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- PDB-1tx0: Dihydropteroate Synthetase, With Bound Product Analogue Pteroic A... -

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Basic information

Entry
Database: PDB / ID: 1tx0
TitleDihydropteroate Synthetase, With Bound Product Analogue Pteroic Acid, From Bacillus anthracis
ComponentsDHPS, Dihydropteroate synthase
KeywordsTRANSFERASE / anthracis / folate biosynthesis / dihydropteroate / pterine
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
PTEROIC ACID / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBabaoglu, K. / Qi, J. / Lee, R.E. / White, S.W.
CitationJournal: STRUCTURE / Year: 2004
Title: Crystal Structure of 7,8-Dihydropteroate Synthase from Bacillus anthracis; Mechanism and Novel Inhibitor Design.
Authors: Babaoglu, K. / Qi, J. / Lee, R.E. / White, S.W.
History
DepositionJul 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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: DHPS, Dihydropteroate synthase
B: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,35314
Polymers65,7672
Non-polymers1,58512
Water2,954164
1
A: DHPS, Dihydropteroate synthase
hetero molecules

A: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,35314
Polymers65,7672
Non-polymers1,58512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
2
B: DHPS, Dihydropteroate synthase
hetero molecules

B: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,35314
Polymers65,7672
Non-polymers1,58512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465-x-1,-y+1,z1
Unit cell
Length a, b, c (Å)97.547, 97.547, 263.158
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLYGLYAA2 - 2422 - 44
21LYSLYSGLYGLYBB2 - 2422 - 44
32SERSERGLYGLYAA38 - 6358 - 83
42SERSERGLYGLYBB38 - 6358 - 83
53SERSERLYSLYSAA75 - 27495 - 294
63SERSERLYSLYSBB75 - 27495 - 294
DetailsThe biological dimer is generated by the two fold axis: x,y,z

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Components

#1: Protein DHPS, Dihydropteroate synthase


Mass: 32883.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: str. A2012 / Gene: folp / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q81VW8, dihydropteroate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PT1 / PTEROIC ACID


Mass: 312.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: lithium sulfate, tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2004 / Details: mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→81.7 Å / Num. all: 38829 / Num. obs: 38829 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rsym value: 0.066 / Net I/σ(I): 18.3
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 38829 / Rsym value: 0.577 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TWS

1tws


Resolution: 2.15→81.7 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.422 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): 0 / ESU R: 0.243 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS REFINEMENT USED THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27963 1954 5 %RANDOM
Rwork0.23057 ---
all0.23298 36872 --
obs0.23298 36872 94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.459 Å2
Baniso -1Baniso -2Baniso -3
1-4.49 Å22.25 Å20 Å2
2--4.49 Å20 Å2
3----6.74 Å2
Refinement stepCycle: LAST / Resolution: 2.15→81.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 96 164 4338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224228
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9925707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9335521
X-RAY DIFFRACTIONr_chiral_restr0.110.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023111
X-RAY DIFFRACTIONr_nbd_refined0.2260.22051
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.25
X-RAY DIFFRACTIONr_mcbond_it0.8751.52605
X-RAY DIFFRACTIONr_mcangle_it1.65824189
X-RAY DIFFRACTIONr_scbond_it2.83631623
X-RAY DIFFRACTIONr_scangle_it4.2424.51518
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
996tight positional0.060.05
949medium positional0.430.5
996tight thermal0.230.5
949medium thermal0.982
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.402 134
Rwork0.367 2670
obs-2894
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)
10.57950.08680.27910.7391-0.11651.6251-0.1249-0.06110.02510.0385-0.0015-0.01290.10620.35260.12640.21590.21580.00830.22730.05830.2151-78.29579.961491.349
20.2142-0.0607-0.07820.6342-0.05621.0691-0.00480.0686-0.0408-0.1323-0.1393-0.0252-0.32710.11940.14410.26710.0686-0.03730.26780.06790.1783-67.723160.9851138.5923
3-0.08190.07470.13430.0565-0.33380.49030.0118-0.03830.0261-0.0228-0.069-0.04-0.09920.05440.05720.28910.18480.00120.20790.05620.302-76.179970.5575112.9455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B2 - 274
3X-RAY DIFFRACTION3A284 - 371
4X-RAY DIFFRACTION3B284 - 359
5X-RAY DIFFRACTION3A278

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