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- PDB-3mwf: Crystal structure of Staphylococcus aureus SirA complexed with st... -

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Basic information

Entry
Database: PDB / ID: 3mwf
TitleCrystal structure of Staphylococcus aureus SirA complexed with staphyloferrin B
ComponentsIron-regulated ABC transporter siderophore-binding protein SirA
KeywordsTRANSPORT PROTEIN / ABC transporter binding protein
Function / homology
Function and homology information


ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-SE8 / Iron-regulated ABC transporter siderophore-binding protein SirA / Iron-regulated ABC transporter siderophore-binding protein SirA
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsGrigg, J.C. / Murphy, M.E.P.
CitationJournal: To be Published
Title: Staphylococcus aureus SirA specificity for staphyloferrin B is driven by localized conformational change
Authors: Grigg, J.C. / Cheung, J. / Heinrichs, D.E. / Murphy, M.E.
History
DepositionMay 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Iron-regulated ABC transporter siderophore-binding protein SirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8373
Polymers33,3331
Non-polymers5042
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.719, 71.588, 72.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Iron-regulated ABC transporter siderophore-binding protein SirA


Mass: 33333.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: N315 / Gene: SA0111, sirA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7A869, UniProt: A0A0H3JJC6*PLUS
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SE8 / 5-[(2-{[(3S)-5-{[(2S)-2-amino-2-carboxyethyl]amino}-3-carboxy-3-hydroxy-5-oxopentanoyl]amino}ethyl)amino]-2,5-dioxopentanoic acid / Staphyloferrin B


Mass: 448.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24N4O11
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: 30% Jeffamine ED-2001, 0.1M Hepes, pH 7.0, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 8, 2008
Details: Sample to detector distance: 100 to 650 mm; Maximum vertical offset: 200mm
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 32691 / % possible obs: 96.6 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.044 / Χ2: 1.012 / Net I/σ(I): 15.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 5.8 / Num. unique all: 2967 / Χ2: 1.034 / % possible all: 89.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.91 Å32.36 Å
Translation1.91 Å32.36 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→32.37 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.841 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1654 5.1 %RANDOM
Rwork0.182 ---
obs0.183 32617 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.44 Å2 / Biso mean: 20.23 Å2 / Biso min: 8.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2---0.65 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 32 185 2518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222449
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9853315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5815309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86526.667102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84215478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.479155
X-RAY DIFFRACTIONr_chiral_restr0.0920.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211814
X-RAY DIFFRACTIONr_mcbond_it0.8381.51508
X-RAY DIFFRACTIONr_mcangle_it1.59322451
X-RAY DIFFRACTIONr_scbond_it2.6553941
X-RAY DIFFRACTIONr_scangle_it4.5774.5864
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 117 -
Rwork0.254 2033 -
all-2150 -
obs--88.11 %

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