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- PDB-4dpp: The structure of dihydrodipicolinate synthase 2 from Arabidopsis ... -

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Basic information

Entry
Database: PDB / ID: 4dpp
TitleThe structure of dihydrodipicolinate synthase 2 from Arabidopsis thaliana
ComponentsDihydrodipicolinate synthase 2, chloroplastic
KeywordsLYASE / Amino-acid biosynthesis / (S)-lysine biosynthesis via DAP pathway / (beta/alpha)8-barrel / Class I aldolase / Chloroplast
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 class I / Aldolase-type TIM barrel ...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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-hydroxy-tetrahydrodipicolinate synthase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsGriffin, M.D.W. / Billakanti, J.M. / Gerrard, J.A. / Dobson, R.C.J. / Pearce, F.G.
CitationJournal: Plos One / Year: 2012
Title: Characterisation of the first enzymes committed to lysine biosynthesis in Arabidopsis thaliana
Authors: Griffin, M.D.W. / Billakanti, J.M. / Wason, A. / Keller, S. / Mertens, H.D.T. / Atkinson, S.C. / Dobson, R.C.J. / Perugini, M.A. / Gerrard, J.A. / Pearce, F.G.
History
DepositionFeb 14, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Mar 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_asym_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.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: Dihydrodipicolinate synthase 2, chloroplastic
B: Dihydrodipicolinate synthase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7727
Polymers79,6572
Non-polymers1155
Water7,837435
1
A: Dihydrodipicolinate synthase 2, chloroplastic
B: Dihydrodipicolinate synthase 2, chloroplastic
hetero molecules

A: Dihydrodipicolinate synthase 2, chloroplastic
B: Dihydrodipicolinate synthase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,54314
Polymers159,3134
Non-polymers23010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area11530 Å2
ΔGint-146 kcal/mol
Surface area39270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.810, 95.810, 174.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-640-

HOH

21B-557-

HOH

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Components

#1: Protein Dihydrodipicolinate synthase 2, chloroplastic / / DHDPS 2


Mass: 39828.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DHDPS2 / Plasmid: pET151/D-Topo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q9FVC8, dihydrodipicolinate synthase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.49 Å3/Da / Density % sol: 50.51 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M sodium malonate, 0.02%(w/v) sodium azide, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2→37.001 Å / Num. all: 55784 / Num. obs: 55784 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Rsym value: 0.096 / Net I/σ(I): 17.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.059.70.750.711.13917340560.240.750.713.4100
2.05-2.119.70.5870.5561.43853139570.1870.5870.5564.4100
2.11-2.179.80.4740.4491.73751738400.1510.4740.4495.4100
2.17-2.249.70.3990.3772.13648437420.1270.3990.3776.4100
2.24-2.319.70.3320.3142.53524236150.1050.3320.3147.6100
2.31-2.399.80.2880.2722.83430535140.0910.2880.2728.8100
2.39-2.489.70.2470.2343.33313834110.0790.2470.23410100
2.48-2.589.80.2130.2023.83196232780.0680.2130.20211.5100
2.58-2.79.70.1720.1634.73056531500.0550.1720.16313.7100
2.7-2.839.70.1380.135.92935830250.0440.1380.1316.8100
2.83-2.989.70.1140.10872793028810.0360.1140.10819.9100
2.98-3.169.70.0870.08292622127170.0280.0870.08224.3100
3.16-3.389.60.0710.06710.72474125780.0230.0710.06728.4100
3.38-3.659.40.0560.05313.22271624090.0180.0560.05334.2100
3.65-490.050.04814.22004522340.0170.050.04836.4100
4-4.478.90.0450.042151811620300.0150.0450.04240.3100
4.47-5.169.10.0440.041151636318050.0140.0440.04143.299.9
5.16-6.329.10.0460.04314.61417415610.0150.0460.04340100
6.32-8.949.10.0390.037161126112440.0130.0390.03742.5100
8.94-37.0018.10.0330.03116.759527370.0120.0330.03145.298.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.72 Å
Translation2.5 Å36.72 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1649 / WRfactor Rwork: 0.1317 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8977 / SU B: 2.698 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1174 / SU Rfree: 0.1155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1813 2826 5.1 %RANDOM
Rwork0.1438 ---
obs0.1457 55699 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.37 Å2 / Biso mean: 26.1045 Å2 / Biso min: 15.25 Å2
Refinement stepCycle: LAST / Resolution: 2→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4737 0 5 435 5177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194843
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.9566582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2145612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79424.286217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80415791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3051528
X-RAY DIFFRACTIONr_chiral_restr0.1350.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213706
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 212 -
Rwork0.187 3509 -
all-3721 -
obs--99.97 %

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