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- PDB-5d87: Staphyloferrin B precursor biosynthetic enzyme SbnA Y152F/S185G v... -

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Basic information

Entry
Database: PDB / ID: 5d87
TitleStaphyloferrin B precursor biosynthetic enzyme SbnA Y152F/S185G variant
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 synthase activity / cysteine biosynthetic process from serine / cytoplasm
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: 1.5 Å
AuthorsKobylarz, M.J. / Grigg, J.C. / 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)36,2927
Polymers35,8941
Non-polymers3986
Water7,242402
1
A: Probable siderophore biosynthesis protein SbnA
hetero molecules

A: Probable siderophore biosynthesis protein SbnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,58514
Polymers71,7882
Non-polymers79712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5530 Å2
ΔGint-48 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.980, 115.170, 44.670
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-774-

HOH

21A-815-

HOH

31A-883-

HOH

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Components

#1: Protein Probable siderophore biosynthesis protein SbnA


Mass: 35894.137 Da / Num. of mol.: 1 / Mutation: Y152F, S185G
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


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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris, pH 8.5, 29-33% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2014 / Details: Rh coated focusing mirror
RadiationMonochromator: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.5→57.585 Å / Num. all: 46619 / Num. obs: 46619 / % possible obs: 98.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 11.17 Å2 / Rpim(I) all: 0.026 / Rrim(I) all: 0.066 / Rsym value: 0.061 / Net I/av σ(I): 7.465 / Net I/σ(I): 19.6 / Num. measured all: 295050
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.5-1.584.30.2423.22705963070.130.2424.993.4
1.58-1.686.40.1983.94084763770.0840.1988.499.5
1.68-1.796.80.145.54163860810.0580.1411.9100
1.79-1.946.80.0947.93868556530.0390.09416.5100
1.94-2.126.80.06710.23538751810.0280.06722.8100
2.12-2.376.80.05412.53226647530.0220.05427.2100
2.37-2.746.70.04514.32807142010.0190.04530.5100
2.74-3.356.50.04911.42313235800.0210.04933.899.9
3.35-4.7460.04712.11704528360.0210.04737.399.8
4.74-38.396.60.04711.21092016500.020.04738.399.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.5 Å34.92 Å
Translation6.48 Å34.92 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.5.5phasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→34.916 Å / FOM work R set: 0.899 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1775 2355 5.06 %
Rwork0.1504 44209 -
obs0.1518 46564 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.1 Å2 / Biso mean: 14.75 Å2 / Biso min: 5.16 Å2
Refinement stepCycle: final / Resolution: 1.5→34.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 20 402 2864
Biso mean--11.58 25.86 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092675
X-RAY DIFFRACTIONf_angle_d1.2213649
X-RAY DIFFRACTIONf_chiral_restr0.051413
X-RAY DIFFRACTIONf_plane_restr0.007474
X-RAY DIFFRACTIONf_dihedral_angle_d13.9261015
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.53070.24631200.18512336245690
1.5307-1.5640.2151340.17452439257394
1.564-1.60030.18751540.16552519267397
1.6003-1.64040.21741350.153725732708100
1.6404-1.68470.20981240.156725812705100
1.6847-1.73430.21511210.158626452766100
1.7343-1.79030.20941620.162225902752100
1.7903-1.85420.18271410.16325912732100
1.8542-1.92850.20731350.157426072742100
1.9285-2.01620.16971550.15225862741100
2.0162-2.12250.1661450.145626122757100
2.1225-2.25550.17671330.146126442777100
2.2555-2.42960.17171250.149326532778100
2.4296-2.6740.18961240.153426692793100
2.674-3.06070.17181420.154426502792100
3.0607-3.85540.15491560.137726742830100
3.8554-34.92550.15351490.13928402989100
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)
14.4967-1.7963-0.29291.92850.42910.8810.14750.26620.2922-0.1685-0.1304-0.0234-0.0859-0.03190.01130.0918-0.00950.00440.08530.01980.086131.8114-6.2334-12.7005
21.860.3575-0.37371.97520.13812.17340.0488-0.0552-0.0820.0859-0.0567-0.0288-0.02860.0029-0.0080.04330.0008-0.00220.0410.00890.08612.768-9.1292-0.2439
35.1933-0.50691.24092.2979-0.27525.2914-0.1007-0.6116-0.06550.47630.0556-0.3650.07240.21560.0340.1836-0.0031-0.05530.12210.0150.136211.3487-20.529113.3098
44.28220.097-2.65910.29410.0362.1126-0.01740.2551-0.0298-0.04110.01530.06880.0355-0.1950.00510.06740.0108-0.02810.0721-0.01130.071216.9569-17.3221-10.3576
50.87190.20920.09711.0720.07870.9310.021-0.039-0.03010.0536-0.02320.0180.05440.0240.00510.0520.01150.00270.04780.00540.059434.4616-19.4201-2.4481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 6:45 )A6 - 45
2X-RAY DIFFRACTION2( CHAIN A AND RESID 46:118 )A46 - 118
3X-RAY DIFFRACTION3( CHAIN A AND RESID 119:142 )A119 - 142
4X-RAY DIFFRACTION4( CHAIN A AND RESID 143:172 )A143 - 172
5X-RAY DIFFRACTION5( CHAIN A AND RESID 173:321 )A173 - 321

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