
E: Protein A


Theoretical massNumber of molelcules
Total (without water)33,8783
Polymers33,8783
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-17 kcal/mol
Surface area12910 Å2
MethodPISA
3
F: 3MNZ Variable heavy chain
G: 3MNZ Variable light chain
I: Protein A


Theoretical massNumber of molelcules
Total (without water)33,8783
Polymers33,8783
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-19 kcal/mol
Surface area13300 Å2
MethodPISA
4
J: 3MNZ Variable heavy chain
K: 3MNZ Variable light chain
L: Protein A


Theoretical massNumber of molelcules
Total (without water)33,8783
Polymers33,8783
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-19 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.951, 95.017, 179.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Antibody
3MNZ Variable heavy chain


Mass: 12752.225 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody
3MNZ Variable light chain


Mass: 12846.358 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#3: Protein
Protein A /


Mass: 8279.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P02976*PLUS

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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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 20% PEG MME 2000, 0.1M MOPS 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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 22763 / % possible obs: 98.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 52.84 Å2 / Rpim(I) all: 0.109 / Net I/σ(I): 7.4
Reflection shellResolution: 3.2→3.3 Å / Num. unique obs: 22763 / Rpim(I) all: 0.346

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MNZ, 1DEE

3mnz

1dee


Resolution: 3.2→33.42 Å / SU ML: 0.4453 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.3089
RfactorNum. reflection% reflectionSelection details
Rfree0.3184 2000 8.79 %RANDOM
Rwork0.2888 ---
obs0.2913 22760 96.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.02 Å2
Refinement stepCycle: LAST / Resolution: 3.2→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8562 0 0 0 8562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028770
X-RAY DIFFRACTIONf_angle_d0.511611896
X-RAY DIFFRACTIONf_chiral_restr0.03881289
X-RAY DIFFRACTIONf_plane_restr0.00391521
X-RAY DIFFRACTIONf_dihedral_angle_d2.1025140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.290.37471440.35911490X-RAY DIFFRACTION98.43
3.29-3.390.39141440.33681485X-RAY DIFFRACTION97.72
3.39-3.50.28881410.31841477X-RAY DIFFRACTION98.42
3.5-3.620.30851470.31941511X-RAY DIFFRACTION98.99
3.62-3.770.38551440.33461497X-RAY DIFFRACTION99.21
3.77-3.940.35161460.32691512X-RAY DIFFRACTION98.69
3.94-4.140.33921430.29771498X-RAY DIFFRACTION97.62
4.14-4.40.30851450.27991491X-RAY DIFFRACTION97.91
4.4-4.740.24961470.25561525X-RAY DIFFRACTION97.55
4.74-5.220.26191450.24381521X-RAY DIFFRACTION99.28
5.22-5.970.29451520.23881563X-RAY DIFFRACTION99.59
5.97-7.510.31031510.27261578X-RAY DIFFRACTION99.37
7.51-33.420.32341560.25581617X-RAY DIFFRACTION97.42

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