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- PDB-3tuu: Structure of dihydrodipicolinate synthase from the common grapevine -

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Basic information

Entry
Database: PDB / ID: 3tuu
TitleStructure of dihydrodipicolinate synthase from the common grapevine
Componentsdihydrodipicolinate synthase
KeywordsLYASE / lysine biosynthesis / TIM Barrel
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate
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
BROMIDE ION / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPerugini, M.A. / Dobson, R.C. / Atkinson, S.C.
CitationJournal: Plos One / Year: 2012
Title: Crystal, Solution and In silico Structural Studies of Dihydrodipicolinate Synthase from the Common Grapevine.
Authors: Atkinson, S.C. / Dogovski, C. / Downton, M.T. / Pearce, F.G. / Reboul, C.F. / Buckle, A.M. / Gerrard, J.A. / Dobson, R.C. / Wagner, J. / Perugini, M.A.
History
DepositionSep 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dihydrodipicolinate synthase
B: dihydrodipicolinate synthase
C: dihydrodipicolinate synthase
D: dihydrodipicolinate synthase
E: dihydrodipicolinate synthase
F: dihydrodipicolinate synthase
G: dihydrodipicolinate synthase
H: dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,40531
Polymers303,9228
Non-polymers1,48223
Water20,5911143
1
A: dihydrodipicolinate synthase
E: dihydrodipicolinate synthase
G: dihydrodipicolinate synthase
H: dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,77817
Polymers151,9614
Non-polymers81613
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-76 kcal/mol
Surface area39250 Å2
MethodPISA
2
B: dihydrodipicolinate synthase
C: dihydrodipicolinate synthase
D: dihydrodipicolinate synthase
F: dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,62714
Polymers151,9614
Non-polymers66610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11300 Å2
ΔGint-75 kcal/mol
Surface area39130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.550, 78.900, 135.350
Angle α, β, γ (deg.)93.19, 95.02, 100.61
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 297
2114B1 - 297
3114C1 - 297
4114D1 - 297
5114E1 - 297
6114F1 - 297
7114G1 - 297
8114H1 - 297

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Components

#1: Protein
dihydrodipicolinate synthase


Mass: 37990.301 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis vinifera (wine grape) / Gene: VIT_15s0048g00750 / Production host: Escherichia coli (E. coli) / References: UniProt: D7U7T8, dihydrodipicolinate synthase
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1143 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: diffracting crystal were obtained by mixing 2 uL of protein solution (10 mg/mL) with 2 uL of reservoir solution: 0.1 M BTP, 0.2 M NaBr, 20 % (w/v) PEG 3350, pH 8.2, VAPOR DIFFUSION, HANGING ...Details: diffracting crystal were obtained by mixing 2 uL of protein solution (10 mg/mL) with 2 uL of reservoir solution: 0.1 M BTP, 0.2 M NaBr, 20 % (w/v) PEG 3350, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→134.47 Å / Num. all: 137442 / Num. obs: 133745 / % possible obs: 97.31 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.257 Å / % possible all: 96.98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→57.17 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.617 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22745 7056 5 %RANDOM
Rwork0.17965 ---
obs0.18205 133745 97.31 %-
all-137442 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.645 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å2-0.23 Å20.14 Å2
2---1.59 Å2-0.36 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.2→57.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18829 0 23 1143 19995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02219237
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.96326188
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1652448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42824.872823
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.532153096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.691587
X-RAY DIFFRACTIONr_chiral_restr0.0880.22984
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114635
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.451.512160
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.887219688
X-RAY DIFFRACTIONr_scbond_it1.58837077
X-RAY DIFFRACTIONr_scangle_it2.7454.56500
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2272 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.210.5
2Bmedium positional0.240.5
3Cmedium positional0.250.5
4Dmedium positional0.240.5
5Emedium positional0.210.5
6Fmedium positional0.220.5
7Gmedium positional0.220.5
8Hmedium positional0.210.5
1Amedium thermal0.62
2Bmedium thermal0.472
3Cmedium thermal0.722
4Dmedium thermal0.632
5Emedium thermal0.532
6Fmedium thermal0.72
7Gmedium thermal0.562
8Hmedium thermal1.122
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 537 -
Rwork0.262 9861 -
obs--96.98 %

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