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- PDB-5h7b: Crystal structure of a repeat protein with five Protein A repeat ... -

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Basic information

Entry
Database: PDB / ID: 5h7b
TitleCrystal structure of a repeat protein with five Protein A repeat modules
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: 3.1 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
A: Immunoglobulin G-binding protein A
B: Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)53,9342
Polymers53,9342
Non-polymers00
Water0
1
A: Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)26,9671
Polymers26,9671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)26,9671
Polymers26,9671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.890, 45.640, 82.140
Angle α, β, γ (deg.)90.00, 105.72, 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: 26966.760 Da / Num. of mol.: 2
Fragment: UNP RESIDUES 215-263,219-263,219-263,219-263,219-267
Mutation: G59A, G104A, G149A, 1G94A, G239A
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

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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: 2.71 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 4.5 / Details: 0.1M sodium acetate pH 4.5, 27.3% PEG MME 2000

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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: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 8687 / % possible obs: 96.9 % / Redundancy: 2.8 % / Net I/σ(I): 7.2
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2.6 % / % possible all: 94.2

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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: 3.1→39.534 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.13
RfactorNum. reflection% reflection
Rfree0.315 420 5.07 %
Rwork0.2686 --
obs0.2711 8286 74.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→39.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3387 0 0 0 3387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033440
X-RAY DIFFRACTIONf_angle_d0.5464651
X-RAY DIFFRACTIONf_dihedral_angle_d13.5522168
X-RAY DIFFRACTIONf_chiral_restr0.036504
X-RAY DIFFRACTIONf_plane_restr0.004644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0678-3.51150.4175630.33491300X-RAY DIFFRACTION37
3.5115-4.42310.34091680.27283095X-RAY DIFFRACTION89
4.4231-39.53710.27081890.2483471X-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)
10.1098-0.00790.01180.1747-0.12240.1222-0.0998-0.0172-0.03860.0124-0.1009-0.07880.13890.1381-0.4670.117-0.01540.04420.1766-0.02660.065164.12581.4326227.3756
20.36810.1335-0.21420.17890.04020.15050.02670.3640.09270.11740.21920.0534-0.0537-0.01960.46480.10890.0226-0.08920.14750.09790.1945185.0771.1722258.0681
30.0383-0.07540.06530.1118-0.13520.3498-0.14160.0753-0.1186-0.028-0.297-0.22020.0590.1263-0.19790.2988-0.10750.09550.12080.00220.0816180.6385-17.529297.4784
40.0158-0.0229-0.00950.05530.01040.0148-0.01890.0523-0.09110.032-0.0433-0.0205-0.01030.033-0.06490.09270.0430.02490.4776-0.1780.2759201.362239.7331264.8015
50.906-0.04850.1820.0374-0.13970.4668-0.2604-0.25660.3081-0.0798-0.1636-0.18140.0975-0.0487-0.43550.0378-0.0578-0.0050.66740.09570.1467202.704228.9238265.6011
60.0230.0119-0.00930.0082-0.00670.00510.0396-0.0628-0.07170.0822-0.02880.0307-0.04320.04830.02540.7966-0.0103-0.1830.11190.1650.4638204.571610.4027259.127
70.0192-0.0038-0.00440.0163-0.01560.0123-0.2152-0.22790.1339-0.00220.0963-0.19730.06780.0618-0.00010.45950.15220.14060.37590.09790.5968210.063512.1353248.486
80.0023-0.00440.00110.0016-0.0017-0.001-0.00110.01890.01670.1034-0.0024-0.0995-0.01740.007701.14110.14960.35411.0451-0.20641.0651212.28931.1156233.0314
9-0.0057-0.0016-0.00020.0226-0.00820.0038-0.02610.0607-0.0740.1402-0.0181-0.0119-0.0165-0.0231-01.1427-0.12270.4190.7593-0.47511.0128209.88917.1606220.9063
10-0.0011-0.00150.00720.00190.00030.0103-0.02290.00930.1040.03740.0591-0.03460.00320.00301.0271-0.0460.13180.9074-0.01310.9682206.432710.203206.0762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 181 )
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 266 )
4X-RAY DIFFRACTION4chain 'B' and (resid 38 through 53 )
5X-RAY DIFFRACTION5chain 'B' and (resid 54 through 98 )
6X-RAY DIFFRACTION6chain 'B' and (resid 99 through 112 )
7X-RAY DIFFRACTION7chain 'B' and (resid 113 through 137 )
8X-RAY DIFFRACTION8chain 'B' and (resid 138 through 157 )
9X-RAY DIFFRACTION9chain 'B' and (resid 158 through 188 )
10X-RAY DIFFRACTION10chain 'B' and (resid 189 through 228 )

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