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- PDB-3wqf: D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23 in t... -

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Basic information

Entry
Database: PDB / ID: 3wqf
TitleD-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23 in the metal-free form
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: 2.3 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 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / 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 / _struct_conn.pdbx_leaving_atom_flag / _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)83,5934
Polymers83,0982
Non-polymers4942
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-10 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.844, 157.844, 157.860
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


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 58.42 %
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 270 / Detector: CCD / Date: Dec 11, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 44400 / Num. obs: 44400 / % possible obs: 100 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 28.63
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 7.13 / Num. unique all: 2198 / % 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: 2.3→49.92 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.639 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23865 2210 5 %RANDOM
Rwork0.19784 ---
obs0.19991 42156 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.553 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20 Å2
2---1.25 Å2-0 Å2
3---2.51 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5635 0 30 228 5893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195759
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.9567824
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5945755
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34522.908251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1215900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1121560
X-RAY DIFFRACTIONr_chiral_restr0.120.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214420
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 150 -
Rwork0.229 2898 -
obs--99.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0768-0.8503-0.12131.0983-0.16440.65080.02210.03610.22920.008-0.02-0.3058-0.08380.1091-0.00210.0634-0.0141-0.00120.0443-0.00260.08960.467-59.6439-21.7979
24.0244-0.294-0.34360.3105-0.03360.3745-0.0591-0.50150.25310.11360.0851-0.2425-0.06750.2953-0.0260.16170.0379-0.05060.3015-0.09440.2049-16.4365-56.87651.5331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 380
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B2 - 380
4X-RAY DIFFRACTION2B401

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