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- PDB-2dzb: Crystal Structure of Dihydropteroate Synthase from Thermus thermo... -

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Basic information

Entry
Database: PDB / ID: 2dzb
TitleCrystal Structure of Dihydropteroate Synthase from Thermus thermophilus HB8 in complex with 6HMPPP
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / Dihydropteroate Synthase / Dimer / 6HMPPP / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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
6-HYDROXYMETHYLPTERIN-DIPHOSPHATE / Dihydropteroate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsBagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Dihydropteroate Synthase (FolP) from Thermus thermophilus HB8
Authors: Bagautdinov, B. / Kunishima, N.
History
DepositionSep 27, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5004
Polymers63,7942
Non-polymers7062
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-25 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.852, 110.852, 87.766
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe biological unit is a dimer and probably identical to the asymmetric unit

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Components

#1: Protein Dihydropteroate synthase


Mass: 31897.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: FolP / Plasmid: pET 11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLV2, dihydropteroate synthase
#2: Chemical ChemComp-HH2 / 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE / [PTERIN-6-YL METHANYL]-PHOSPHONOPHOSPHATE


Mass: 353.123 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N5O8P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.8
Details: PEG 20K, Mes, NaOH, 6HMPPP, pH 5.8, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 5, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 48314 / Num. obs: 46124 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 33.65 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.046 / Net I/σ(I): 15.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.82 / Num. unique all: 4425 / Rsym value: 0.431 / % possible all: 92.3

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2DQW

2dqw


Resolution: 1.9→39.91 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2291 -RANDOM
Rwork0.212 ---
obs0.212 46124 95.3 %-
all-48314 --
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å21.84 Å20 Å2
2--2.02 Å20 Å2
3----4.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3841 0 44 383 4268
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.3 192 -
Rwork0.286 --
obs-4081 88.6 %

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