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- PDB-5d85: Staphyloferrin B precursor biosynthetic enzyme SbnA bound to amin... -

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Basic information

Entry
Database: PDB / ID: 5d85
TitleStaphyloferrin B precursor biosynthetic enzyme SbnA bound to aminoacrylate intermediate
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
CITRATE ANION / Chem-P1T / N-(2-amino-2-carboxyethyl)-L-glutamate synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 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 1.2Sep 6, 2017Group: 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
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable siderophore biosynthesis protein SbnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5404
Polymers35,9401
Non-polymers5993
Water3,153175
1
A: Probable siderophore biosynthesis protein SbnA
hetero molecules

A: Probable siderophore biosynthesis protein SbnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0798
Polymers71,8802
Non-polymers1,1996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area4080 Å2
ΔGint-9 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.741, 117.408, 47.818
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-588-

HOH

21A-636-

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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-P1T / 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID


Mass: 318.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O7P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.9-1.1 M Sodium citrate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2013 / 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: 1.1587 Å / Relative weight: 1
ReflectionResolution: 1.92→39.14 Å / Num. obs: 25115 / % possible obs: 99.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 22.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.037 / Net I/σ(I): 13.1 / Num. measured all: 148794 / Scaling rejects: 83
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.92-1.965.50.5362.6839115330.9360.24593.2
9-39.144.90.02135.114923020.9990.0199

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.59 Å37.07 Å
Translation6.59 Å37.07 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIX(phenix.refine: 1.8.4_1496)phasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→37.075 Å / FOM work R set: 0.8441 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 2000 7.98 %
Rwork0.1707 23049 -
obs0.1741 25049 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.68 Å2 / Biso mean: 28.16 Å2 / Biso min: 14.32 Å2
Refinement stepCycle: final / Resolution: 1.92→37.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 40 175 2640
Biso mean--29.62 35.27 -
Num. residues----313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132547
X-RAY DIFFRACTIONf_angle_d1.2863457
X-RAY DIFFRACTIONf_chiral_restr0.06388
X-RAY DIFFRACTIONf_plane_restr0.007444
X-RAY DIFFRACTIONf_dihedral_angle_d16.181977
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-1.96640.32641300.2611500163093
1.9664-2.01950.3311420.235816291771100
2.0195-2.0790.25041420.206716361778100
2.079-2.14610.27841390.195816041743100
2.1461-2.22270.28071410.193316311772100
2.2227-2.31170.21861430.188716421785100
2.3117-2.41690.21151410.179416301771100
2.4169-2.54430.20091430.175816381781100
2.5443-2.70370.24161430.178416601803100
2.7037-2.91240.21471430.178616311774100
2.9124-3.20530.20361460.170316841830100
3.2053-3.66870.19671440.160116651809100
3.6687-4.62080.17411470.130817001847100
4.6208-37.08170.19061560.15717991955100
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)
17.4587-3.12320.42433.9411-0.72651.43440.21960.6111-0.4363-0.324-0.22280.04850.06310.0189-0.0110.18410.00090.00830.2313-0.0420.2091-33.16517.3291-13.6504
21.96250.267-0.03011.26770.18691.4962-0.00010.13560.1041-0.0493-0.0004-0.2577-0.01080.203-0.00940.12860.00130.01750.15850.0150.2808-12.181610.2457-4.7781
32.5329-0.18420.21432.50140.57831.0092-0.0075-0.30260.20430.36690.0291-0.1132-0.0902-0.007-0.0240.25620.0011-0.03310.2178-0.01250.2009-14.920614.9138.6217
43.4217-0.82090.84321.9667-0.15811.67230.02090.32350.3598-0.0743-0.0648-0.189-0.0450.11680.03130.17550.00960.03920.14490.0560.2184-25.816421.1928-10.3233
52.2314-0.0007-0.11261.7795-0.23070.8955-0.00220.08350.37410.05010.03560.0332-0.2048-0.0678-0.0330.1750.030.00590.14640.01360.2032-36.27119.6091-3.0339
62.6026-0.79160.5342.7366-0.55743.9331-0.2136-0.30640.05550.51360.0647-0.0413-0.3385-0.16280.10620.2110.0166-0.0170.136-0.01780.1913-37.628912.6681.2395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:45 )A9 - 45
2X-RAY DIFFRACTION2( CHAIN A AND RESID 46:102 )A46 - 102
3X-RAY DIFFRACTION3( CHAIN A AND RESID 103:142 )A103 - 142
4X-RAY DIFFRACTION4( CHAIN A AND RESID 143:227 )A143 - 227
5X-RAY DIFFRACTION5( CHAIN A AND RESID 228:286 )A228 - 286
6X-RAY DIFFRACTION6( CHAIN A AND RESID 287:321 )A287 - 321

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