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- PDB-4u82: Structure of S. aureus undecaprenyl diphosphate synthase in compl... -

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Basic information

Entry
Database: PDB / ID: 4u82
TitleStructure of S. aureus undecaprenyl diphosphate synthase in complex with FSPP and sulfate
ComponentsIsoprenyl transferase
KeywordsTRANSFERASE / Alkyl and Aryl Transferases / Anti-Bacterial Agents / Benzoates / Biosynthetic Pathways / Cell Wall / Diphosphonates / Drug Discovery / High-Throughput Screening Assays / Methicillin / Microbial Sensitivity Tests / Pyrrolidinones / Staphylococcus aureus / Terpenes
Function / homology
Function and homology information


Transferases; Transferring alkyl or aryl groups, other than methyl groups / prenyltransferase activity / magnesium ion binding
Similarity search - Function
Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FPS / Isoprenyl transferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsZhu, W. / Oldfield, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM065307 United States
CitationJournal: J.Med.Chem. / Year: 2015
Title: Antibacterial drug leads: DNA and enzyme multitargeting.
Authors: Zhu, W. / Wang, Y. / Li, K. / Gao, J. / Huang, C.H. / Chen, C.C. / Ko, T.P. / Zhang, Y. / Guo, R.T. / Oldfield, E.
History
DepositionJul 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_symmetry / _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_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoprenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4214
Polymers29,9021
Non-polymers5193
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-24 kcal/mol
Surface area11920 Å2
2
A: Isoprenyl transferase
hetero molecules

A: Isoprenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8428
Polymers59,8042
Non-polymers1,0386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7290 Å2
ΔGint-95 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.079, 57.079, 158.618
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Isoprenyl transferase


Mass: 29902.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: uppS, SA1103 / Production host: Escherichia coli (E. coli)
References: UniProt: P60477, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O6P2S
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / 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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 100 mM MES sodium, pH 6.5, 200 mM ammonium sulfate, 25% PEG5000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2012
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 32040 / % possible obs: 99.5 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 34.5714
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 4.5714

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H8E

4h8e


Resolution: 1.66→46.33 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.627 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 1616 5.1 %RANDOM
Rwork0.1873 30352 --
obs0.1889 31968 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.02 Å2 / Biso mean: 20.106 Å2 / Biso min: 10.08 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.66→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 30 84 2044
Biso mean--23.78 23.74 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022016
X-RAY DIFFRACTIONr_angle_refined_deg2.4231.9682721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5525237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88124.79698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38615375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6511511
X-RAY DIFFRACTIONr_chiral_restr0.1760.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211509
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 109 -
Rwork0.201 1958 -
all-2067 -
obs--99.95 %

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