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- PDB-7lvl: Dihydrodipicolinate synthase bound with allosteric inhibitor (S)-... -

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Basic information

Entry
Database: PDB / ID: 7lvl
TitleDihydrodipicolinate synthase bound with allosteric inhibitor (S)-lysine from Candidatus Liberibacter solanacearum
Components4-hydroxy-tetrahydrodipicolinate synthaseDihydrodipicolinate synthase
KeywordsLYASE / 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 / cytoplasm
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-type TIM barrel
Similarity search - Domain/homology
LYSINE / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCandidatus Liberibacter solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsGilkes, J.M. / Frampton, R.A. / Board, A.J. / Sheen, C.R. / Smith, G.R. / Dobson, R.C.J.D.
CitationJournal: To Be Published
Title: Dihydrodipicolinate synthase bound with allosteric inhibitor (S)-lysine from Candidatus Liberibacter solanacearum
Authors: Gilkes, J.M. / Frampton, R.A. / Board, A.J. / Sheen, C.R. / Smith, G.R. / Dobson, R.C.J.D.
History
DepositionFeb 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,05912
Polymers196,1766
Non-polymers8836
Water15,781876
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,3738
Polymers130,7844
Non-polymers5894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9870 Å2
ΔGint-57 kcal/mol
Surface area39580 Å2
MethodPISA
2
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,3738
Polymers130,7844
Non-polymers5894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-55 kcal/mol
Surface area39320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.763, 133.484, 155.778
Angle α, β, γ (deg.)90.00, 100.45, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-572-

HOH

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Components

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase / Dihydrodipicolinate synthase / HTPA synthase


Mass: 32695.988 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Liberibacter solanacearum (bacteria)
Gene: dapA, DJ66_0589 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A0F4VK59, 4-hydroxy-tetrahydrodipicolinate synthase
#2: Chemical
ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 876 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.64 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20% w/v PEG3000, 0.1 M sodium citrate, pH 5.5

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Data collection

DiffractionMean temperature: 210 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.01→46.24 Å / Num. obs: 135620 / % possible obs: 99.92 % / Redundancy: 4 % / Biso Wilson estimate: 31.38 Å2 / CC1/2: 0.954 / Net I/σ(I): 13.45
Reflection shellResolution: 2.01→2.082 Å / Num. unique obs: 13469 / CC1/2: 0.802

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7LOY

7loy


Resolution: 2.01→46.202 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 19.74 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.206 6892 5.08 %RANDOM
Rwork0.1685 ---
obs0.1704 135599 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→46.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13404 0 60 876 14340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713692
X-RAY DIFFRACTIONf_angle_d0.84118570
X-RAY DIFFRACTIONf_dihedral_angle_d3.698262
X-RAY DIFFRACTIONf_chiral_restr0.0582160
X-RAY DIFFRACTIONf_plane_restr0.0052418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.03280.2922260.25334236X-RAY DIFFRACTION99
2.0328-2.05680.27512290.23184292X-RAY DIFFRACTION100
2.0568-2.08180.26862260.22374259X-RAY DIFFRACTION100
2.0818-2.10820.23092250.20824279X-RAY DIFFRACTION100
2.1082-2.13590.25772520.20514243X-RAY DIFFRACTION100
2.1359-2.16520.24742380.20094291X-RAY DIFFRACTION100
2.1652-2.19610.24572390.19634262X-RAY DIFFRACTION100
2.1961-2.22890.24522260.2014277X-RAY DIFFRACTION100
2.2289-2.26370.23172440.18834280X-RAY DIFFRACTION100
2.2637-2.30080.22922140.18454269X-RAY DIFFRACTION100
2.3008-2.34050.2342480.18244299X-RAY DIFFRACTION100
2.3405-2.38310.22752580.1784227X-RAY DIFFRACTION100
2.3831-2.42890.2392400.17834259X-RAY DIFFRACTION100
2.4289-2.47850.22242290.17194316X-RAY DIFFRACTION100
2.4785-2.53240.22082440.17384274X-RAY DIFFRACTION100
2.5324-2.59130.23992500.17494223X-RAY DIFFRACTION100
2.5913-2.65610.22152320.17794265X-RAY DIFFRACTION100
2.6561-2.72790.21812230.17474334X-RAY DIFFRACTION100
2.7279-2.80810.23672050.18464337X-RAY DIFFRACTION100
2.8081-2.89880.22742160.18054308X-RAY DIFFRACTION100
2.8988-3.00230.22852210.18764294X-RAY DIFFRACTION100
3.0023-3.12250.24082250.18674286X-RAY DIFFRACTION100
3.1225-3.26460.23441850.19754329X-RAY DIFFRACTION100
3.2646-3.43670.20352010.18044318X-RAY DIFFRACTION100
3.4367-3.65190.20552490.17514313X-RAY DIFFRACTION100
3.6519-3.93370.19062220.15374299X-RAY DIFFRACTION100
3.9337-4.32930.16142280.13594303X-RAY DIFFRACTION100
4.3293-4.95520.14722320.12644329X-RAY DIFFRACTION100
4.9552-6.24060.17812320.14694319X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.2875 Å / Origin y: -2.2409 Å / Origin z: 42.7079 Å
111213212223313233
T0.1619 Å2-0.0075 Å20.0085 Å2-0.1975 Å20.022 Å2--0.2185 Å2
L0.2041 °2-0.0519 °20.1744 °2-0.071 °2-0.0496 °2--0.6486 °2
S-0.0341 Å °0.0919 Å °0.0493 Å °-0.0051 Å °-0.0152 Å °0.0169 Å °-0.0566 Å °-0.0329 Å °-0.0389 Å °
Refinement TLS groupSelection details: all

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