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- PDB-3tzn: Crystal Structure of the Yersinia pestis Dihydropteroate synthase. -

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Basic information

Entry
Database: PDB / ID: 3tzn
TitleCrystal Structure of the Yersinia pestis Dihydropteroate synthase.
Components7,8-dihydropteroate synthase
KeywordsTRANSFERASE / Dihydropteroate synthase / Tim barrel
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 / Dihydropteroate synthase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.083 Å
AuthorsWu, Y.
CitationJournal: Science / Year: 2012
Title: Catalysis and sulfa drug resistance in dihydropteroate synthase.
Authors: Yun, M.K. / Wu, Y. / Li, Z. / Zhao, Y. / Waddell, M.B. / Ferreira, A.M. / Lee, R.E. / Bashford, D. / White, S.W.
History
DepositionSep 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7,8-dihydropteroate synthase
B: 7,8-dihydropteroate synthase


Theoretical massNumber of molelcules
Total (without water)60,6352
Polymers60,6352
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-27 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.429, 49.936, 75.512
Angle α, β, γ (deg.)90.000, 90.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 7,8-dihydropteroate synthase / Dihydropteroate synthase


Mass: 30317.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: KIM D27 / Gene: dhpS, folP, y0683, YPO3501, YP_0582 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7CKJ1, UniProt: A0A2S9PLG4*PLUS, dihydropteroate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: PEG 20,000, MES(pH6.5), pH 6-7, VAPOR DIFFUSION, SITTING DROP, temperature 291K
PH range: 6-7

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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: Dec 3, 2009
RadiationMonochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 27369 / % possible obs: 85.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.098 / Χ2: 2.127 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.08-2.122.30.21711470.444173.2
2.12-2.152.40.21512620.429177.9
2.15-2.22.30.18612780.408180.8
2.2-2.242.40.15913050.412183
2.24-2.292.50.14113540.443183.8
2.29-2.342.50.12613250.467183.8
2.34-2.42.50.12213570.515184.5
2.4-2.472.60.12913180.614184.1
2.47-2.542.90.18813480.806184.8
2.54-2.623.20.20513930.699185.8
2.62-2.713.50.2413711.583185.8
2.71-2.823.90.20513920.907186.8
2.82-2.954.30.18214170.879188
2.95-3.114.50.16614431.269189.9
3.11-3.34.60.14314511.574190.8
3.3-3.564.70.13514502.643189.8
3.56-3.914.70.11514403.993189.6
3.91-4.484.80.09514474.722188.7
4.48-5.644.80.08214334.534187.6
5.64-504.80.06314384.387184.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.083→41.652 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.813 / SU ML: 0.3 / σ(F): 1.33 / Phase error: 26.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 1387 5.07 %
Rwork0.208 --
obs0.2103 27350 85.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.087 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 154.76 Å2 / Biso mean: 66.119 Å2 / Biso min: 23.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.8606 Å20 Å2-0.4346 Å2
2---0.8191 Å2-0 Å2
3---2.6798 Å2
Refinement stepCycle: LAST / Resolution: 2.083→41.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 0 84 3554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0223532
X-RAY DIFFRACTIONf_angle_d1.6724779
X-RAY DIFFRACTIONf_chiral_restr0.128571
X-RAY DIFFRACTIONf_plane_restr0.009613
X-RAY DIFFRACTIONf_dihedral_angle_d18.5381281
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.083-2.15730.32641010.23632268236974
2.1573-2.24360.29331340.22052453258782
2.2436-2.34570.26011400.20292541268184
2.3457-2.46940.24541290.19512561269084
2.4694-2.62410.27011430.20262591273485
2.6241-2.82670.23561300.20832638276886
2.8267-3.1110.23761540.21232704285889
3.111-3.5610.26111380.212768290690
3.561-4.48560.21091560.18532731288789
4.4856-41.66040.25831620.21022708287086
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)
10.0410.0279-0.07470.048-0.00360.0152-0.18930.22150.06670.2095-0.2061-0.3408-0.29820.5051-00.4285-0.1214-0.0880.43850.08990.4752-6.104524.4511-3.0701
20.23280.00350.1760.29920.17480.2395-0.0496-0.1865-0.03520.62970.096-0.38340.22050.1086-00.49690.006-0.10220.4105-0.00580.4185-7.635916.675211.401
31.4822-0.4274-0.08550.63380.23640.54960.0712-0.00970.1240.0751-0.0585-0.0276-0.0745-0.03700.29470.00370.03870.26840.01070.3221-21.57321.5643-2.0772
40.16890.051-0.21290.1526-0.07620.12520.15620.48-0.5161-0.2826-0.35360.21610.96-0.392400.90630.0353-0.19540.6243-0.19970.7584-27.7076-9.471-25.9975
50.0324-0.05250.01170.07260.00910.62140.53860.8832-0.1509-0.7076-0.28260.0680.35140.46650.00010.82620.3422-0.13090.9902-0.01040.3041-20.34674.2566-36.7821
60.16270.28420.15080.51170.28390.61120.27310.1844-0.15840.0075-0.1988-0.20740.17640.2654-00.38970.1175-0.02210.421-0.03150.3836-17.23934.1527-18.1755
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -1:20)A-1 - 20
2X-RAY DIFFRACTION2(chain A and resid 21:116)A21 - 116
3X-RAY DIFFRACTION3(chain A and resid 117:275)A117 - 275
4X-RAY DIFFRACTION4(chain B and resid 1:97)B1 - 97
5X-RAY DIFFRACTION5(chain B and resid 98:218)B98 - 218
6X-RAY DIFFRACTION6(chain B and resid 219:275)B219 - 275

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