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- PDB-4zmd: C domain of staphylococcal protein A mutant - Q9W -

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Basic information

Entry
Database: PDB / ID: 4zmd
TitleC domain of staphylococcal protein A mutant - Q9W
ComponentsImmunoglobulin G-binding protein A
KeywordsPROTEIN BINDING / Staphylococcal protein A / SpA / three-helix-bundle / antibody / IgG / protein-binding domain
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: 1.87 Å
AuthorsDeis, L.N. / Oas, T.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Suppression of conformational heterogeneity at a protein-protein interface.
Authors: Deis, L.N. / Wu, Q. / Wang, Y. / Qi, Y. / Daniels, K.G. / Zhou, P. / Oas, T.G.
History
DepositionMay 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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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)13,3912
Polymers13,3912
Non-polymers00
Water39622
1
A: Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)6,6951
Polymers6,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)6,6951
Polymers6,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.492, 44.492, 116.165
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 6695.434 Da / Num. of mol.: 2 / Fragment: UNP residues 270-327 / Mutation: Q9W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spa / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38507
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.48 Å3/Da / Density % sol: 50.38 % / Description: Rodlike.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Mar 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 9609 / % possible obs: 99.9 % / Redundancy: 17 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 54.7
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1664refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NPD

4npd


Resolution: 1.87→36.572 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 41.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 977 10.17 %Random selection
Rwork0.1985 ---
obs0.2047 9603 88.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→36.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 0 22 932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012940
X-RAY DIFFRACTIONf_angle_d1.1891268
X-RAY DIFFRACTIONf_dihedral_angle_d15.513365
X-RAY DIFFRACTIONf_chiral_restr0.049132
X-RAY DIFFRACTIONf_plane_restr0.006171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.96020.38311070.3352945X-RAY DIFFRACTION68
1.9602-2.0830.30131260.28251070X-RAY DIFFRACTION77
2.083-2.24390.36761320.26721198X-RAY DIFFRACTION86
2.2439-2.46960.29551400.24071287X-RAY DIFFRACTION91
2.4696-2.82690.30531510.25381332X-RAY DIFFRACTION96
2.8269-3.56110.30691560.21291389X-RAY DIFFRACTION99
3.5611-36.57890.20251650.15671405X-RAY DIFFRACTION100

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