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- PDB-5ua0: Dimeric crystal structure of HTPA reductase from arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 5ua0
TitleDimeric crystal structure of HTPA reductase from arabidopsis thaliana
Components4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic
KeywordsOXIDOREDUCTASE / HTPA Reductase DHDPR Lysine biosynthesis
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase activity / diaminopimelate biosynthetic process / L-lysine biosynthetic process via diaminopimelate / NADPH binding / chloroplast
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 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsKeown, J.K. / Pearce, F.G. / Goldstone, D.C.
CitationJournal: Biochem. J. / Year: 2018
Title: Plant DHDPR forms a dimer with unique secondary structure features that preclude higher-order assembly.
Authors: Watkin, S.A.J. / Keown, J.R. / Richards, E. / Goldstone, D.C. / Devenish, S.R.A. / Grant Pearce, F.
History
DepositionDec 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic
B: 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic
C: 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7905
Polymers107,5973
Non-polymers1922
Water70339
1
A: 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic

A: 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic


Theoretical massNumber of molelcules
Total (without water)71,7322
Polymers71,7322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3890 Å2
ΔGint-27 kcal/mol
Surface area21610 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic
C: 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9244
Polymers71,7322
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-49 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.549, 80.620, 92.790
Angle α, β, γ (deg.)90.000, 95.840, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYMETMETAA21 - 29554 - 328
21GLYGLYMETMETBB21 - 29554 - 328
12GLYGLYMETMETAA21 - 29554 - 328
22GLYGLYMETMETCC21 - 29554 - 328
13ASNASNARGARGBB20 - 29653 - 329
23ASNASNARGARGCC20 - 29653 - 329

NCS ensembles :
ID
1
2
3

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Components

#1: Protein 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic / HTPA reductase 2


Mass: 35865.832 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DAPB2, At3g59890, F24G16.160 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8LB01, 4-hydroxy-tetrahydrodipicolinate reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1.6 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→61.95 Å / Num. obs: 40722 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.042 / Rrim(I) all: 0.114 / Net I/σ(I): 13.6 / Num. measured all: 300898 / Scaling rejects: 110
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.3-2.387.21.8360.499199.8
8.91-61.956.50.0241199

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å54.05 Å
Translation2.3 Å54.05 Å

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHASER2.5.7phasing
REFMACrefinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U5I

5u5i


Resolution: 2.3→61.95 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 23.347 / SU ML: 0.241 / SU R Cruickshank DPI: 0.3395 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.238
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 2012 4.9 %RANDOM
Rwork0.2261 ---
obs0.2277 38707 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 137.81 Å2 / Biso mean: 59.756 Å2 / Biso min: 36.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20.26 Å2
2---0.62 Å2-0 Å2
3---0.79 Å2
Refinement stepCycle: final / Resolution: 2.3→61.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5973 0 10 39 6022
Biso mean--75.25 53.84 -
Num. residues----815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196088
X-RAY DIFFRACTIONr_bond_other_d0.0070.025718
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9598264
X-RAY DIFFRACTIONr_angle_other_deg1.259313117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21724.558226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06115950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1291520
X-RAY DIFFRACTIONr_chiral_restr0.080.2970
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216970
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021314
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A282400.05
12B282400.05
21A282080.07
22C282080.07
31B277660.08
32C277660.08
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 162 -
Rwork0.352 2798 -
all-2960 -
obs--99.8 %
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)
110.4057-0.1342-0.38856.8684-1.46126.6353-0.11280.9718-0.6226-0.1376-0.17810.34460.5424-0.36650.29090.2804-0.03140.03580.5411-0.09930.07279.6055101.3519-29.5412
24.0901-0.0876-2.00341.30610.62213.9887-0.02770.45950.0887-0.21210.01130.08020.1023-0.17180.01630.24360.0510.01460.44510.06590.016816.0533108.5048-26.053
36.339-2.0661-4.20544.3323.52185.05290.10670.0195-0.4772-0.6351-0.2287-0.6405-0.20990.64530.1220.34970.11410.1330.82070.19910.346310.383698.31680.7293
42.1885-2.0599-2.9555.92182.2936.37-0.5393-0.3454-0.4960.32330.0109-0.75040.98660.90860.52840.3880.14630.20770.61380.15010.53778.166291.44872.1043
52.57640.993-2.50352.6846-2.8926.4335-0.10160.3465-0.04690.06720.11350.2628-0.2212-0.4718-0.01190.140.06280.01820.4203-0.02720.05334.2408106.9197-13.009
62.8369-1.25811.64383.6034-3.10864.7868-0.143-0.36840.20320.449-0.1801-0.4182-0.31110.27740.32310.35760.0051-0.00350.53660.01140.059645.266684.44770.6832
72.7938-2.2444-0.04074.2666-2.97427.19580.13580.19930.0381-0.0958-0.04740.08240.7068-0.1838-0.08830.27720.0189-0.02450.38830.00010.018837.362380.5534-11.1014
81.0898-0.2691-0.172.22170.14345.0371-0.2742-0.1536-0.2947-0.0069-0.0443-0.45190.28490.27970.31850.31480.06310.17290.29590.08050.243845.75992.1274-32.8655
91.5850.7801-1.15421.2187-2.06096.1751-0.2208-0.2175-0.00430.035-0.427-0.6105-0.25891.01890.64790.31460.02390.00020.49290.18590.541553.720697.7042-27.5032
108.18050.5324-1.34087.3713-3.80618.64960.2012-0.49740.36860.09710.01590.4484-0.4147-0.5458-0.21710.16750.10740.02470.4811-0.00640.043331.803191.4501-11.6581
113.8371-1.42721.02127.254-3.27096.3845-0.09220.20250.0321-0.8593-0.2458-0.37640.20330.1190.33810.5132-0.01060.1620.3935-0.0030.063338.8123108.1096-63.0809
121.6436-0.0787-0.29516.253-0.94024.49780.0420.33-0.0189-0.29380.13870.34880.063-0.4182-0.18080.4037-0.02260.06570.41290.03910.04428.1475113.341-59.5443
131.837-0.28270.80641.7836-0.70715.5897-0.29360.08320.4376-0.03460.0727-0.2144-0.3594-0.13110.2210.38290.03470.02610.23310.03140.141336.3336105.6418-35.1091
143.50152.9786-0.28858.4075-0.4730.7561-0.06780.62781.0740.160.2184-0.3074-0.8862-0.0351-0.15051.10050.03350.04140.42950.13810.646439.881112.6067-30.7117
150.2529-0.7518-0.26859.5932-1.81042.16460.1689-0.29950.23570.26740.01110.0314-1.46160.5983-0.181.2424-0.3451-0.1660.87070.02360.854.7901114.3257-28.2078
163.3289-0.39812.49461.8323-1.70936.0203-0.00510.0636-0.0882-0.1799-0.059-0.40860.1334-0.14370.06410.37680.02050.14110.23230.03010.14139.7731102.9879-41.848
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 43
2X-RAY DIFFRACTION2A44 - 160
3X-RAY DIFFRACTION3A161 - 191
4X-RAY DIFFRACTION4A192 - 238
5X-RAY DIFFRACTION5A239 - 295
6X-RAY DIFFRACTION6B20 - 127
7X-RAY DIFFRACTION7B128 - 147
8X-RAY DIFFRACTION8B148 - 205
9X-RAY DIFFRACTION9B206 - 272
10X-RAY DIFFRACTION10B273 - 296
11X-RAY DIFFRACTION11C17 - 64
12X-RAY DIFFRACTION12C65 - 134
13X-RAY DIFFRACTION13C135 - 178
14X-RAY DIFFRACTION14C179 - 205
15X-RAY DIFFRACTION15C206 - 228
16X-RAY DIFFRACTION16C229 - 296

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