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- PDB-7l6p: Crystal structure of dihydropteroate synthase from Stenotrophomon... -

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Basic information

Entry
Database: PDB / ID: 7l6p
TitleCrystal structure of dihydropteroate synthase from Stenotrophomonas maltophilia with active site-bound imidazole
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / SSGCID / PMM / dihydropteroate synthase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding
Similarity search - Function
Dihydropteroate synthase signature 1. / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like
Similarity search - Domain/homology
IMIDAZOLE / Dihydropteroate synthase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of dihydropteroate synthase from Stenotrophomonas maltophilia with active site-bound imidazole
Authors: Bolejack, M.J. / Delker, S.L. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,9114
Polymers65,7732
Non-polymers1382
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-12 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.740, 68.810, 155.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 13 through 38 or (resid 48...
21(chain B and (resid 13 through 102 or (resid 103...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 13 through 38 or (resid 48...A13 - 38
121(chain A and (resid 13 through 38 or (resid 48...A48
131(chain A and (resid 13 through 38 or (resid 48...A5 - 283
141(chain A and (resid 13 through 38 or (resid 48...A5 - 283
151(chain A and (resid 13 through 38 or (resid 48...A5 - 283
161(chain A and (resid 13 through 38 or (resid 48...A5 - 283
211(chain B and (resid 13 through 102 or (resid 103...B13 - 102
221(chain B and (resid 13 through 102 or (resid 103...B103
231(chain B and (resid 13 through 102 or (resid 103...B13 - 291
241(chain B and (resid 13 through 102 or (resid 103...B13 - 291
251(chain B and (resid 13 through 102 or (resid 103...B13 - 291
261(chain B and (resid 13 through 102 or (resid 103...B13 - 291

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Components

#1: Protein Dihydropteroate synthase / / DHPS / Dihydropteroate pyrophosphorylase


Mass: 32886.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: folP, Smlt1734 / Plasmid: StmaA.01019.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2FL24, dihydropteroate synthase
#2: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: StmaA.01019.a.B1.PW38739 at 16.2 mg/ml was mixed 1:1 with 0.1 M Tris/Bicine pH 8.5, 0.1 M amino acids, 10% (w/v) PEG4000, and 20% (v/v) glycerol (Morpheus H11). Stored at 14C. Cryo: direct. ...Details: StmaA.01019.a.B1.PW38739 at 16.2 mg/ml was mixed 1:1 with 0.1 M Tris/Bicine pH 8.5, 0.1 M amino acids, 10% (w/v) PEG4000, and 20% (v/v) glycerol (Morpheus H11). Stored at 14C. Cryo: direct. Tray 314007h11: puck cbg9-2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 12, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→41.34 Å / Num. obs: 28734 / % possible obs: 99.9 % / Redundancy: 5.141 % / Biso Wilson estimate: 51.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.055 / Χ2: 1.084 / Net I/σ(I): 18.23 / Num. measured all: 147717
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.414.0890.5632.178525208520850.90.644100
2.41-2.485.0030.5022.9310121202520230.9420.56199.9
2.48-2.555.4040.3963.8310760199119910.9530.439100
2.55-2.635.3760.3424.510348192519250.9630.38100
2.63-2.715.3880.2526.0510032186318620.9790.2899.9
2.71-2.815.3880.1857.819774181418140.9890.205100
2.81-2.915.3790.1519.59478176217620.9920.168100
2.91-3.035.3340.11612.428967168216810.9950.12999.9
3.03-3.175.3230.08615.768644162416240.9970.095100
3.17-3.325.2870.06620.138316157315730.9980.073100
3.32-3.55.2270.05424.127715147614760.9990.06100
3.5-3.725.1760.04429.737308141214120.9990.049100
3.72-3.975.1820.03833.136830131813180.9990.042100
3.97-4.295.1240.03537.196384124612460.9990.038100
4.29-4.75.0990.03240.325844114711460.9990.03599.9
4.7-5.255.0540.02941.775342105710570.9990.033100
5.25-6.075.0320.02940.8546709289280.9990.032100
6.07-7.434.9880.02742.8740008028020.9990.03100
7.43-10.514.790.02147.1930856456440.9990.02499.8
10.51-41.344.3120.0244.0215743823650.9990.02295.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19rc4-4035refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5uur

5uur
PDB Unreleased entry


Resolution: 2.35→41.34 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 2058 7.18 %
Rwork0.1975 26606 -
obs0.2014 28664 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.34 Å2 / Biso mean: 66.7543 Å2 / Biso min: 40.79 Å2
Refinement stepCycle: final / Resolution: 2.35→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3885 0 10 66 3961
Biso mean--62.01 59.26 -
Num. residues----530
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2330X-RAY DIFFRACTION6.666TORSIONAL
12B2330X-RAY DIFFRACTION6.666TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.40.38941250.339617281853100
2.4-2.460.35851340.307617541888100
2.46-2.530.35121290.279917461875100
2.53-2.610.34521390.270217511890100
2.61-2.690.31141310.282417331864100
2.69-2.790.32111320.254217621894100
2.79-2.90.32481270.243917561883100
2.9-3.030.30911450.23717541899100
3.03-3.190.28741480.242717581906100
3.19-3.390.31661520.237117471899100
3.39-3.650.22871290.197417901919100
3.65-4.020.25871360.182617981934100
4.02-4.60.19111450.15218031948100
4.6-5.790.22221300.151818311961100
5.79-41.340.19951560.16331895205199
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)
16.53680.1781-2.42715.0929-0.03753.80420.2538-0.13650.3230.00520.07050.0135-0.03410.29-0.30980.6113-0.0371-0.13070.5352-0.04080.6058-11.8719.781-25.108
24.1552-0.09860.55021.99830.77882.8574-0.08740.17040.0816-0.37890.1539-0.4812-0.03090.3823-0.02470.6211-0.03190.12890.5399-0.03940.6285-12.9774.42-37.057
31.4194-0.5305-0.58640.95991.62753.26280.0519-0.0197-0.004-0.088-0.0351-0.16140.0999-0.0566-0.01650.4505-0.05650.02970.31390.01620.4654-27.9288.32-28.95
46.1758-1.7727-1.80016.4584-2.10396.62310.1445-0.7180.0269-0.2018-0.0171-0.6261-0.41450.2394-0.11140.53210.00860.1110.4296-0.02530.4284-41.59737.09-15.409
52.8147-0.80751.05364.9711-1.60151.4620.0367-0.68680.42280.38390.19190.0718-0.3087-0.1863-0.24260.7501-0.01280.22390.6832-0.12670.5222-47.47940.594-6.354
65.7538-6.3869-1.86397.53951.30751.9899-0.231-1.1840.53341.55570.5894-0.9264-0.07990.0681-0.32011.0232-0.1702-0.02091.13310.04330.6039-38.87723.3477.189
72.5564-1.4421-0.34321.9474-0.00912.0290.1724-0.4397-0.11560.0359-0.0477-0.1354-0.0423-0.1797-0.12150.5349-0.12740.03620.46470.04670.4166-40.65521.672-9.812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 13:83 )A13 - 83
2X-RAY DIFFRACTION2( CHAIN A AND RESID 84:169 )A84 - 169
3X-RAY DIFFRACTION3( CHAIN A AND RESID 170:283 )A170 - 283
4X-RAY DIFFRACTION4( CHAIN B AND RESID 13:83 )B13 - 83
5X-RAY DIFFRACTION5( CHAIN B AND RESID 84:152 )B84 - 152
6X-RAY DIFFRACTION6( CHAIN B AND RESID 153:169 )B153 - 169
7X-RAY DIFFRACTION7( CHAIN B AND RESID 170:291 )B170 - 291

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