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- PDB-4h8e: Structure of S. aureus undecaprenyl diphosphate synthase in compl... -

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Basic information

Entry
Database: PDB / ID: 4h8e
TitleStructure of S. aureus undecaprenyl diphosphate synthase in complex with FPP and sulfate
ComponentsUndecaprenyl pyrophosphate synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / alpha-helix / prenyl transferase / cell wall biosynthesis / farnesyl diphosphate binding / isopentenyl diphosphate binding / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity / polyprenol biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / manganese ion binding / magnesium ion binding / cytosol
Similarity search - Function
Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FARNESYL DIPHOSPHATE / Isoprenyl transferase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsZhu, W. / Oldfield, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Antibacterial drug leads targeting isoprenoid biosynthesis.
Authors: Zhu, W. / Zhang, Y. / Sinko, W. / Hensler, M.E. / Olson, J. / Molohon, K.J. / Lindert, S. / Cao, R. / Li, K. / Wang, K. / Wang, Y. / Liu, Y.L. / Sankovsky, A. / de Oliveira, C.A. / Mitchell, ...Authors: Zhu, W. / Zhang, Y. / Sinko, W. / Hensler, M.E. / Olson, J. / Molohon, K.J. / Lindert, S. / Cao, R. / Li, K. / Wang, K. / Wang, Y. / Liu, Y.L. / Sankovsky, A. / de Oliveira, C.A. / Mitchell, D.A. / Nizet, V. / McCammon, J.A. / Oldfield, E.
History
DepositionSep 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_label_seq_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_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_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_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: Undecaprenyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4054
Polymers29,9021
Non-polymers5033
Water2,414134
1
A: Undecaprenyl pyrophosphate synthase
hetero molecules

A: Undecaprenyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8108
Polymers59,8042
Non-polymers1,0056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7240 Å2
ΔGint-89 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.303, 57.303, 158.824
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 Undecaprenyl pyrophosphate synthase / UPP synthase / Di-trans / poly-cis-decaprenylcistransferase / Ditrans / polycis-undecaprenyl- ...UPP synthase / Di-trans / poly-cis-decaprenylcistransferase / Ditrans / polycis-undecaprenyl-diphosphate synthase / Undecaprenyl diphosphate synthase / UDS


Mass: 29902.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: N315 / Gene: uppS, SA1103 / Production host: Escherichia coli (E. coli)
References: UniProt: P60477, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#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.: 134 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
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: Jun 16, 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: 1.3→50 Å / Num. obs: 66126 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 13.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 33.9
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→32.64 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.565 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 3349 5.1 %RANDOM
Rwork0.1741 ---
all0.1751 69372 --
obs0.1751 66023 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.36 Å2 / Biso mean: 13.6007 Å2 / Biso min: 6.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.3→32.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1918 0 30 134 2082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.021988
X-RAY DIFFRACTIONr_angle_refined_deg2.6551.9672683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7475234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00724.63295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42315369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5931511
X-RAY DIFFRACTIONr_chiral_restr0.1870.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211481
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 220 -
Rwork0.2 4161 -
all-4381 -
obs--99.3 %

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