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

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Basic information

Entry
Database: PDB / ID: 4dpq
TitleThe structure of dihydrodipicolinate synthase 2 from Arabidopsis thaliana in complex with (S)-lysine
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
LYSINE / 4-hydroxy-tetrahydrodipicolinate synthase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.202 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)80,0669
Polymers79,6572
Non-polymers4097
Water5,783321
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)160,13218
Polymers159,3134
Non-polymers81914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11730 Å2
ΔGint-139 kcal/mol
Surface area37950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.480, 95.480, 174.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.46 Å3/Da / Density % sol: 50.09 % / 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: 2.202→36.641 Å / Num. all: 41684 / Num. obs: 41684 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rsym value: 0.121 / Net I/σ(I): 13.3
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
2.202-2.266.90.6920.6381.12094330260.2640.6920.6384.199.4
2.26-2.327.20.5370.4971.42140529590.2010.5370.4975.4100
2.32-2.397.30.4890.4531.62069228520.1830.4890.4535.8100
2.39-2.467.20.4370.4041.82015327890.1640.4370.4046.3100
2.46-2.547.20.3910.36221952727050.1470.3910.3626.9100
2.54-2.637.20.3190.2952.41891126170.120.3190.2957.9100
2.63-2.737.20.2620.24231845525660.0980.2620.2429.1100
2.73-2.847.20.2170.23.61751924400.0810.2170.210.5100
2.84-2.977.20.1780.1654.41694323600.0670.1780.16512.1100
2.97-3.117.20.1370.1275.81608522410.0510.1370.12714.5100
3.11-3.287.20.1190.116.71552021590.0440.1190.1115.9100
3.28-3.487.10.0930.0868.41448020290.0350.0930.08619.3100
3.48-3.727.10.0820.0769.31374619280.0310.0820.07621100
3.72-4.0270.0730.06710.31263818100.0270.0730.06723100
4.02-4.46.90.0640.05911.41153016600.0240.0640.05925.2100
4.4-4.926.90.0580.05411.91045615220.0220.0580.05427100
4.92-5.696.70.060.05611.1905713610.0230.060.05625.399.8
5.69-6.966.90.0630.05811.6800311680.0240.0630.05823.7100
6.96-9.856.50.0430.0414.660329340.0170.0430.0427.899.9
9.85-36.6415.70.0420.03912.232075580.0160.0420.03926.997.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.64 Å
Translation2.5 Å36.64 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: 2.202→36.64 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1766 / WRfactor Rwork: 0.1394 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8954 / SU B: 3.737 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1602 / SU Rfree: 0.1417 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1766 2090 5 %RANDOM
Rwork0.1394 ---
obs0.1413 41606 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.1 Å2 / Biso mean: 23.8616 Å2 / Biso min: 13.04 Å2
Refinement stepCycle: LAST / Resolution: 2.202→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4719 0 25 321 5065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194843
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.9566580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3975612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15724.178213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14815789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8471528
X-RAY DIFFRACTIONr_chiral_restr0.1280.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213698
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 140 -
Rwork0.178 2608 -
all-2748 -
obs--99.35 %

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