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

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Basic information

Entry
Database: PDB / ID: 3wqd
TitleD-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23 complexed with D-erythro-3-hydroxyaspartate
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 / PLP-binding barrel ...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
(3S)-3-hydroxy-D-aspartic acid / 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
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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)84,01211
Polymers83,0982
Non-polymers9149
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-58 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.834, 157.834, 158.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#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
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal 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-999 / (3S)-3-hydroxy-D-aspartic acid


Type: D-peptide linking / Mass: 149.102 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O
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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12% 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: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 156137 / Num. obs: 156137 / % possible obs: 99.6 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 37.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 6.54 / Num. unique all: 7721 / % 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→28.88 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.868 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17586 7785 5 %RANDOM
Rwork0.14352 ---
obs0.14517 147246 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.155 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5731 0 55 672 6458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0195999
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1021.9548160
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9765796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26922.714269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29515951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.731566
X-RAY DIFFRACTIONr_chiral_restr0.1630.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214638
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr8.47235999
X-RAY DIFFRACTIONr_sphericity_free27.7775179
X-RAY DIFFRACTIONr_sphericity_bonded19.58556380
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 556 -
Rwork0.251 10184 -
obs--97.01 %

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