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- PDB-3na8: Crystal Structure of a putative dihydrodipicolinate synthetase fr... -

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Basic information

Entry
Database: PDB / ID: 3na8
TitleCrystal Structure of a putative dihydrodipicolinate synthetase from Pseudomonas aeruginosa
Componentsputative dihydrodipicolinate synthetase
KeywordsLYASE
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase activity / metal ion binding / cytosol
Similarity search - Function
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
D-MALATE / Probable dihydrodipicolinate synthetase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsQiu, W. / Lam, R. / Romanov, V. / Jones, K. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: To be Published
Title: Crystal Structure of a putative dihydrodipicolinate synthetase from Pseudomonas aeruginosa
Authors: Qiu, W. / Lam, R. / Romanov, V. / Jones, K. / Pai, E.F. / Chirgadze, N.Y.
History
DepositionJun 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2012Group: Non-polymer description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative dihydrodipicolinate synthetase
B: putative dihydrodipicolinate synthetase
C: putative dihydrodipicolinate synthetase
D: putative dihydrodipicolinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,87211
Polymers137,3734
Non-polymers4997
Water14,934829
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-104 kcal/mol
Surface area40700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.370, 156.210, 76.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
putative dihydrodipicolinate synthetase


Mass: 34343.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA0223 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I6R5, dihydrodipicolinate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 829 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 17% PEG6000, 0.4M Malic Acid, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 8, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.85→48.73 Å / Num. all: 125665 / Num. obs: 106856 / % possible obs: 96.5 % / Redundancy: 7.27 % / Rmerge(I) obs: 0.1044 / Rsym value: 0.0556 / Net I/σ(I): 11.89
Reflection shellResolution: 1.85→1.94 Å / Redundancy: 6.78 % / Rmerge(I) obs: 0.7143 / Mean I/σ(I) obs: 1.99 / Num. unique all: 13416 / Rsym value: 0.5008 / % possible all: 90.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.5.0066refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→43.06 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.432 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26972 5334 5 %RANDOM
Rwork0.23498 ---
obs0.23674 101217 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.413 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8846 0 31 829 9706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0229221
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.5271.98712565
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4975.0661213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.89423.091385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.739151527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6931583
X-RAY DIFFRACTIONr_chiral_restr0.0360.21455
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216988
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_it0.1951.55825
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.36629381
X-RAY DIFFRACTIONr_scbond_it0.40333396
X-RAY DIFFRACTIONr_scangle_it0.7194.53161
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 360 -
Rwork0.375 6586 -
obs--85.95 %

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