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- PDB-6pz2: Crystal Structure of FolP (dihydropteroate synthase) from Colstri... -

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Basic information

Entry
Database: PDB / ID: 6pz2
TitleCrystal Structure of FolP (dihydropteroate synthase) from Colstridium difficile in the presence of pteroic acid
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / clostridium / DHPS / dihydropteroate synthase / antibiotic resistance
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding
Similarity search - Function
Dihydropteroate synthase signature 1. / 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
PTEROIC ACID / Dihydropteroate synthase
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGirardi, N.M. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)gm115921 United States
CitationJournal: To Be Published
Title: Crystal Structure of FolP (dihydropteroate synthase) from Colstridium difficile in the presence of pteroic acid
Authors: Girardi, N.M. / Thoden, J.B. / Holden, H.M.
History
DepositionJul 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)31,15412
Polymers29,7701
Non-polymers1,38411
Water2,666148
1
A: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,30924
Polymers59,5402
Non-polymers2,76822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area7270 Å2
ΔGint-237 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.258, 156.258, 84.708
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-305-

SO4

21A-305-

SO4

31A-534-

HOH

41A-538-

HOH

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Components

#1: Protein Dihydropteroate synthase / DHPS / Dihydropteroate pyrophosphorylase


Mass: 29770.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: folP, SAMEA3374989_02220 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A160WS51, dihydropteroate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PT1 / PTEROIC ACID


Mass: 312.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 5.01 Å3/Da / Density % sol: 75.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.4-2.6 M ammonium sulfate, 200 mM LiCl, 100 mM CHES (pH 9), 4 mM pteroic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.99861 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99861 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 41365 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 45.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 2026 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hb7

4hb7


Resolution: 2→37.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.064 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.111
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 2116 5.1 %RANDOM
Rwork0.1876 ---
obs0.1895 39244 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.23 Å2 / Biso mean: 39.817 Å2 / Biso min: 23.66 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å2-0.81 Å20 Å2
2---1.63 Å20 Å2
3---5.27 Å2
Refinement stepCycle: final / Resolution: 2→37.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 81 148 2290
Biso mean--67.67 46.59 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0152183
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172013
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.7792950
X-RAY DIFFRACTIONr_angle_other_deg0.5491.7284723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4935268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.69817.96964
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96415346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2071514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022393
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02368
LS refinement shellResolution: 2→2.048 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.357 160 -
Rwork0.378 2746 -
obs--95.66 %

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