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- PDB-3wqc: D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23 -

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Basic information

Entry
Database: PDB / ID: 3wqc
TitleD-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23
ComponentsD-threo-3-hydroxyaspartate dehydratase
KeywordsLYASE / Dehydratase / PLP
Function / homology
Function and homology information


threo-3-hydroxy-D-aspartate ammonia-lyase / ammonia-lyase activity / D-serine ammonia-lyase activity / D-serine catabolic process / pyridoxal phosphate binding
Similarity search - Function
: / D-serine dehydratase-like domain / D-serine dehydratase-like domain / D-serine dehydratase-like domain superfamily / Putative serine dehydratase domain / Putative serine dehydratase domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase ...: / D-serine dehydratase-like domain / D-serine dehydratase-like domain / D-serine dehydratase-like domain superfamily / Putative serine dehydratase domain / Putative serine dehydratase domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / D-threo-3-hydroxyaspartate dehydratase
Similarity search - Component
Biological speciesDelftia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsYasutake, Y. / Matsumoto, Y. / Wada, M.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2015
Title: Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and D- ...Title: Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and D-erythro-3-hydroxyaspartate
Authors: Matsumoto, Y. / Yasutake, Y. / Takeda, Y. / Tamura, T. / Yokota, A. / Wada, M.
History
DepositionJan 25, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-threo-3-hydroxyaspartate dehydratase
B: D-threo-3-hydroxyaspartate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,06114
Polymers83,0982
Non-polymers96312
Water11,710650
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-76 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.689, 157.689, 158.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-789-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein D-threo-3-hydroxyaspartate dehydratase / D-THA DH / D-THA dehydratase / Threo-3-hydroxy-D-aspartate ammonia-lyase


Mass: 41549.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Delftia (bacteria) / Strain: HT23 / Gene: dthadh / Plasmid: pTip-QC2 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): L88
References: UniProt: B2DFG5, threo-3-hydroxy-D-aspartate ammonia-lyase

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Non-polymers , 5 types, 662 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsSG ATOM OF CYS 353 AND NE2 ATOM OF HIS 351 ARE COORDINATED TO THE ACTIVE-SITE METAL MG.

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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: 2.97 Å3/Da / Density % sol: 58.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 13% PEG3350, 0.2M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 157557 / Num. obs: 157557 / % possible obs: 100 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 33.66
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 4.99 / Num. unique all: 7806 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXCDphasing
SHELXEmodel building
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→45.63 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.585 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1518 7908 5 %RANDOM
Rwork0.1211 ---
obs0.1227 149594 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 164.66 Å2 / Biso mean: 21.614 Å2 / Biso min: 7.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5731 0 55 650 6436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0195987
X-RAY DIFFRACTIONr_angle_refined_deg2.1771.9538133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9125794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30122.734267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92715950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2951565
X-RAY DIFFRACTIONr_chiral_restr0.170.2920
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214605
X-RAY DIFFRACTIONr_rigid_bond_restr8.95435987
X-RAY DIFFRACTIONr_sphericity_free29.7595185
X-RAY DIFFRACTIONr_sphericity_bonded19.21356341
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 550 -
Rwork0.154 10413 -
all-10963 -
obs--98.87 %

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