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- PDB-6vvi: Arabidopsis thaliana dihydrodipicolinate synthase isoform 1 (DHDPS1) -

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Basic information

Entry
Database: PDB / ID: 6vvi
TitleArabidopsis thaliana dihydrodipicolinate synthase isoform 1 (DHDPS1)
Components4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic
KeywordsLYASE / Dihydrodipicolinate Synthase
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / chloroplast
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.145 Å
AuthorsLee, M. / Hall, C.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE190100806 Australia
CitationJournal: Febs J. / Year: 2021
Title: Differential lysine-mediated allosteric regulation of plant dihydrodipicolinate synthase isoforms.
Authors: Hall, C.J. / Lee, M. / Boarder, M.P. / Mangion, A.M. / Gendall, A.R. / Panjikar, S. / Perugini, M.A. / Soares da Costa, T.P.
History
DepositionFeb 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: 4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic
BBB: 4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic
CCC: 4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic
DDD: 4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,09817
Polymers142,1574
Non-polymers94113
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13130 Å2
ΔGint-176 kcal/mol
Surface area40180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.468, 98.100, 176.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic / HTPA synthase 1


Mass: 35539.355 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DHDPS1, DHDPS, DHPS1, At3g60880, T4C21_290 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9LZX6, 4-hydroxy-tetrahydrodipicolinate synthase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES (pH 7.5), 0.1 M NaCl, and 1.4 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.14→49.1 Å / Num. obs: 90994 / % possible obs: 99.4 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 11.5
Reflection shellResolution: 2.14→2.2 Å / Num. unique obs: 4163 / CC1/2: 0.865

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DPP

4dpp


Resolution: 2.145→49.098 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.617 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.157
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2091 4371 4.807 %
Rwork0.1715 --
all0.173 --
obs-90925 99.238 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.455 Å2
Baniso -1Baniso -2Baniso -3
1--1.039 Å20 Å20 Å2
2--3.471 Å20 Å2
3----2.431 Å2
Refinement stepCycle: LAST / Resolution: 2.145→49.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9633 0 53 465 10151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0139947
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179114
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.6413515
X-RAY DIFFRACTIONr_angle_other_deg1.2871.57421151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.92651252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48722.5540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.108151647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7591568
X-RAY DIFFRACTIONr_chiral_restr0.0680.21287
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022046
X-RAY DIFFRACTIONr_nbd_refined0.1930.21965
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.28785
X-RAY DIFFRACTIONr_nbtor_refined0.1530.24839
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.24328
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2473
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0850.27
X-RAY DIFFRACTIONr_metal_ion_refined0.0130.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.020.23
X-RAY DIFFRACTIONr_nbd_other0.1290.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1070.210
X-RAY DIFFRACTIONr_mcbond_it2.2994.1294972
X-RAY DIFFRACTIONr_mcbond_other2.2924.1284971
X-RAY DIFFRACTIONr_mcangle_it3.2766.1856212
X-RAY DIFFRACTIONr_mcangle_other3.2776.1866213
X-RAY DIFFRACTIONr_scbond_it3.1984.5724975
X-RAY DIFFRACTIONr_scbond_other3.1984.5714956
X-RAY DIFFRACTIONr_scangle_it5.0236.77295
X-RAY DIFFRACTIONr_scangle_other5.0256.6987266
X-RAY DIFFRACTIONr_lrange_it6.32149.51711057
X-RAY DIFFRACTIONr_lrange_other6.31749.41210989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.145-2.20.2942910.2716051X-RAY DIFFRACTION94.8691
2.2-2.260.2793280.2536178X-RAY DIFFRACTION99.4801
2.26-2.3260.2473090.2236028X-RAY DIFFRACTION99.3727
2.326-2.3970.2732980.2135836X-RAY DIFFRACTION99.4972
2.397-2.4760.2552570.2015681X-RAY DIFFRACTION99.6978
2.476-2.5630.242590.2045526X-RAY DIFFRACTION99.6383
2.563-2.660.2392610.195339X-RAY DIFFRACTION99.804
2.66-2.7680.2472400.1855109X-RAY DIFFRACTION99.7018
2.768-2.8910.2292250.1894973X-RAY DIFFRACTION99.7314
2.891-3.0320.2332280.1854698X-RAY DIFFRACTION99.6561
3.032-3.1960.252550.1894478X-RAY DIFFRACTION99.4955
3.196-3.3890.2272460.1784212X-RAY DIFFRACTION99.6201
3.389-3.6230.1882280.1593958X-RAY DIFFRACTION99.4063
3.623-3.9130.1761960.1533736X-RAY DIFFRACTION99.4185
3.913-4.2850.1691810.1333438X-RAY DIFFRACTION99.4504
4.285-4.790.1581620.1243140X-RAY DIFFRACTION99.6981
4.79-5.5280.1851500.1322784X-RAY DIFFRACTION99.8979
5.528-6.7640.2131180.1682392X-RAY DIFFRACTION99.7219
6.764-9.5380.144870.1451882X-RAY DIFFRACTION99.3942
9.538-49.0980.225520.1981115X-RAY DIFFRACTION98.9822

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