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- PDB-3a5f: High-resolution structure of DHDPS from Clostridium botulinum in ... -

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Basic information

Entry
Database: PDB / ID: 3a5f
TitleHigh-resolution structure of DHDPS from Clostridium botulinum in complex with pyruvate
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / TIM barrel / enzyme / Amino-acid biosynthesis / Diaminopimelate biosynthesis / Lysine biosynthesis / Schiff base
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / :
Function and homology information
Biological speciesClostridium botulinum A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsAtkinson, S.C. / Dobson, R.C.J. / Perugini, M.A.
CitationJournal: To be Published
Title: The high resolution structure of DHDPS from Clostridium botulinum
Authors: Dobson, R.C.J. / Atkinson, S.C.
History
DepositionAug 6, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 26, 2012Group: Structure summary
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4264
Polymers63,2412
Non-polymers1842
Water18,1411007
1
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules

A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8518
Polymers126,4834
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area9130 Å2
ΔGint-70 kcal/mol
Surface area38500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.358, 54.836, 94.304
Angle α, β, γ (deg.)90.00, 126.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dihydrodipicolinate synthase


Mass: 31620.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum A (bacteria) / Gene: dapA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7FYA1, dihydrodipicolinate synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1007 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsKPI IS LYS MODIFIED WITH PYRUVIC ACID.

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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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 200mM NaCl, 20%(w/v) PEG 3350, pH 8, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9536 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 1.19→25.79 Å / Num. all: 188454 / Num. obs: 188454 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.6
Reflection shellResolution: 1.19→1.25 Å / Redundancy: 5 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.8 / Num. unique all: 27400 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASESphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BI8

3bi8
PDB Unreleased entry


Resolution: 1.19→25.79 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.887 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13985 3773 2 %RANDOM
Rwork0.11234 ---
obs0.1129 184727 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.724 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å2-0.14 Å2
2--0.24 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.19→25.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4403 0 12 1007 5422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224689
X-RAY DIFFRACTIONr_bond_other_d0.0010.023095
X-RAY DIFFRACTIONr_angle_refined_deg2.0761.9866404
X-RAY DIFFRACTIONr_angle_other_deg1.42537747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1665639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.30826.667180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99615874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7061511
X-RAY DIFFRACTIONr_chiral_restr0.1480.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215180
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02797
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_it2.2651.52985
X-RAY DIFFRACTIONr_mcbond_other1.0031.51211
X-RAY DIFFRACTIONr_mcangle_it3.08424894
X-RAY DIFFRACTIONr_scbond_it5.27131704
X-RAY DIFFRACTIONr_scangle_it7.7194.51479
X-RAY DIFFRACTIONr_rigid_bond_restr2.1937784
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.19→1.221 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 246 -
Rwork0.166 13605 -
obs--100 %

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