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- PDB-2y5j: Crystal structure of Burkholderia cenocepacia dihydropteroate syn... -

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Basic information

Entry
Database: PDB / ID: 2y5j
TitleCrystal structure of Burkholderia cenocepacia dihydropteroate synthase.
ComponentsDIHYDROPTEROATE SYNTHASE
KeywordsTRANSFERASE / FOLATE BIOSYNTHESIS
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding / cytosol
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
Dihydropteroate synthase
Similarity search - Component
Biological speciesBURKHOLDERIA CENOCEPACIA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsMorgan, R.E. / Batot, G.O. / Dement, J.M. / Rao, V.A. / Eadsforth, T.C. / Hunter, W.N.
CitationJournal: Bmc Struct.Biol. / Year: 2011
Title: Crystal Structures of Burkholderia Cenocepacia Dihydropteroate Synthase in the Apo-Form and Complexed with the Product 7,8-Dihydropteroate.
Authors: Morgan, R.E. / Batot, G.O. / Dement, J.M. / Rao, V.A. / Eadsforth, T.C. / Hunter, W.N.
History
DepositionJan 13, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: DIHYDROPTEROATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2515
Polymers31,0031
Non-polymers2484
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.952, 89.433, 87.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DIHYDROPTEROATE SYNTHASE / DHPS


Mass: 31002.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA CENOCEPACIA (bacteria) / Strain: LMG 16656
Description: BELGIAN CO-ORDINATED COLLECTIONS OF MICRO-ORGANISMS, BACTERIA COLLECTION (BCCM/LMG)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4E5F5, dihydropteroate synthase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 7.8
Details: RESERVOIR CONDITIONS 0.3 M TRIS/HCL PH8, 10% PEG 8000. PROTEIN SOLUTION BCDHPS AT 7.5 MGML-1, 2MM SULPHADOXINE, 50MM TRIS/HCL PH7.5, 250 MM NACL., pH 7.8

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Aug 6, 2009 / Details: MIRRORS
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→57.28 Å / Num. obs: 12564 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AJ2

1aj2


Resolution: 2.33→56.99 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / SU B: 7.975 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.392 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.27403 610 4.9 %RANDOM
Rwork0.20748 ---
obs0.21063 11865 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å20 Å2
2--3.06 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.33→56.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 16 89 2101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222065
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.161.9892809
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3735274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47522.84188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49915317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4331524
X-RAY DIFFRACTIONr_chiral_restr0.1350.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211589
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.2081.51353
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.09222159
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3343712
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8064.5646
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.391 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 47 -
Rwork0.325 723 -
obs--83.42 %

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