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- PDB-3daq: Crystal structure of dihydrodipicolinate synthase from methicilli... -

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Basic information

Entry
Database: PDB / ID: 3daq
TitleCrystal structure of dihydrodipicolinate synthase from methicillin-resistant Staphylococcus aureus
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / dihydrodipicolinate synthase / lysine biosynthesis / Amino-acid biosynthesis / Diaminopimelate biosynthesis / Schiff base
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsDobson, R.C.J. / Burgess, B.R. / Jameson, G.B. / Gerrard, J.A. / Parker, M.W. / Perugini, M.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure and evolution of a novel dimeric enzyme from a clinically-important bacterial pathogen.
Authors: Burgess, B.R. / Dobson, R.C.J. / Bailey, M.F. / Atkinson, S.C. / Griffin, M.D.W. / Jameson, G.B. / Parker, M.W. / Gerrard, J.A. / Perugini, M.A.
History
DepositionMay 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
C: Dihydrodipicolinate synthase
D: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,51217
Polymers128,5414
Non-polymers97113
Water32,3371795
1
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7108
Polymers64,2712
Non-polymers4396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-39 kcal/mol
Surface area21470 Å2
MethodPISA
2
C: Dihydrodipicolinate synthase
D: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8029
Polymers64,2712
Non-polymers5317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-39 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.410, 67.573, 77.998
Angle α, β, γ (deg.)90.13, 68.85, 72.29
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLYSLYS3AA225 - 235224 - 234
21GLNGLNLYSLYS3BB225 - 235224 - 234
31GLNGLNLYSLYS3CC225 - 235224 - 234
41GLNGLNLYSLYS3DD225 - 235224 - 234
12ALAALAGLYGLY3AA291 - 292290 - 291
22ALAALAGLYGLY3BB291 - 292290 - 291
32ALAALAGLYGLY3CC291 - 292290 - 291
42ALAALAGLYGLY3DD291 - 292290 - 291
13PHEPHEASNASN5AA262 - 264261 - 263
23PHEPHEASNASN5BB262 - 264261 - 263
33PHEPHEASNASN5CC262 - 264261 - 263
43PHEPHEASNASN5DD262 - 264261 - 263

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Dihydrodipicolinate synthase / DHDPS


Mass: 32135.295 Da / Num. of mol.: 4 / Fragment: residues 2-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: dapA, SAR1407 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6GH13, dihydrodipicolinate synthase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1795 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 16.7% PEG6000, NaF 135mM, LiCl 296mM, NaAC 100mM, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9536 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 1.45→30.25 Å / Num. obs: 190869 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 9.84 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 18.8
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 8.4 / Num. unique all: 21900 / Rsym value: 0.147 / % possible all: 71.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yxc

1yxc


Resolution: 1.45→30.25 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.84 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16084 9610 5 %RANDOM
Rwork0.13229 ---
obs0.13371 181258 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: 8.073 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0.08 Å2-0.34 Å2
2---0.38 Å2-0.13 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9024 0 58 1795 10877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229356
X-RAY DIFFRACTIONr_bond_other_d0.0010.026044
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.97712776
X-RAY DIFFRACTIONr_angle_other_deg0.887314997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.92751207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06926.145415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27151589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0771528
X-RAY DIFFRACTIONr_chiral_restr0.0720.21542
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021670
X-RAY DIFFRACTIONr_nbd_refined0.2160.22285
X-RAY DIFFRACTIONr_nbd_other0.1790.26872
X-RAY DIFFRACTIONr_nbtor_refined0.1790.24999
X-RAY DIFFRACTIONr_nbtor_other0.0870.24638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.21493
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.296
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7671.56070
X-RAY DIFFRACTIONr_mcbond_other0.2441.52366
X-RAY DIFFRACTIONr_mcangle_it1.0829625
X-RAY DIFFRACTIONr_scbond_it1.76233648
X-RAY DIFFRACTIONr_scangle_it2.634.53130
X-RAY DIFFRACTIONr_rigid_bond_restr0.772316594
X-RAY DIFFRACTIONr_sphericity_free2.81231799
X-RAY DIFFRACTIONr_sphericity_bonded1.329315236
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A63tight positional0.060.05
12B63tight positional0.060.05
13C63tight positional0.040.05
14D63tight positional0.020.05
21A11tight positional0.120.05
22B11tight positional0.040.05
23C11tight positional0.040.05
24D11tight positional0.040.05
31A17medium positional0.260.5
32B17medium positional0.080.5
33C17medium positional0.10.5
34D17medium positional0.080.5
11A58loose positional0.245
12B58loose positional0.195
13C58loose positional0.385
14D58loose positional0.175
21A3loose positional0.25
22B3loose positional0.075
23C3loose positional0.065
24D3loose positional0.075
31A22loose positional0.125
32B22loose positional0.055
33C22loose positional0.075
34D22loose positional0.055
11A63tight thermal0.080.5
12B63tight thermal0.050.5
13C63tight thermal0.090.5
14D63tight thermal0.040.5
21A11tight thermal0.030.5
22B11tight thermal0.040.5
23C11tight thermal0.050.5
24D11tight thermal0.030.5
31A17medium thermal0.332
32B17medium thermal0.342
33C17medium thermal0.332
34D17medium thermal0.272
11A58loose thermal0.5410
12B58loose thermal0.4410
13C58loose thermal0.7210
14D58loose thermal0.310
21A3loose thermal0.0910
22B3loose thermal0.110
23C3loose thermal0.110
24D3loose thermal0.0710
31A22loose thermal0.4210
32B22loose thermal0.610
33C22loose thermal0.6510
34D22loose thermal0.5110
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 475 -
Rwork0.13 9117 -
obs--100 %

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