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- PDB-4npe: High-resolution structure of C domain of staphylococcal protein A... -

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Basic information

Entry
Database: PDB / ID: 4npe
TitleHigh-resolution structure of C domain of staphylococcal protein A at room temperature
ComponentsImmunoglobulin G-binding protein A
KeywordsPROTEIN BINDING / SpA / three-helix bundle / conformational heterogeneity / rapidly unfolding and folding / RUF / Antibody binding / Antibody
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 / LysM domain superfamily / Lysin motif / LysM domain / LysM domain profile. / LysM domain ...Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / LysM domain superfamily / Lysin motif / 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
THIOCYANATE ION / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.42 Å
AuthorsDeis, L.N. / Pemble IV, C.W. / Oas, T.G. / Richardson, J.S. / Richardson, D.C.
CitationJournal: Structure / Year: 2014
Title: Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity.
Authors: Deis, L.N. / Pemble, C.W. / Qi, Y. / Hagarman, A. / Richardson, D.C. / Richardson, J.S. / Oas, T.G.
History
DepositionNov 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7613
Polymers6,6371
Non-polymers1232
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.840, 38.560, 28.960
Angle α, β, γ (deg.)90.00, 118.20, 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: 6637.353 Da / Num. of mol.: 1 / Fragment: UNP residues 270-327
Source method: isolated from a genetically manipulated source
Details: C domain of staphylococcal protein A / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: 8325-4 / Gene: protein A, spa / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38507
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Na Thiocyanate, PEG 3350, Glycerol, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. all: 10199 / Num. obs: 9893 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 12.65 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.42-1.442.90.33173.6
1.44-1.473.30.295186.2
1.47-1.53.60.307191
1.5-1.533.90.269194.2
1.53-1.564.20.251198
1.56-1.64.70.241199
1.6-1.645.20.237199.4
1.64-1.685.50.221199.4
1.68-1.735.80.21100
1.73-1.796.20.186199.8
1.79-1.856.40.171100
1.85-1.936.50.1421100
1.93-2.016.70.1241100
2.01-2.126.70.0961100
2.12-2.256.70.0861100
2.25-2.436.70.0741100
2.43-2.676.70.0661100
2.67-3.066.80.0611100
3.06-3.856.70.0491100
3.85-506.40.049199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.42→25.52 Å / Occupancy max: 1 / Occupancy min: 0.19 / SU ML: 0.1 / σ(F): 0 / Phase error: 14.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.143 953 10.02 %
Rwork0.111 --
obs0.114 9512 93.2 %
all-10199 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.24 Å2
Refinement stepCycle: LAST / Resolution: 1.42→25.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms468 0 4 50 522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013760
X-RAY DIFFRACTIONf_angle_d1.4441031
X-RAY DIFFRACTIONf_dihedral_angle_d15.922302
X-RAY DIFFRACTIONf_chiral_restr0.069112
X-RAY DIFFRACTIONf_plane_restr0.007142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.49930.1948990.1114943X-RAY DIFFRACTION73
1.4993-1.59320.15931290.0921181X-RAY DIFFRACTION90
1.5932-1.71620.17241320.09081262X-RAY DIFFRACTION95
1.7162-1.88880.14721530.0871244X-RAY DIFFRACTION96
1.8888-2.1620.12731450.09151281X-RAY DIFFRACTION98
2.162-2.72340.15181510.11251301X-RAY DIFFRACTION99
2.7234-25.5230.13221440.12921347X-RAY DIFFRACTION100

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