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- PDB-1tx2: Dihydropteroate Synthetase, With Bound Inhibitor MANIC, From Baci... -

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Basic information

Entry
Database: PDB / ID: 1tx2
TitleDihydropteroate Synthetase, With Bound Inhibitor MANIC, From Bacillus anthracis
ComponentsDHPS, Dihydropteroate synthase
KeywordsTRANSFERASE / anthracis / folate biosynthesis / dihydropteroate / pterine / MANIC
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-METHYLAMINO-5-NITROISOCYTOSINE / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 / Derived calculations ...Advisory / Derived calculations / 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_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_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

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Assembly

Deposited unit
A: DHPS, Dihydropteroate synthase
B: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,09814
Polymers65,7672
Non-polymers1,33112
Water7,188399
1
A: DHPS, Dihydropteroate synthase
hetero molecules

A: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,09814
Polymers65,7672
Non-polymers1,33112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
Buried area4880 Å2
ΔGint-113 kcal/mol
Surface area22070 Å2
MethodPISA, PQS
2
B: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5497
Polymers32,8841
Non-polymers6656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: DHPS, Dihydropteroate synthase
hetero molecules

A: DHPS, Dihydropteroate synthase
hetero molecules

B: DHPS, Dihydropteroate synthase
hetero molecules

B: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,19728
Polymers131,5354
Non-polymers2,66224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
crystal symmetry operation2_574-y,x-y+2,z-1/31
crystal symmetry operation5_454y-1,-x+y,z-1/31
Buried area12040 Å2
ΔGint-230 kcal/mol
Surface area41120 Å2
MethodPISA
4
B: DHPS, Dihydropteroate synthase
hetero molecules

B: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,09814
Polymers65,7672
Non-polymers1,33112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465-x-1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.387, 98.387, 263.235
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-692-

HOH

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-680 / 6-METHYLAMINO-5-NITROISOCYTOSINE


Mass: 185.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H7N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 1.83→81.7 Å / Num. all: 63046 / Num. obs: 63046 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rsym value: 0.071 / Net I/σ(I): 23.6
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 63046 / Rsym value: 0.273 / % possible all: 68.9

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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: 1.83→81.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.475 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): 0 / ESU R: 0.116 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT USED THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20878 3220 5.1 %RANDOM
Rwork0.18249 ---
all0.18382 59753 --
obs0.18382 59753 93.57 %-
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: 19.723 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å21.34 Å20 Å2
2--2.69 Å20 Å2
3----4.03 Å2
Refinement stepCycle: LAST / Resolution: 1.83→81.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4109 0 76 399 4584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224236
X-RAY DIFFRACTIONr_bond_other_d0.0030.023896
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.9855716
X-RAY DIFFRACTIONr_angle_other_deg0.92239079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715525
X-RAY DIFFRACTIONr_chiral_restr0.1070.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024643
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02767
X-RAY DIFFRACTIONr_nbd_refined0.2360.2924
X-RAY DIFFRACTIONr_nbd_other0.2590.24559
X-RAY DIFFRACTIONr_nbtor_other0.0890.22529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2313
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4580.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.214
X-RAY DIFFRACTIONr_mcbond_it1.1071.52625
X-RAY DIFFRACTIONr_mcangle_it2.00424220
X-RAY DIFFRACTIONr_scbond_it3.37631611
X-RAY DIFFRACTIONr_scangle_it5.2854.51496
LS refinement shellResolution: 1.83→1.878 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.282 166
Rwork0.249 3169
obs-3335
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)
10.84680.09520.40130.47490.1791.2660.0026-0.0792-0.03340.0179-0.0232-0.05380.05450.17560.02060.19550.11520.00120.15780.03920.1887-79.05680.813391.7911
20.58050.15660.01190.9067-0.06661.0867-0.03570.05590.0534-0.1341-0.0413-0.0176-0.19710.08580.07690.18430.0489-0.01960.20470.03550.1771-68.451861.3375138.7453
3-0.0285-0.08420.25390.2025-0.65240.93980.0091-0.0030.0397-0.0121-0.0753-0.0461-0.07490.13970.06620.11330.1055-0.00760.10370.01770.1124-74.546171.1187114.2869
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B2 - 274
3X-RAY DIFFRACTION3A503 - 713
4X-RAY DIFFRACTION3B502 - 689
5X-RAY DIFFRACTION3A401 - 409
6X-RAY DIFFRACTION3B402 - 410

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