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- PDB-5ktl: Dihydrodipicolinate synthase from the industrial and evolutionari... -

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Basic information

Entry
Database: PDB / ID: 5ktl
TitleDihydrodipicolinate synthase from the industrial and evolutionarily important cyanobacteria Anabaena variabilis.
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / DHDPS / enzyme / cyanobacteria / Diaminopimelate biosynthesis pathway
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / metal ion binding / cytosol
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / 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
: / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesAnabaena variabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsChristensen, J.B. / Panjikar, S. / Perugini, M.
CitationJournal: Sci Rep / Year: 2016
Title: Structure and Function of Cyanobacterial DHDPS and DHDPR.
Authors: Christensen, J.B. / Soares da Costa, T.P. / Faou, P. / Pearce, F.G. / Panjikar, S. / Perugini, M.A.
History
DepositionJul 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2719
Polymers70,8862
Non-polymers3857
Water5,026279
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)142,54218
Polymers141,7724
Non-polymers76914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area10910 Å2
ΔGint-128 kcal/mol
Surface area39490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.727, 154.347, 55.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 35443.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: mismatch at 201 position due naming of modified lysine (here called KPI)
Source: (gene. exp.) Anabaena variabilis (bacteria) / Strain: ATCC 29413 / PCC 7937 / Gene: dapA, Ava_3607 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): pLys
References: UniProt: Q3M723, 4-hydroxy-tetrahydrodipicolinate synthase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: 16% PEG3350, 0.4 M trisodium citrate, 0.1 M bis-tris propane chloride pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2013 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.92→19.97 Å / Num. obs: 49312 / % possible obs: 99.1 % / Redundancy: 6.85 % / Biso Wilson estimate: 25.841 Å2 / Net I/σ(I): 14.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→19.97 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.799 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.133 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1016 2 %RANDOM
Rwork0.17536 ---
obs0.17629 49312 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.304 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å20 Å2
2--0.18 Å20 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.92→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4410 0 7 279 4696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194494
X-RAY DIFFRACTIONr_bond_other_d0.0010.024391
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.9716127
X-RAY DIFFRACTIONr_angle_other_deg0.884310107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79925.977174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01515723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5061512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02937
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_it2.052.562360
X-RAY DIFFRACTIONr_mcbond_other2.042.5582359
X-RAY DIFFRACTIONr_mcangle_it2.8873.8272947
X-RAY DIFFRACTIONr_mcangle_other2.8893.8282948
X-RAY DIFFRACTIONr_scbond_it3.7232.9992134
X-RAY DIFFRACTIONr_scbond_other3.72332135
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7624.3173180
X-RAY DIFFRACTIONr_long_range_B_refined6.97221.5345251
X-RAY DIFFRACTIONr_long_range_B_other6.91921.3455168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.921→1.971 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 72 -
Rwork0.371 3248 -
obs--91.18 %

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