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- PDB-5d84: Staphyloferrin B precursor biosynthetic enzyme SbnA bound to PLP -

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Basic information

Entry
Database: PDB / ID: 5d84
TitleStaphyloferrin B precursor biosynthetic enzyme SbnA bound to PLP
ComponentsProbable siderophore biosynthesis protein SbnA
KeywordsBIOSYNTHETIC PROTEIN / siderophore / iron / plp
Function / homology
Function and homology information


N-(2-amino-2-carboxyethyl)-L-glutamate synthase / cysteine biosynthetic process from serine / transferase activity, transferring alkyl or aryl (other than methyl) groups
Similarity search - Function
2,3-diaminopropionate biosynthesis protein SbnA / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / N-(2-amino-2-carboxyethyl)-L-glutamate synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsGrigg, J.C. / Kobylarz, M.J. / Liu, Y. / Lee, M.S.F. / Heinrichs, D.E. / Murphy, M.E.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-102596 Canada
CitationJournal: Biochemistry / Year: 2016
Title: Deciphering the Substrate Specificity of SbnA, the Enzyme Catalyzing the First Step in Staphyloferrin B Biosynthesis.
Authors: Kobylarz, M.J. / Grigg, J.C. / Liu, Y. / Lee, M.S. / Heinrichs, D.E. / Murphy, M.E.
History
DepositionAug 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _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: Probable siderophore biosynthesis protein SbnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2123
Polymers35,9401
Non-polymers2712
Water6,557364
1
A: Probable siderophore biosynthesis protein SbnA
hetero molecules

A: Probable siderophore biosynthesis protein SbnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4236
Polymers71,8802
Non-polymers5434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4350 Å2
ΔGint-26 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.080, 115.828, 45.138
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1236-

HOH

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Components

#1: Protein Probable siderophore biosynthesis protein SbnA


Mass: 35940.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Newman / Gene: sbnA, NWMN_0060 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6QDA0
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 0.2 M MgCl2, 20-25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97952 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 15, 2010
Details: Vertical Focusing Mirror: ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 51631 / % possible obs: 97.3 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.055 / Χ2: 1.006 / Net I/av σ(I): 28.097 / Net I/σ(I): 13 / Num. measured all: 302661
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.45-1.55.60.41349541.01994.7
1.5-1.565.70.31849420.99994.6
1.56-1.635.70.25949571.00394.8
1.63-1.725.70.19850051.01795.6
1.72-1.835.70.15450990.95997.3
1.83-1.975.80.10952280.93698.7
1.97-2.1760.0752690.99399.7
2.17-2.486.20.05553171.00499.8
2.48-3.126.20.04153770.991100
3.12-5060.02854831.13197.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.8 Å40.12 Å
Translation1.8 Å40.12 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX2.2.4phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.585 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 2598 5.1 %RANDOM
Rwork0.1239 ---
obs0.1265 48724 96.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.86 Å2 / Biso mean: 18.813 Å2 / Biso min: 7.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.59 Å20 Å2
3----0.35 Å2
Refinement stepCycle: final / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 16 364 2836
Biso mean--12.9 32.78 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192714
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9693705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4365358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92325.089112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46215492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1781512
X-RAY DIFFRACTIONr_chiral_restr0.0920.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212061
X-RAY DIFFRACTIONr_mcbond_it2.6271.4851375
X-RAY DIFFRACTIONr_mcangle_it3.3272.2451752
X-RAY DIFFRACTIONr_scbond_it3.3541.7821339
X-RAY DIFFRACTIONr_rigid_bond_restr3.04932714
X-RAY DIFFRACTIONr_sphericity_free42.449589
X-RAY DIFFRACTIONr_sphericity_bonded16.27852922
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 192 -
Rwork0.19 3421 -
all-3613 -
obs--94.53 %

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