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- PDB-4bih: Crystal structure of the conserved staphylococcal antigen 1A, Csa1A -

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Basic information

Entry
Database: PDB / ID: 4bih
TitleCrystal structure of the conserved staphylococcal antigen 1A, Csa1A
ComponentsUNCHARACTERIZED LIPOPROTEIN SAOUHSC_00053
KeywordsIMMUNE SYSTEM / TANDEM LIPOPROTEIN / PROTECTIVE IMMUNITY
Function / homologyCsa family / Csa superfamily / Csa1 family / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / Uncharacterized lipoprotein SAOUHSC_00052
Function and homology information
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.459 Å
AuthorsMalito, E. / Bottomley, M.J. / Spraggon, G. / Schluepen, C. / Liberatori, S.
CitationJournal: Biochem.J. / Year: 2013
Title: Mining the Bacterial Unknown Proteome: Identification and Characterization of a Novel Family of Highly Conserved Protective Antigens in Staphylococcus Aureus
Authors: Schluepen, C. / Malito, E. / Marongiu, A. / Schirle, M. / Mcwhinnie, E. / Lo Surdo, P. / Biancucci, M. / Falugi, F. / Nardi-Dei, V. / Marchi, S. / Fontana, M.R. / Lombardi, B. / De Falco, M. ...Authors: Schluepen, C. / Malito, E. / Marongiu, A. / Schirle, M. / Mcwhinnie, E. / Lo Surdo, P. / Biancucci, M. / Falugi, F. / Nardi-Dei, V. / Marchi, S. / Fontana, M.R. / Lombardi, B. / De Falco, M.G. / Rinaudo, C.D. / Spraggon, G. / Nissum, M. / Bagnoli, F. / Grandi, G. / Bottomley, M.J. / Liberatori, S.
History
DepositionApr 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Atomic model / Other
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_conn.ptnr2_label_seq_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: UNCHARACTERIZED LIPOPROTEIN SAOUHSC_00053
B: UNCHARACTERIZED LIPOPROTEIN SAOUHSC_00053
C: UNCHARACTERIZED LIPOPROTEIN SAOUHSC_00053
D: UNCHARACTERIZED LIPOPROTEIN SAOUHSC_00053
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0635
Polymers117,0234
Non-polymers401
Water1,856103
1
A: UNCHARACTERIZED LIPOPROTEIN SAOUHSC_00053
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2962
Polymers29,2561
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UNCHARACTERIZED LIPOPROTEIN SAOUHSC_00053


Theoretical massNumber of molelcules
Total (without water)29,2561
Polymers29,2561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: UNCHARACTERIZED LIPOPROTEIN SAOUHSC_00053


Theoretical massNumber of molelcules
Total (without water)29,2561
Polymers29,2561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: UNCHARACTERIZED LIPOPROTEIN SAOUHSC_00053


Theoretical massNumber of molelcules
Total (without water)29,2561
Polymers29,2561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.130, 49.250, 137.370
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
UNCHARACTERIZED LIPOPROTEIN SAOUHSC_00053 / CONSERVED STAPHYLOCOCCAL LIPOPROTEIN 1B


Mass: 29255.828 Da / Num. of mol.: 4 / Fragment: RESIDUES 23-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: NCTC 8325 / Plasmid: PET TEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): T7 EXPRESS / References: UniProt: Q2G1Q1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.23 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.9 / Details: 28% PEG 3350, 0.157 M NA-THIOCYANATE, PH 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.49
ReflectionResolution: 2.46→68.68 Å / Num. obs: 32851 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.3
Reflection shellResolution: 2.46→2.59 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.7 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BIG

4big


Resolution: 2.459→68.685 Å / σ(F): 1.35 / Phase error: 24.52 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2563 1760 5.4 %
Rwork0.2073 --
obs0.2094 32839 93.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.13 Å2
Refinement stepCycle: LAST / Resolution: 2.459→68.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5722 0 1 103 5826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085821
X-RAY DIFFRACTIONf_angle_d1.1837791
X-RAY DIFFRACTIONf_dihedral_angle_d18.242291
X-RAY DIFFRACTIONf_chiral_restr0.081825
X-RAY DIFFRACTIONf_plane_restr0.006983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4593-2.53170.37111110.26112556X-RAY DIFFRACTION89
2.5317-2.61340.32941480.24572634X-RAY DIFFRACTION90
2.6134-2.70680.26241350.24222634X-RAY DIFFRACTION91
2.7068-2.81510.27351370.23762587X-RAY DIFFRACTION90
2.8151-2.94320.2871200.22622637X-RAY DIFFRACTION91
2.9432-3.09840.28671350.21782650X-RAY DIFFRACTION90
3.0984-3.29250.26451330.2132604X-RAY DIFFRACTION90
3.2925-3.54660.24641460.20692589X-RAY DIFFRACTION89
3.5466-3.90340.24071530.19372555X-RAY DIFFRACTION88
3.9034-4.46790.22131370.16622611X-RAY DIFFRACTION88
4.4679-5.62780.20351420.16442535X-RAY DIFFRACTION86
5.6278-49.42370.27971470.24192593X-RAY DIFFRACTION85
Refinement TLS params.Method: refined / Origin x: -31.1253 Å / Origin y: 6.5995 Å / Origin z: -34.01 Å
111213212223313233
T0.2364 Å2-0.0218 Å2-0.0189 Å2-0.1403 Å20.0256 Å2--0.2975 Å2
L0.305 °2-0.0787 °2-0.3302 °2-0.2016 °20.0934 °2--0.1176 °2
S0.0244 Å °0.0144 Å °0.0619 Å °-0.0344 Å °0.0026 Å °-0.0566 Å °0.0058 Å °-0.0485 Å °-0.0317 Å °
Refinement TLS groupSelection details: ALL

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