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- PDB-3to3: Crystal Structure of Petrobactin Biosynthesis Protein AsbB from B... -

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Basic information

Entry
Database: PDB / ID: 3to3
TitleCrystal Structure of Petrobactin Biosynthesis Protein AsbB from Bacillus anthracis str. Sterne
ComponentsPetrobactin biosynthesis protein AsbB
KeywordsBIOSYNTHETIC PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta structure / adenylation / cytosol
Function / homology
Function and homology information


Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / siderophore biosynthetic process / ligase activity / catalytic activity / ATP binding
Similarity search - Function
Aerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like / IucA / IucC family / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Citryl-spermidine/3,4-dihydroxybenzoyl-citryl-spermidine:spermidine ligase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.382 Å
AuthorsKim, Y. / Eschenfeldt, W. / Stols, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Functional and Structural Analysis of the Siderophore Synthetase AsbB through Reconstitution of the Petrobactin Biosynthetic Pathway from Bacillus anthracis.
Authors: Nusca, T.D. / Kim, Y. / Maltseva, N. / Lee, J.Y. / Eschenfeldt, W. / Stols, L. / Schofield, M.M. / Scaglione, J.B. / Dixon, S.D. / Oves-Costales, D. / Challis, G.L. / Hanna, P.C. / Pfleger, ...Authors: Nusca, T.D. / Kim, Y. / Maltseva, N. / Lee, J.Y. / Eschenfeldt, W. / Stols, L. / Schofield, M.M. / Scaglione, J.B. / Dixon, S.D. / Oves-Costales, D. / Challis, G.L. / Hanna, P.C. / Pfleger, B.F. / Joachimiak, A. / Sherman, D.H.
History
DepositionSep 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Petrobactin biosynthesis protein AsbB
B: Petrobactin biosynthesis protein AsbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,7889
Polymers146,9992
Non-polymers7897
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-44 kcal/mol
Surface area47380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.259, 155.923, 156.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsas in the asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Petrobactin biosynthesis protein AsbB


Mass: 73499.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: asbB, BA_1982, GBAA_1982 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q81RQ8

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Non-polymers , 5 types, 331 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M L-Proline, 0.1 M HEPES pH 7.5, 10 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.382→50 Å / Num. all: 62971 / Num. obs: 62971 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 50.83 Å2 / Rsym value: 0.09 / Net I/σ(I): 10.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 3081 / Rsym value: 0.631 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
BUCCANEERmodel building
PHENIX(phenix.refine: dev_851)refinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.382→49.627 Å / SU ML: 0.66 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.31 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3178 5.06 %random
Rwork0.172 ---
all0.174 62858 --
obs0.174 62858 98.76 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.108 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso mean: 59.8 Å2
Baniso -1Baniso -2Baniso -3
1-8.5069 Å2-0 Å2-0 Å2
2---5.1772 Å20 Å2
3----3.3297 Å2
Refinement stepCycle: LAST / Resolution: 2.382→49.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9881 0 42 324 10247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210356
X-RAY DIFFRACTIONf_angle_d1.48514023
X-RAY DIFFRACTIONf_dihedral_angle_d17.2193930
X-RAY DIFFRACTIONf_chiral_restr0.1171491
X-RAY DIFFRACTIONf_plane_restr0.0081806
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3819-2.41750.30691090.2491955206477
2.4175-2.45520.28751520.226225722724100
2.4552-2.49550.29831390.227825952734100
2.4955-2.53850.32531530.220225492702100
2.5385-2.58470.27471390.218926202759100
2.5847-2.63440.27741420.200625862728100
2.6344-2.68810.26281290.194326292758100
2.6881-2.74660.23461290.19625622691100
2.7466-2.81050.30031490.193126122761100
2.8105-2.88080.29141430.203725782721100
2.8808-2.95860.27931170.213826432760100
2.9586-3.04570.2781550.202225832738100
3.0457-3.1440.26621390.194526012740100
3.144-3.25630.29881560.205726292785100
3.2563-3.38670.25721220.193326352757100
3.3867-3.54080.23741580.175326062764100
3.5408-3.72740.19241300.159726122742100
3.7274-3.96080.20831310.146226562787100
3.9608-4.26650.18461470.139126412788100
4.2665-4.69550.16071350.120426712806100
4.6955-5.37430.18141210.131926892810100
5.3743-6.76830.22831410.187526992840100
6.7683-49.63810.20041420.17692757287997
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.46490.35110.12823.4511.161.334-0.0025-0.05270.00890.20480.0997-0.1592-0.07520.1375-0.11180.25250.00410.07120.27990.03340.272422.3804-5.338218.6676
20.2630.7586-0.17594.06920.24771.29-0.07650.0564-0.0352-0.58650.09580.0563-0.06540.0532-0.01210.4285-0.03820.08760.35760.00030.297227.57622.85260.5901
31.5758-0.3231-1.44892.3225-1.50435.4254-0.09240.1420.2631-0.29540.2061-0.0166-0.52670.0121-0.06660.5-0.10830.02270.2579-0.01850.350726.532621.7197.4562
44.18140.06140.44432.0920.10422.049-0.0718-0.002-0.0535-0.0528-0.0148-0.10970.01410.15890.05560.2831-0.03930.04270.1741-0.00970.1986-2.6349-28.548414.5542
53.7421.4576-1.49182.1586-1.13972.12520.1313-0.17620.01780.2059-0.157-0.1314-0.07350.0116-0.0090.3123-0.0373-0.04080.2768-0.010.24279.7762-21.065845.6354
62.54791.22930.97622.23450.91522.80720.0542-0.36760.1690.2147-0.19180.0366-0.1598-0.18360.1170.286-0.0530.04870.27550.02740.2555-10.4613-31.239641.2386
73.55720.3111-2.57241.0283-1.25864.56310.1873-0.08170.28640.19480.04520.6188-0.0237-0.3955-0.2150.2744-0.0350.0040.4222-0.02150.4648-24.0074-32.245833.2199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:286)
2X-RAY DIFFRACTION2chain 'A' and (resseq 287:513)
3X-RAY DIFFRACTION3chain 'A' and (resseq 514:600)
4X-RAY DIFFRACTION4chain 'B' and (resseq 0:183)
5X-RAY DIFFRACTION5chain 'B' and (resseq 184:366)
6X-RAY DIFFRACTION6chain 'B' and (resseq 367:519)
7X-RAY DIFFRACTION7chain 'B' and (resseq 520:600)

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