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- PDB-7loy: Dihydrodipicolinate synthase with pyruvate from Candidatus Liberi... -

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Basic information

Entry
Database: PDB / ID: 7loy
TitleDihydrodipicolinate synthase with pyruvate from Candidatus Liberibacter solanacearum
Components4-hydroxy-tetrahydrodipicolinate 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 / cytosol
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 speciesCandidatus Liberibacter solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGilkes, J.M. / Frampton, R.A. / Board, A. / Sheen, C.R. / Smith, G.R. / Dobson, R.C.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Dihydrodipicolinate synthase with pyruvate from the plant pathogen, Candidatus Liberibacter solanacearum
Authors: Gilkes, J.M. / Frampton, R.A. / Board, A. / Sheen, C.R. / Smith, G.R. / Dobson, R.C.J.
History
DepositionFeb 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 2.0Mar 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_sites.fract_transf_matrix[1][3] / _database_2.pdbx_DOI ..._atom_sites.fract_transf_matrix[1][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _pdbx_struct_special_symmetry.auth_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.d_resolution_low / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Ligand geometry
Details: We have fixed errors we discovered in the ligand bound into the active site.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details
Revision 2.2Nov 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

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


Theoretical massNumber of molelcules
Total (without water)191,2756
Polymers191,2756
Non-polymers00
Water8,071448
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)63,7582
Polymers63,7582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-13 kcal/mol
Surface area21710 Å2
MethodPISA
2
C: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)63,7582
Polymers63,7582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-14 kcal/mol
Surface area21910 Å2
MethodPISA
3
D: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)63,7582
Polymers63,7582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-13 kcal/mol
Surface area21590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.777, 133.581, 155.988
Angle α, β, γ (deg.)90.00, 100.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-361-

HOH

21B-340-

HOH

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Components

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase


Mass: 31879.105 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Liberibacter solanacearum (bacteria)
Gene: dapA / Plasmid: pGRO7
Details (production host): GroEL/GroES chaperone co-expression
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0F4VK59
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG3000, 0.1 M sodium citrate, pH 5.5

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953723 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: 0.953723 Å / Relative weight: 1
ReflectionResolution: 2.4→46.32 Å / Num. obs: 79992 / % possible obs: 99.82 % / Redundancy: 4 % / CC1/2: 0.917 / Net I/σ(I): 1.04
Reflection shellResolution: 2.4→2.486 Å / Num. unique obs: 79992 / CC1/2: 0.702

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
pointlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4I7U

4i7u


Resolution: 2.4→46.27 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU B: 10.132 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25191 4050 5.1 %RANDOM
Rwork0.20054 ---
obs0.20313 75861 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.948 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.05 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.4→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13416 0 0 448 13864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01313651
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712678
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.63718500
X-RAY DIFFRACTIONr_angle_other_deg1.2171.57829436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1651752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49423.302636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.245152244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9191566
X-RAY DIFFRACTIONr_chiral_restr0.0610.21854
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022658
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_it2.0453.7657074
X-RAY DIFFRACTIONr_mcbond_other2.0453.7657073
X-RAY DIFFRACTIONr_mcangle_it3.1425.6478796
X-RAY DIFFRACTIONr_mcangle_other3.1425.6488797
X-RAY DIFFRACTIONr_scbond_it2.3334.036577
X-RAY DIFFRACTIONr_scbond_other2.3314.0316577
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7015.9359704
X-RAY DIFFRACTIONr_long_range_B_refined5.11945.50115113
X-RAY DIFFRACTIONr_long_range_B_other5.11945.50515114
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 295 -
Rwork0.29 5576 -
obs--99.97 %

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