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- PDB-1aj2: CRYSTAL STRUCTURE OF A BINARY COMPLEX OF E. COLI DIHYDROPTEROATE ... -

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Basic information

Entry
Database: PDB / ID: 1aj2
TitleCRYSTAL STRUCTURE OF A BINARY COMPLEX OF E. COLI DIHYDROPTEROATE SYNTHASE
ComponentsDIHYDROPTEROATE SYNTHASE
KeywordsSYNTHASE / ANTIBIOTIC / RESISTANCE / TRANSFERASE / FOLATE / BIOSYNTHESIS
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / response to xenobiotic stimulus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel ...Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-2PH / Dihydropteroate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsAchari, A. / Somers, D.O. / Champness, J.N. / Bryant, P.K. / Rosemond, J. / Stammers, D.K.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of the anti-bacterial sulfonamide drug target dihydropteroate synthase.
Authors: Achari, A. / Somers, D.O. / Champness, J.N. / Bryant, P.K. / Rosemond, J. / Stammers, D.K.
History
DepositionMay 14, 1997Processing site: BNL
Revision 1.0May 20, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROPTEROATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1033
Polymers30,6521
Non-polymers4512
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.500, 60.940, 59.930
Angle α, β, γ (deg.)90.00, 114.80, 90.00
Int Tables number5
Space group name H-MC1211

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Components

#1: Protein DIHYDROPTEROATE SYNTHASE / / DHPS


Mass: 30652.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AC13, dihydropteroate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-2PH / [7,8-DIHYDRO-PTERIN-6-YL METHANYL]-PHOSPHONOPHOSPHATE / 2-Amino-4-hydroxy-6-pyrophosphoryl-methylpteridine


Mass: 355.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N5O8P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growpH: 8.4
Details: PROTEIN WAS CRYSTALLIZED FROM 42% AMMONIUM SULFATE, 50MM TRIS-HCL, PH 8.4.
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
142 %satammonium sulfate11
250 mMTris-HCl11

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 14242 / % possible obs: 69.2 % / Observed criterion σ(I): 2 / Rsym value: 0.067
Reflection shellResolution: 1.95→2.2 Å
Reflection
*PLUS
Num. measured all: 23600 / Rmerge(I) obs: 0.067

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefinementResolution: 2→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / σ(F): 0 /
Rfactor% reflection
Rwork0.169 -
obs0.169 69.2 %
Refine analyzeLuzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2147 0 27 152 2326
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.18
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→10 Å / Total num. of bins used: 8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ENGH.PROTOPENGH.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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