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- PDB-2dqw: Crystal Structure of Dihydropteroate Synthase (FolP) from Thermus... -

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Basic information

Entry
Database: PDB / ID: 2dqw
TitleCrystal Structure of Dihydropteroate Synthase (FolP) from Thermus thermophilus HB8
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / Dihydropteroate Synthase / Dimer / 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
Dihydropteroate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionMay 31, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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
B: Dihydropteroate synthase


Theoretical massNumber of molelcules
Total (without water)63,7942
Polymers63,7942
Non-polymers00
Water11,007611
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-25 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.994, 109.994, 88.321
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) / Strain: HB8 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.8
Details: PEG 20000, Mes, NaOH, 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: May 21, 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: 1.65→40 Å / Num. all: 72924 / Num. obs: 72756 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.056 / Net I/σ(I): 17.7
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.8 / Num. unique all: 7277 / Rsym value: 0.443 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EYE

1eye


Resolution: 1.65→29.88 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3683 -RANDOM
Rwork0.213 ---
obs0.213 72756 99.8 %-
all-72924 --
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å22.9 Å20 Å2
2--2.27 Å20 Å2
3----4.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.65→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 0 611 4445
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
LS refinement shellResolution: 1.65→1.71 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.29 355 -
Rwork0.294 --
obs-7263 4.9 %

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