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- PDB-6ue0: Crystal structure of dihydrodipicolinate synthase from Klebsiella... -

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Basic information

Entry
Database: PDB / ID: 6ue0
TitleCrystal structure of dihydrodipicolinate synthase from Klebsiella pneumoniae bound to pyruvate
Components4-hydroxy-tetrahydrodipicolinate synthaseDihydrodipicolinate synthase
KeywordsLYASE / DHDPS / Lysine biosynthesis / tetramer
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
4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsImpey, R.E. / Lee, M. / Hawkins, D.A. / Sutton, J.M. / Panjikar, S. / Perugini, M.A. / Soares da Costa, T.P.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE190100806 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1091976 Australia
Australian Research Council (ARC)DP150103313 Australia
CitationJournal: Febs Lett. / Year: 2020
Title: Mis-annotations of a promising antibiotic target in high-priority gram-negative pathogens.
Authors: Impey, R.E. / Lee, M. / Hawkins, D.A. / Sutton, J.M. / Panjikar, S. / Perugini, M.A. / Soares da Costa, T.P.
History
DepositionSep 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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
Revision 1.3Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: 4-hydroxy-tetrahydrodipicolinate synthase
BBB: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,03910
Polymers69,6342
Non-polymers4058
Water7,620423
1
AAA: 4-hydroxy-tetrahydrodipicolinate synthase
BBB: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules

AAA: 4-hydroxy-tetrahydrodipicolinate synthase
BBB: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,07720
Polymers139,2674
Non-polymers81016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10360 Å2
ΔGint-268 kcal/mol
Surface area38900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.634, 114.230, 55.298
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 34816.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: dapA_2, dapA_3, dapA_4, dapA_5, dapA_6, dapA_7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: W9BBZ5, 4-hydroxy-tetrahydrodipicolinate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris, ph 7.5, 2 M Ammonium Sulfate, 5 mM Pyruvate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.89→49.039 Å / Num. obs: 54112 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.998 / Net I/σ(I): 11.4
Reflection shellResolution: 1.89→1.93 Å / Num. unique obs: 3259 / CC1/2: 0.827 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YXC

1yxc


Resolution: 1.892→48.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.582 / SU ML: 0.076 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1982 2562 4.741 %
Rwork0.1693 --
all0.171 --
obs-54037 99.666 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.372 Å2
Baniso -1Baniso -2Baniso -3
1--0.034 Å20 Å20 Å2
2---0.847 Å20 Å2
3---0.881 Å2
Refinement stepCycle: LAST / Resolution: 1.892→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 16 423 4809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134464
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174242
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.6416074
X-RAY DIFFRACTIONr_angle_other_deg1.3591.5689830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6665590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12522.2200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19115744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8291526
X-RAY DIFFRACTIONr_chiral_restr0.0680.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02850
X-RAY DIFFRACTIONr_nbd_refined0.2050.2879
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.23886
X-RAY DIFFRACTIONr_nbtor_refined0.1490.22253
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21917
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2334
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.28
X-RAY DIFFRACTIONr_nbd_other0.1520.216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0980.218
X-RAY DIFFRACTIONr_mcbond_it1.322.1952342
X-RAY DIFFRACTIONr_mcbond_other1.3082.1932341
X-RAY DIFFRACTIONr_mcangle_it1.9443.2832926
X-RAY DIFFRACTIONr_mcangle_other1.9473.2842927
X-RAY DIFFRACTIONr_scbond_it2.2032.5252122
X-RAY DIFFRACTIONr_scbond_other2.1792.522114
X-RAY DIFFRACTIONr_scangle_it3.5223.6653144
X-RAY DIFFRACTIONr_scangle_other3.4883.6573132
X-RAY DIFFRACTIONr_lrange_it4.52527.6624975
X-RAY DIFFRACTIONr_lrange_other4.39327.2184875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.892-1.9410.3151650.2963608X-RAY DIFFRACTION96.25
1.941-1.9940.2442130.1973661X-RAY DIFFRACTION100
1.994-2.0520.2161760.1773596X-RAY DIFFRACTION100
2.052-2.1150.1981710.163462X-RAY DIFFRACTION100
2.115-2.1850.1981610.1523357X-RAY DIFFRACTION99.9432
2.185-2.2610.2631610.2193271X-RAY DIFFRACTION99.9127
2.261-2.3460.21550.1583143X-RAY DIFFRACTION99.9394
2.346-2.4420.1851490.1463041X-RAY DIFFRACTION100
2.442-2.5510.191630.1462909X-RAY DIFFRACTION100
2.551-2.6750.191460.152774X-RAY DIFFRACTION100
2.675-2.8190.1811340.172661X-RAY DIFFRACTION100
2.819-2.990.241060.182554X-RAY DIFFRACTION99.9249
2.99-3.1960.2061160.1832386X-RAY DIFFRACTION99.8802
3.196-3.4520.216930.182249X-RAY DIFFRACTION100
3.452-3.7810.2011350.1662008X-RAY DIFFRACTION99.8137
3.781-4.2260.1561200.1471866X-RAY DIFFRACTION100
4.226-4.8770.152650.1381667X-RAY DIFFRACTION100
4.877-5.9670.209450.1711458X-RAY DIFFRACTION99.9335
5.967-8.4140.156700.1551114X-RAY DIFFRACTION100
8.414-48.990.174180.19691X-RAY DIFFRACTION98.7465

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