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- PDB-3mwg: Crystal structure of Staphylococcus aureus SirA -

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Basic information

Entry
Database: PDB / ID: 3mwg
TitleCrystal structure of Staphylococcus aureus SirA
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
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 / MAD / Resolution: 2.1 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

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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
B: Iron-regulated ABC transporter siderophore-binding protein SirA


Theoretical massNumber of molelcules
Total (without water)62,7432
Polymers62,7432
Non-polymers00
Water4,432246
1
A: Iron-regulated ABC transporter siderophore-binding protein SirA


Theoretical massNumber of molelcules
Total (without water)31,3711
Polymers31,3711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Iron-regulated ABC transporter siderophore-binding protein SirA


Theoretical massNumber of molelcules
Total (without water)31,3711
Polymers31,3711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.136, 61.513, 114.649
Angle α, β, γ (deg.)90.000, 100.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 31371.432 Da / Num. of mol.: 2 / Fragment: UNP residues 54-330
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6.5
Details: 24% Polyethylene glycol 3350, 0.1M Bis-Tris, pH 6.5, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97882, 0.97947
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2010
Details: Sample to detector distance: 100 to 650 mm; Maximum vertical offset: 75mm
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978821
20.979471
ReflectionResolution: 2.1→40 Å / Num. obs: 34267 / % possible obs: 99.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.066 / Χ2: 0.986 / Net I/σ(I): 11.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3394 / Χ2: 1.001 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
2 wavelength110.97884.02-6.88
2 wavelength120.97952.34-8.27
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se43.2520.1130.9980.1591.563
2Se32.1290.260.7520.331.305
3Se49.2520.5160.3230.381.875
4Se600.2880.5120.0970.961
Phasing dmFOM : 0.59 / FOM acentric: 0.59 / FOM centric: 0.6 / Reflection: 28808 / Reflection acentric: 27448 / Reflection centric: 1360
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.3-31.6460.950.960.913021125177
3.9-6.30.930.940.8339453659286
3.1-3.90.860.870.7349134672241
2.8-3.10.680.690.5648464641205
2.4-2.80.410.410.3585168232284
2.2-2.40.210.210.252865119167

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementResolution: 2.1→31.65 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.358 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23588 1702 5 %RANDOM
Rwork0.19188 ---
obs0.1941 32066 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.331 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.09 Å2
2--0.01 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4351 0 0 246 4597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224423
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9745962
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8555548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87626.508189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74115871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.51510
X-RAY DIFFRACTIONr_chiral_restr0.0930.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213212
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7011.52740
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31324424
X-RAY DIFFRACTIONr_scbond_it2.09931683
X-RAY DIFFRACTIONr_scangle_it3.4644.51538
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 120 -
Rwork0.21 2323 -
obs--99.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4447-0.1068-0.07221.0641.25712.02920.0009-0.0003-0.03930.1117-0.08650.05880.0954-0.10690.08570.0907-0.02250.0280.0268-0.00490.05890.13132.034119.2415
20.5589-0.6315-0.04040.72620.03042.313-0.0726-0.00470.05550.08280.0339-0.0799-0.0116-0.15730.03860.0106-0.003-0.00730.0674-0.01540.10367.0813-2.1346-5.1988
31.2054-0.10090.02321.43860.51181.739-0.0024-0.12720.00310.13970.0128-0.183-0.01260.1941-0.01040.1355-0.00210.00260.13010.01130.142514.365118.338634.2653
40.1351-0.0611-0.23541.51040.82031.8361-0.1062-0.1134-0.03650.3743-0.0170.26130.1891-0.07210.12320.31790.01120.00220.33190.01220.32132.357314.700251.3552
50.23270.0475-0.11240.3905-0.33550.87840.0345-0.2425-0.12980.28630.01630.21410.0012-0.1976-0.05080.4727-0.01720.04680.48290.03250.4598-5.670435.088458.4614
61.8191.1545-0.31180.9878-0.21130.1421-0.13330.36230.0693-0.3410.1207-0.1416-0.0440.08610.01260.45480.0110.02930.43080.01380.42587.283442.569940.1232
72.6787-1.579-1.00421.30190.69420.7063-0.0712-0.08870.01210.1050.00690.3388-0.1408-0.25360.06430.33520.05050.02840.37020.01190.3758-3.935332.240346.9423
81.4997-0.05530.79510.1514-0.01030.5123-0.02650.3570.0939-0.23290.0284-0.023-0.09070.0624-0.00190.43480.00720.01710.3780.00030.3816-0.525141.986642.3479
90.1774-0.0829-0.02270.10480.06080.04180.08990.22170.2075-0.188-0.0092-0.1516-0.11260.0511-0.08070.54930.01890.04080.54180.03220.56688.08950.008547.3417
100.793-0.48680.24832.08370.64071.0063-0.0816-0.45420.09130.47950.06190.3239-0.1275-0.19460.01970.3576-0.05930.07920.3436-0.05910.33657.268830.656554.4163
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 160
2X-RAY DIFFRACTION2A161 - 329
3X-RAY DIFFRACTION3C54 - 157
4X-RAY DIFFRACTION4C158 - 181
5X-RAY DIFFRACTION5C182 - 198
6X-RAY DIFFRACTION6C199 - 209
7X-RAY DIFFRACTION7C210 - 227
8X-RAY DIFFRACTION8C228 - 261
9X-RAY DIFFRACTION9C262 - 292
10X-RAY DIFFRACTION10C293 - 329

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