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- PDB-3dx5: Crystal structure of the probable 3-DHS dehydratase AsbF involved... -

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Basic information

Entry
Database: PDB / ID: 3dx5
TitleCrystal structure of the probable 3-DHS dehydratase AsbF involved in the petrobactin synthesis from Bacillus anthracis
Componentsuncharacterized protein AsbF
KeywordsLYASE / beta-alpha barrel / petrobactin synthesis / Asb locus / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / unknown function
Function / homology
Function and homology information


3-dehydroshikimate dehydratase / 3-dehydroshikimate dehydratase activity / 3,4-dihydroxybenzoate biosynthetic process / metal ion binding
Similarity search - Function
: / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3,4-DIHYDROXYBENZOIC ACID / : / 3-dehydroshikimate dehydratase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.12 Å
AuthorsKim, Y. / Maltseva, N. / Stols, L. / Eschenfeldt, W. / Pfleger, B.F. / Sherman, D.H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structural and functional analysis of AsbF: origin of the stealth 3,4-dihydroxybenzoic acid subunit for petrobactin biosynthesis.
Authors: Pfleger, B.F. / Kim, Y. / Nusca, T.D. / Maltseva, N. / Lee, J.Y. / Rath, C.M. / Scaglione, J.B. / Janes, B.K. / Anderson, E.C. / Bergman, N.H. / Hanna, P.C. / Joachimiak, A. / Sherman, D.H.
History
DepositionJul 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein AsbF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2056
Polymers33,7461
Non-polymers4595
Water4,161231
1
A: uncharacterized protein AsbF
hetero molecules

A: uncharacterized protein AsbF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,40912
Polymers67,4922
Non-polymers91710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area4800 Å2
ΔGint-30 kcal/mol
Surface area22710 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.483, 134.483, 72.806
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-299-

HOH

21A-387-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein uncharacterized protein AsbF


Mass: 33745.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tag with TEV protease cleavage site / Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS1843, BA_1986, GBAA1986 / Plasmid: pMCSG26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81RQ4

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Non-polymers , 6 types, 236 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH8.5, 3.2 M soudium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.11→49.4 Å / Num. all: 22726 / Num. obs: 22726 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 9.1
Reflection shellResolution: 2.11→2.19 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 6.7 / Num. unique all: 2210 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.4.0078refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDphasing
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.12→49.4 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.044 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.165 / ESU R Free: 0.138
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.178 1151 5.1 %RANDOM
Rwork0.148 ---
all0.15 21342 --
obs0.15 21342 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.061 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.13 Å20 Å2
2--0.25 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.12→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 27 231 2508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212587
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.943531
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6765319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.36925.448145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44515447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8341511
X-RAY DIFFRACTIONr_chiral_restr0.1090.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022054
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_it0.7351.51530
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41222498
X-RAY DIFFRACTIONr_scbond_it2.51131057
X-RAY DIFFRACTIONr_scangle_it4.0234.51033
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 85 -
Rwork0.157 1525 -
obs-1610 99.32 %
Refinement TLS params.Method: refined / Origin x: 65.6262 Å / Origin y: 70.4113 Å / Origin z: 2.1516 Å
111213212223313233
T0.0256 Å2-0.0096 Å20.0176 Å2-0.0299 Å20.0098 Å2--0.0228 Å2
L0.7774 °2-0.0827 °20.0616 °2-0.8213 °20.1661 °2--1.4143 °2
S-0.0144 Å °0.0356 Å °0.0189 Å °-0.0669 Å °-0.0041 Å °0.0357 Å °0.0663 Å °-0.0232 Å °0.0185 Å °

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