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- PDB-3tzf: Crystal Structure of the Yersinia pestis Dihydropteroate Synthase... -

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Basic information

Entry
Database: PDB / ID: 3tzf
TitleCrystal Structure of the Yersinia pestis Dihydropteroate Synthase with Sulfonamide Drug Complex.
Components7,8-dihydropteroate synthase
KeywordsTRANSFERASE/ANTIBIOTIC/INHIBITOR / Dihydropteroate synthase / sulfonamide complex / Tim barrel / TRANSFERASE-INHIBITOR-ANTIBIOTIC complex / TRANSFERASE-ANTIBIOTIC-INHIBITOR complex
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
Sulfamethoxazole / 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE / Dihydropteroate synthase / Dihydropteroate synthase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,6447
Polymers60,6352
Non-polymers1,0085
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-55 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.245, 50.582, 74.988
Angle α, β, γ (deg.)90.000, 90.800, 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 / Fragment: DHPS
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: Chemical ChemComp-HH2 / 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE / [PTERIN-6-YL METHANYL]-PHOSPHONOPHOSPHATE


Mass: 353.123 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N5O8P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-08D / Sulfamethoxazole / 4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide / SMX / SMZ


Mass: 253.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11N3O3S / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.2 Å3/Da / Density % sol: 44.01 %
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-BM / Wavelength: 0.97954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2011
RadiationMonochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 30631 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.074 / Χ2: 0.849 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.143.30.39914750.851196.5
2.14-2.183.70.38514720.922195.8
2.18-2.224.10.34814980.887197.2
2.22-2.264.30.3115500.917198.7
2.26-2.314.60.28114480.863196.4
2.31-2.374.70.24215410.891199.5
2.37-2.424.90.22915280.823197
2.42-2.494.90.21715150.856199.8
2.49-2.565.10.19315100.846197.5
2.56-2.655.10.16715390.839198.9
2.65-2.745.20.15515380.921199.1
2.74-2.855.10.12315110.844198.4
2.85-2.985.10.10515460.844198.8
2.98-3.145.10.08215590.821199.9
3.14-3.335.20.06415450.865199.2
3.33-3.595.10.05315470.903199.2
3.59-3.955.10.05115570.882199.2
3.95-4.525.10.0415600.814199.7
4.52-5.750.03615770.785199.7
5.7-504.90.02316150.656198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.676 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 1550 5.1 %RANDOM
Rwork0.1994 ---
obs0.2015 30629 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 68.9 Å2 / Biso mean: 33.2524 Å2 / Biso min: 7.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å2-0.51 Å2
2--1.2 Å2-0 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 63 207 4356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214286
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.9635841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8975564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11924.42181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0715684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5871524
X-RAY DIFFRACTIONr_chiral_restr0.0750.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213257
X-RAY DIFFRACTIONr_mcbond_it0.4131.52762
X-RAY DIFFRACTIONr_mcangle_it0.7724407
X-RAY DIFFRACTIONr_scbond_it1.06431524
X-RAY DIFFRACTIONr_scangle_it1.7914.51428
LS refinement shellResolution: 2.1→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 88 -
Rwork0.232 2043 -
all-2131 -
obs--94.17 %
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)
11.08650.08870.3280.64880.40780.92790.0124-0.09790.07380.0691-0.029-0.0488-0.0442-0.05850.01660.02470.00480.00630.01760.01450.063817.759418.661640.0076
20.67470.12640.0930.74260.44982.13380.07560.2431-0.0605-0.10.0118-0.02180.2035-0.0825-0.08740.06860.0069-0.01560.127-0.00740.030615.977-1.59647.2987
33.9975-15.27459.2158.3658-35.191821.2201-0.0413-0.1624-0.24580.16220.61150.9429-0.0985-0.3807-0.57020.01150.01030.02360.1420.03460.055514.800114.52543.0272
40.85380.1599-1.85580.0301-0.34714.0363-0.14120.0369-0.061-0.02650.0144-0.01560.3244-0.05970.12680.04090.0426-0.01160.1519-0.06550.096424.3395-3.49418.2604
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 275
2X-RAY DIFFRACTION2B1 - 276
3X-RAY DIFFRACTION3A278 - 279
4X-RAY DIFFRACTION4B278 - 280

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