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- PDB-6nva: Crystal structure of Escherichia coli dihydrodipicolinate synthas... -

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Basic information

Entry
Database: PDB / ID: 6nva
TitleCrystal structure of Escherichia coli dihydrodipicolinate synthase and propionate covalently bound to K161.
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsBIOSYNTHETIC PROTEIN / Synthase Lysine Biosynthesis Propionate
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 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
4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsThomas, L.M. / Chooback, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103447 United States
CitationJournal: To Be Published
Title: Crystal structure of Escherichia coli dihydrodipicolinate synthase and propionate covalently bound to K161.
Authors: Chooback, L. / Thomas, L.M. / Karsten, W. / Sultana, F. / Mesiya, S.
History
DepositionFeb 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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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
G: 4-hydroxy-tetrahydrodipicolinate synthase
H: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,90917
Polymers253,2188
Non-polymers6919
Water44,1192449
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


  • defined by author&software
  • Evidence: Mirwaldt, C., Korndorfer, I., &Huber, R. (1995). The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 angstrom resolution. J. Mol. Biol. 246, 227-239. ...Evidence: Mirwaldt, C., Korndorfer, I., &Huber, R. (1995). The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 angstrom resolution. J. Mol. Biol. 246, 227-239. Blickling, S., Renner, C., Laber, B., Pohlenz, HD, Holak, TA, and Huber, R. (1997) Reaction Mechanism of Escerichia coli Dihydrodipicolinate Synthase Investigated by X-ray Crystallography and NMR Spectroscopy. Biochemistry, 36, 24-33. Dobson, R. C., Griffin, M.D.W., Jameson, G.B., and Gerrard, J.A.(2005) The crystal structure of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance. Acta. Cryst. D61, 1116-1124.
  • 63.5 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)63,4894
Polymers63,3052
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-21 kcal/mol
Surface area20830 Å2
MethodPISA
2
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4204
Polymers63,3052
Non-polymers1152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-30 kcal/mol
Surface area20840 Å2
MethodPISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5125
Polymers63,3052
Non-polymers2073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-34 kcal/mol
Surface area20680 Å2
MethodPISA
4
G: 4-hydroxy-tetrahydrodipicolinate synthase
H: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4894
Polymers63,3052
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-21 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.140, 86.333, 107.002
Angle α, β, γ (deg.)109.72, 104.24, 99.18
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 31652.281 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dapA, A8C65_04230 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A066Q637, 4-hydroxy-tetrahydrodipicolinate synthase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2449 / 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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350 8 mM spermidine 200 mM sodium tartrate 8 mM 2-bromopropionic acid pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 15, 2017 / Details: VeriMax HF mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. all: 443797 / Num. obs: 142605 / % possible obs: 97.6 % / Redundancy: 3.2 % / CC1/2: 0.524 / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Χ2: 1.135 / Net I/σ(I): 7.781
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.756 / Num. unique obs: 6709 / CC1/2: 0.524 / Rsym value: 0.756 / Χ2: 0.848 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T26

5t26


Resolution: 2.16→25.173 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.64
RfactorNum. reflection% reflection
Rfree0.2388 3492 1.4 %
Rwork0.1832 --
obs0.184 142552 85.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.16→25.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17685 0 44 2449 20178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818041
X-RAY DIFFRACTIONf_angle_d0.93324464
X-RAY DIFFRACTIONf_dihedral_angle_d6.01112932
X-RAY DIFFRACTIONf_chiral_restr0.0532946
X-RAY DIFFRACTIONf_plane_restr0.0063161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1546-2.18410.34791060.2737189X-RAY DIFFRACTION63
2.1841-2.21530.28591170.25188649X-RAY DIFFRACTION74
2.2153-2.24830.26791270.24738726X-RAY DIFFRACTION76
2.2483-2.28340.28381300.2458909X-RAY DIFFRACTION77
2.2834-2.32090.26331210.24589202X-RAY DIFFRACTION80
2.3209-2.36080.29921350.24079310X-RAY DIFFRACTION81
2.3608-2.40370.30441250.23159820X-RAY DIFFRACTION84
2.4037-2.44990.27581310.230310057X-RAY DIFFRACTION87
2.4499-2.49990.29571540.226110216X-RAY DIFFRACTION88
2.4999-2.55420.27311460.21610398X-RAY DIFFRACTION90
2.5542-2.61360.27281570.20910518X-RAY DIFFRACTION91
2.6136-2.67890.31211370.202810543X-RAY DIFFRACTION91
2.6789-2.75120.24161560.200710553X-RAY DIFFRACTION92
2.7512-2.83210.27281600.20710804X-RAY DIFFRACTION93
2.8321-2.92330.30821510.211210483X-RAY DIFFRACTION91
2.9233-3.02760.23811240.19819339X-RAY DIFFRACTION81
3.0276-3.14870.26821270.19248171X-RAY DIFFRACTION71
3.1487-3.29170.2081210.18639012X-RAY DIFFRACTION78
3.2917-3.46480.23281630.164110544X-RAY DIFFRACTION91
3.4648-3.68120.18811410.152710913X-RAY DIFFRACTION94
3.6812-3.96450.22881520.146210972X-RAY DIFFRACTION95
3.9645-4.36160.18821500.141510864X-RAY DIFFRACTION94
4.3616-4.98840.20711600.13510836X-RAY DIFFRACTION94
4.9884-6.26880.19061490.155810697X-RAY DIFFRACTION93
6.2688-25.17420.18531520.14799967X-RAY DIFFRACTION87

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