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- PDB-3sgx: Crystal Structure of E. coli undecaprenyl pyrophosphate synthase ... -

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Basic information

Entry
Database: PDB / ID: 3sgx
TitleCrystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1100
ComponentsUndecaprenyl pyrophosphate synthase
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / Alpha/beta / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


Gram-negative-bacterium-type cell wall biogenesis / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity / polyprenol biosynthetic process / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium ion binding ...Gram-negative-bacterium-type cell wall biogenesis / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity / polyprenol biosynthetic process / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium ion binding / protein homodimerization activity / cytoplasm / 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
Chem-0FW / Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsCao, R. / Liu, Y.-L. / 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
DepositionJun 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Sep 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Undecaprenyl pyrophosphate synthase
B: Undecaprenyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8694
Polymers56,9622
Non-polymers9072
Water1,35175
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-14 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.950, 68.135, 111.608
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Undecaprenyl pyrophosphate synthase / UPP synthase / Di-trans / poly-cis-decaprenylcistransferase / Undecaprenyl diphosphate synthase / UDS


Mass: 28481.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0174, ispU, JW0169, rth, uppS, yaeS / Plasmid: pET32 / Production host: Escherichia coli (E. coli)
References: UniProt: P60472, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical ChemComp-0FW / 4-{3-[(biphenyl-4-ylcarbonyl)amino]phenoxy}benzene-1,2-dicarboxylic acid


Mass: 453.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H19NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50mM HEPES, pH 7.5, 5% PEG 4,000, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 23, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 17225 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.092 / Χ2: 1.715 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.45-2.494.70.4517860.95190.7
2.49-2.544.80.4578521.008196.3
2.54-2.595.20.4368120.953197.5
2.59-2.645.50.378791.042198.9
2.64-2.75.70.3498451.045199.3
2.7-2.765.80.3218811.055199.1
2.76-2.835.90.2748641.19199.1
2.83-2.960.248651.2198.7
2.9-2.9960.2088571.265198.6
2.99-3.0960.1828661.319198.1
3.09-3.260.1568711.402198.4
3.2-3.3260.1298621.63198.7
3.32-3.485.90.1088721.844198.6
3.48-3.6660.0948822.237198.2
3.66-3.8960.0818712.387197.2
3.89-4.1960.0728522.501196.7
4.19-4.615.80.068722.7196.2
4.61-5.285.90.0558742.501195.8
5.28-6.655.80.0538782.338194.7
6.65-505.40.0528843.23188.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2E98

2e98


Resolution: 2.45→32.65 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.824 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.717 / SU ML: 0.272 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3275 865 5 %RANDOM
Rwork0.2417 ---
all0.2458 18005 --
obs0.2458 17140 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 131.97 Å2 / Biso mean: 45.5567 Å2 / Biso min: 14.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.45→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 68 75 3399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213428
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9454632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.455416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4223.626182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.57815574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6741533
X-RAY DIFFRACTIONr_chiral_restr0.1070.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022690
X-RAY DIFFRACTIONr_mcbond_it0.7911.52037
X-RAY DIFFRACTIONr_mcangle_it1.48723239
X-RAY DIFFRACTIONr_scbond_it2.28531391
X-RAY DIFFRACTIONr_scangle_it3.7644.51388
LS refinement shellResolution: 2.447→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 58 -
Rwork0.321 1097 -
all-1155 -
obs--91.3 %

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