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- PDB-5t25: Kinetic, Spectral and Structural Characterization of the Slow Bin... -

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Basic information

Entry
Database: PDB / ID: 5t25
TitleKinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase from Escherichia coli.
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsHYDROLASE / Dihydrodipicolinate Synthase / Kinetics / Acetopyruvate modification
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 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
LYSINE / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesEscherichia coli O8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.991 Å
AuthorsChooback, L. / Thomas, L.M. / Karsten, W.E. / Fleming, C.D. / Seabourn, P.
Funding support United States, 1items
OrganizationGrant numberCountry
OK-INBRE RPIRS20132225112 United States
CitationJournal: To Be Published
Title: Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase from Escherichia coli.
Authors: Chooback, L. / Thomas, L.M. / Karsten, W.E. / Fleming, C.D. / Seabourn, P.
History
DepositionAug 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Non-polymer description
Revision 1.2Nov 7, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.3Oct 4, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_type.id
Revision 1.4Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,63314
Polymers63,1082
Non-polymers52412
Water11,890660
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-116 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.647, 56.385, 101.530
Angle α, β, γ (deg.)90.00, 127.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 31554.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O8 (strain IAI1) (bacteria)
Strain: IAI1 / Gene: dapA, ECIAI1_2529 / Production host: Escherichia coli (E. coli)
References: UniProt: B7M7I1, 4-hydroxy-tetrahydrodipicolinate synthase
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 20% PEG3350 200mM Sodium Tartarate 14.7 mM HEPES pH 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 10, 2015 / Details: VeriMaxHF
RadiationMonochromator: Multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→81 Å / Num. obs: 193325 / % possible obs: 100 % / Redundancy: 4.5 % / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.911 / CC1/2: 0.809 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yxc

1yxc


Resolution: 1.991→26.806 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2114 2083 5.06 %RANDOM
Rwork0.1581 ---
obs0.1608 41146 97.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.991→26.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4406 0 30 660 5096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074495
X-RAY DIFFRACTIONf_angle_d0.8916105
X-RAY DIFFRACTIONf_dihedral_angle_d3.5552731
X-RAY DIFFRACTIONf_chiral_restr0.053735
X-RAY DIFFRACTIONf_plane_restr0.006794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9915-2.03780.27381350.222462X-RAY DIFFRACTION94
2.0378-2.08870.28411370.18342658X-RAY DIFFRACTION100
2.0887-2.14520.21971340.17812619X-RAY DIFFRACTION100
2.1452-2.20830.21521520.16992621X-RAY DIFFRACTION100
2.2083-2.27950.24371450.16632659X-RAY DIFFRACTION100
2.2795-2.36090.24151350.16492664X-RAY DIFFRACTION100
2.3609-2.45540.20881310.17032685X-RAY DIFFRACTION100
2.4554-2.56710.22371360.16492659X-RAY DIFFRACTION100
2.5671-2.70230.23791460.15932633X-RAY DIFFRACTION100
2.7023-2.87140.26771410.1682646X-RAY DIFFRACTION100
2.8714-3.09280.21331170.16262350X-RAY DIFFRACTION87
3.0928-3.40350.18021160.15422334X-RAY DIFFRACTION87
3.4035-3.89470.20531560.13342666X-RAY DIFFRACTION99
3.8947-4.9020.16651600.13292641X-RAY DIFFRACTION99
4.902-26.80860.19231420.15962766X-RAY DIFFRACTION100

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