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- PDB-2y5s: Crystal structure of Burkholderia cenocepacia dihydropteroate syn... -

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Basic information

Entry
Database: PDB / ID: 2y5s
TitleCrystal structure of Burkholderia cenocepacia dihydropteroate synthase complexed with 7,8-dihydropteroate.
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
7,8-DIHYDROPTEROATE / Dihydropteroate synthase
Similarity search - Component
Biological speciesBURKHOLDERIA CENOCEPACIA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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 17, 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

Downloads & links

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Assembly

Deposited unit
A: DIHYDROPTEROATE SYNTHASE
B: DIHYDROPTEROATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,69822
Polymers62,0052
Non-polymers1,69320
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint11.3 kcal/mol
Surface area21390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.662, 86.920, 88.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DIHYDROPTEROATE SYNTHASE / DHPS


Mass: 31002.512 Da / Num. of mol.: 2
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-78H / 7,8-DIHYDROPTEROATE


Mass: 314.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14N6O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.29 Å3/Da / Density % sol: 46.39 % / Description: NONE
Crystal growpH: 7.8
Details: RESERVOIR: 0.1 M TRIS/HCL PH 8, 10 % PEG 8000, 0.3 M MGCL2 PROTEIN SOLUTIONS: BCDHPS AT 7.5 MG/ML, 2 MM DIHYDROPTEROATE, 50 MM TRIS/HCL PH 7.5, 250 MM NACL.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / 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: 1.95→29.6 Å / Num. obs: 41750 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.4
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.1 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AJ2

1aj2


Resolution: 1.95→62.11 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.01 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21114 2027 5.1 %RANDOM
Rwork0.17564 ---
obs0.17742 37961 94.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.049 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å20 Å2
2---1.41 Å20 Å2
3---2.76 Å2
Refinement stepCycle: LAST / Resolution: 1.95→62.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4142 0 112 305 4559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224436
X-RAY DIFFRACTIONr_bond_other_d0.0010.023083
X-RAY DIFFRACTIONr_angle_refined_deg1.2322.0056036
X-RAY DIFFRACTIONr_angle_other_deg0.8823.0017436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0025588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56622.513187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48515674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6371555
X-RAY DIFFRACTIONr_chiral_restr0.0730.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02887
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_it0.5721.52856
X-RAY DIFFRACTIONr_mcbond_other0.1281.51143
X-RAY DIFFRACTIONr_mcangle_it1.05224575
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.69131580
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7084.51448
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 145 -
Rwork0.304 2381 -
obs--82.39 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2418-1.53510.35722.5512-0.52471.50910.23690.5624-0.0214-0.3792-0.2595-0.04180.1550.00930.02260.10410.0166-0.00290.0887-0.0070.074356.9477-6.9779-7.3704
22.1954-0.87530.09881.298-0.09150.2614-0.0023-0.1152-0.03760.0120.0031-0.1031-0.00340.0097-0.00080.0537-0.0045-0.01340.0564-0.00290.039353.3039-10.56612.0002
34.4368-1.49550.04342.58120.60882.58740.20670.5365-0.0159-0.3762-0.2230.1794-0.28210.0670.01640.13060.0179-0.04470.0706-0.01240.076516.8235.1533-8.0197
42.5187-0.75110.11441.65220.07810.3375-0.0153-0.12660.0681-0.00810.00530.1521-0.0451-0.00230.010.05590.0042-0.00940.048-0.00130.027720.554310.23731.56
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 81
2X-RAY DIFFRACTION2A82 - 292
3X-RAY DIFFRACTION3B2 - 85
4X-RAY DIFFRACTION4B86 - 292

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