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- PDB-4npf: High-resolution structure of two tandem B domains of staphylococc... -

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Basic information

Entry
Database: PDB / ID: 4npf
TitleHigh-resolution structure of two tandem B domains of staphylococcal protein A connected by the conserved linker
ComponentsImmunoglobulin G-binding protein A
KeywordsPROTEIN BINDING / SpA / three-helix bundle / conformational heterogeneity / rapidly unfolding and folding / RUF / Antibody binding / Antibody / TNFR1 / von Willebrand factor
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 speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Y: Immunoglobulin G-binding protein A
X: Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)26,5452
Polymers26,5452
Non-polymers00
Water7,296405
1
Y: Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)13,2731
Polymers13,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
X: Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)13,2731
Polymers13,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.412, 44.412, 214.790
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 13272.528 Da / Num. of mol.: 2 / Fragment: UNP residues 212-323 / Mutation: W13F, W113F
Source method: isolated from a genetically manipulated source
Details: Double B construct 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS USED AN UNUSUAL RESIDUE-NUMBERING SCHEME FOR RESIDUES 101-158 OF BOTH CHAIN X AND OF ...THE AUTHORS USED AN UNUSUAL RESIDUE-NUMBERING SCHEME FOR RESIDUES 101-158 OF BOTH CHAIN X AND OF CHAIN Y TO SIMPLIFY DESCRIPTIONS IN THE PAPER OF THE TWO IDENTICAL MODULAR DOMAINS CONTAINED WITHIN EACH CHAIN OF THE AU

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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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Ammonium Sulfate, MES, pH 6, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 29, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. all: 39170 / Num. obs: 39130 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 13.56 Å2 / Rmerge(I) obs: 0.101 / Χ2: 1.392 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.49-1.524.40.61619090.963199.6
1.52-1.545.20.60819660.955199.5
1.54-1.575.70.56519360.9861100
1.57-1.616.10.49419411.0051100
1.61-1.646.60.44519850.9811100
1.64-1.6870.396192811100
1.68-1.727.30.419600.961100
1.72-1.777.60.34719551.041100
1.77-1.8280.33919371.1331100
1.82-1.888.10.26819591.0811100
1.88-1.948.10.21719781.1721100
1.94-2.028.10.16719841.27199.9
2.02-2.117.90.12719451.4661100
2.11-2.237.80.10419601.4831100
2.23-2.377.50.09119261.6151100
2.37-2.557.10.0819541.6761100
2.55-2.86.70.0719831.8291100
2.8-3.216.20.06319592.1941100
3.21-4.045.40.05719802.603199.8
4.04-505.30.05919852.994199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
PHENIX1.8.3_1479phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→37.86 Å / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.8895 / SU ML: 0.16 / σ(F): 0 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1847 1872 5.06 %RANDOM
Rwork0.1424 ---
all0.1446 39170 --
obs0.1446 36984 94.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.54 Å2 / Biso mean: 20.6137 Å2 / Biso min: 5.7 Å2
Refinement stepCycle: LAST / Resolution: 1.49→37.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 0 405 2274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033290
X-RAY DIFFRACTIONf_angle_d0.6924474
X-RAY DIFFRACTIONf_chiral_restr0.044460
X-RAY DIFFRACTIONf_plane_restr0.003630
X-RAY DIFFRACTIONf_dihedral_angle_d12.2961292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.49-1.52770.26021310.17762435256685
1.5277-1.57270.24291360.15622501263788
1.5727-1.62340.21211320.14132519265189
1.6234-1.68150.23211310.1352638276992
1.6815-1.74880.20431400.13632643278393
1.7488-1.82840.21031390.1372673281293
1.8284-1.92480.18111480.13352758290696
1.9248-2.04530.16631520.12212746289898
2.0453-2.20320.16641510.1192829298099
2.2032-2.42490.18581530.12712825297899
2.4249-2.77570.19551560.14822841299799
2.7757-3.49680.17521440.150928472991100
3.4968-37.860.1651590.15522857301699

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