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- PDB-7t34: Crystal structure of AtDHDPR1 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 7t34
TitleCrystal structure of AtDHDPR1 from Arabidopsis thaliana
Components4-hydroxy-tetrahydrodipicolinate reductase 1, chloroplastic
KeywordsPLANT PROTEIN / dihydrodipicolinate reductase / DHDPR / Arabidopsis thaliana
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / chloroplast stroma / lysine biosynthetic process via diaminopimelate / NADPH binding / chloroplast / cytosol
Similarity search - Function
Dihydrodipicolinate reductase, plant-type / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
4-hydroxy-tetrahydrodipicolinate reductase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsMackie, E.R.R. / Panjikar, S. / Soares da Costa, T.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)IH180100006 Australia
CitationJournal: To be published
Title: From bacteria to plants: a repurposing strategy in the pursuit for novel herbicides
Authors: Mackie, E.R.R. / Barrow, A.S. / Giel, M.C. / Hulett, M.D. / Gendall, A.R. / Panjikar, S. / Soares da Costa, T.P.
History
DepositionDec 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate reductase 1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)32,2751
Polymers32,2751
Non-polymers00
Water0
1
A: 4-hydroxy-tetrahydrodipicolinate reductase 1, chloroplastic

A: 4-hydroxy-tetrahydrodipicolinate reductase 1, chloroplastic

A: 4-hydroxy-tetrahydrodipicolinate reductase 1, chloroplastic

A: 4-hydroxy-tetrahydrodipicolinate reductase 1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)129,0994
Polymers129,0994
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area9620 Å2
ΔGint-80 kcal/mol
Surface area41130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.840, 118.840, 127.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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


Mass: 32274.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DAPB1, At2g44040, F6E13.17 / Production host: Escherichia coli (E. coli)
References: UniProt: O80574, 4-hydroxy-tetrahydrodipicolinate reductase

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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: 3.5 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M bis-tris hydrochloride (pH 6.5), 0.245 M magnesium formate, 22% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2021
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.889→49.05 Å / Num. obs: 11082 / % possible obs: 99.68 % / Redundancy: 13.09 % / Biso Wilson estimate: 116.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.046 / Net I/σ(I): 30.28
Reflection shellResolution: 2.889→2.993 Å / Rmerge(I) obs: 0.1197 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 11082 / CC1/2: 0.846 / Rrim(I) all: 0.1244 / % possible all: 97.74

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ARZ

1arz


Resolution: 2.89→49.05 Å / SU ML: 0.4003 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.7357 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2202 1032 9.81 %
Rwork0.1876 9487 -
obs0.1908 10519 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 119.92 Å2
Refinement stepCycle: LAST / Resolution: 2.89→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 0 0 1793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861825
X-RAY DIFFRACTIONf_angle_d0.96812464
X-RAY DIFFRACTIONf_chiral_restr0.054282
X-RAY DIFFRACTIONf_plane_restr0.007316
X-RAY DIFFRACTIONf_dihedral_angle_d16.18121091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.040.29991340.27191317X-RAY DIFFRACTION98.44
3.04-3.230.34291490.25481326X-RAY DIFFRACTION99.8
3.23-3.480.28841460.22421342X-RAY DIFFRACTION100
3.48-3.830.23661530.18591324X-RAY DIFFRACTION100
3.83-4.390.23911490.18051356X-RAY DIFFRACTION100
4.39-5.520.19531450.17621378X-RAY DIFFRACTION100
5.52-49.050.19811560.18061444X-RAY DIFFRACTION99.75
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)
13.53487852931-0.355338616041-0.7436817392692.998093951040.3863828636576.09697462757-0.0659599717719-0.7869769037980.04947252418410.9485406828930.02909812996490.3540538373740.602312036288-0.534825571851-0.09206515190471.11777953514-0.04856366090610.0915821048650.8731346768440.0050082354060.882315797416-18.809789135312.919135030128.3193659507
25.81971647617-3.110528430441.555127086516.04651136789-2.299703869572.98695570864-0.354069876788-0.224286656098-1.203046190880.0851193346140.6831168792230.621926334409-0.6652236129520.288215374429-0.3334769449740.9546624802480.0104807326628-0.04185901728911.13590659581-0.04483930994411.22244193782-14.90271485520.445460899065-2.154737862
33.67779133884-1.60242404993-1.631332984481.903445694442.869122660926.23249411670.2686486749210.08199733901290.1291603587150.05588803441630.0743775570407-0.2081988671560.135416477358-0.355527963251-0.3128729583910.820331100391-0.0929585803004-0.002283623971520.8301639359250.05580584640220.896322433884-14.031434031710.22325600689.97516573204
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 67 through 214 )
2X-RAY DIFFRACTION2chain 'A' and (resid 215 through 240 )
3X-RAY DIFFRACTION3chain 'A' and (resid 241 through 347 )

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