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- PDB-5h79: Crystal structure of a repeat protein with three Protein A repeat... -

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Basic information

Entry
Database: PDB / ID: 5h79
TitleCrystal structure of a repeat protein with three Protein A repeat module
ComponentsImmunoglobulin G-binding protein A
KeywordsIMMUNE SYSTEM / synthetic protein
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
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 ...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
Similarity search - Domain/homology
Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYoun, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Lee, H. / Lee, J.O.
CitationJournal: Sci Rep / Year: 2017
Title: Construction of novel repeat proteins with rigid and predictable structures using a shared helix method.
Authors: Youn, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Choi, J. / Lee, H. / Lee, J.O.
History
DepositionNov 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
D: Immunoglobulin G-binding protein A
C: Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)33,0642
Polymers33,0642
Non-polymers00
Water30617
1
D: Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)16,5321
Polymers16,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)16,5321
Polymers16,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.689, 46.614, 74.311
Angle α, β, γ (deg.)90.00, 107.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A


Mass: 16532.178 Da / Num. of mol.: 2
Fragment: UNP RESIDUES 217-263,UNP RESIDUES 219-263,UNP RESIDUES 219-268
Mutation: G59A, N131A, G149A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: P38507
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 4.5 / Details: 0.1M sodium acetate pH 4.5, 13.5%(w/v) PEG 1000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 10513 / % possible obs: 98.7 % / Redundancy: 3.3 % / Net I/σ(I): 15.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.14 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZNC, 5COC

4znc

5coc


Resolution: 2.7→28.018 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 33.48
RfactorNum. reflection% reflection
Rfree0.2778 500 4.77 %
Rwork0.2298 --
obs0.2321 10491 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→28.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2265 0 0 17 2282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032298
X-RAY DIFFRACTIONf_angle_d0.633106
X-RAY DIFFRACTIONf_dihedral_angle_d15.1291456
X-RAY DIFFRACTIONf_chiral_restr0.038337
X-RAY DIFFRACTIONf_plane_restr0.005432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6968-2.96790.37951250.31892347X-RAY DIFFRACTION92
2.9679-3.39670.3431250.28722538X-RAY DIFFRACTION99
3.3967-4.2770.29821250.20462539X-RAY DIFFRACTION99
4.277-28.01940.22041250.20772567X-RAY DIFFRACTION97
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)
13.3851-1.4528-2.34891.21610.27282.47260.00040.543-0.7590.07380.3613-0.23280.88930.3848-0.2680.59360.0131-0.00410.6416-0.38560.6935149.6589-0.7981161.552
21.9222-0.9889-2.46492.0151-1.00986.60880.2020.5534-0.1367-0.1580.00070.1485-0.3299-0.70880.11290.43840.07610.04890.2498-0.10640.6125151.66488.4319164.6346
34.69680.0458-2.51580.4929-0.65372.659-0.358-0.3073-0.96660.02110.1451-0.15860.54430.0458-0.02140.6133-0.02950.01060.2634-0.09180.5175142.5010.1921175.1339
45.02061.50320.85152.5539-0.40372.3376-0.7405-0.28630.1743-0.21550.7885-0.1735-0.44620.36960.01660.4929-0.11360.05340.5577-0.22560.5283130.9669-3.3091186.9144
53.09772.0581.42873.19710.16543.16470.4161-0.5969-1.110.34950.1479-0.5363-0.14520.1739-0.340.4605-0.0555-0.0620.56140.06310.5698113.0112-15.373187.8489
63.88140.82640.89262.4908-0.09931.6847-0.21912.11060.7155-0.19410.2252-0.06-0.51480.4180.01670.58180.00110.00780.76420.2590.4416167.41320.7116158.3971
73.42462.2260.45545.23840.23571.1514-0.19621.9941-0.1728-0.4610.2228-0.08990.18621.10150.20570.57920.0891-0.03511.5923-0.10630.4636162.188414.4852149.9987
83.6749-0.9748-0.13394.1267-0.72511.8913-0.02230.634-0.7208-0.83910.29780.1940.59480.5214-0.15690.78290.1132-0.05571.6746-0.39410.812147.30991.0228144.4194
90.2643-0.03260.29731.7627-0.09550.3235-0.23060.6355-0.4963-1.15882.14982.33280.9405-1.6022-0.89712.0182-0.186-0.49122.25420.40881.883125.61721.4408141.0208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 36 through 53 )
2X-RAY DIFFRACTION2chain 'D' and (resid 54 through 67 )
3X-RAY DIFFRACTION3chain 'D' and (resid 68 through 98 )
4X-RAY DIFFRACTION4chain 'D' and (resid 99 through 138 )
5X-RAY DIFFRACTION5chain 'D' and (resid 139 through 177 )
6X-RAY DIFFRACTION6chain 'C' and (resid 36 through 67 )
7X-RAY DIFFRACTION7chain 'C' and (resid 68 through 93 )
8X-RAY DIFFRACTION8chain 'C' and (resid 94 through 137 )
9X-RAY DIFFRACTION9chain 'C' and (resid 138 through 176 )

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