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- PDB-3ugs: Crystal structure of a probable undecaprenyl diphosphate synthase... -

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Basic information

Entry
Database: PDB / ID: 3ugs
TitleCrystal structure of a probable undecaprenyl diphosphate synthase (uppS) from Campylobacter jejuni
ComponentsUndecaprenyl pyrophosphate synthase
KeywordsTRANSFERASE / NIAID / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / farnesyl monophosphate
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-FFT / Isoprenyl transferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.457 Å
AuthorsNocek, B. / Gu, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a probable undecaprenyl diphosphate synthase (uppS) from Campylobacter jejuni
Authors: Nocek, B. / Gu, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,4084
Polymers52,8032
Non-polymers6052
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-13 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.643, 67.234, 118.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 26401.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: uppS, Cj0824 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: Q9PP99, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical ChemComp-FFT / (2Z,6Z)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl dihydrogen phosphate / farnesyl monophosphate


Mass: 302.346 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H27O4P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDURING MODEL BUILDING AND REFINEMENT, AN UNIDENTIFIED LIGAND WAS OBSERVED IN THE ACTIVE SITE AREA. ...DURING MODEL BUILDING AND REFINEMENT, AN UNIDENTIFIED LIGAND WAS OBSERVED IN THE ACTIVE SITE AREA. BASED ON DENSITY FEATURES AND THE BEST FIT, IT WAS MODELED AS FARNESYL MONOPHOSPHATE. IT WAS LIKELY CO-PURIFIED WITH THE PROTEIN, NOT HAVING BEEN ADDED TO THE PROTEIN DURING CRYSTALLIZATION.

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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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 45% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2009 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.457→40 Å / Num. all: 18358 / Num. obs: 18362 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 28
Reflection shellResolution: 2.45→2.49 Å / Num. unique all: 908 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DR2

2dr2


Resolution: 2.457→40 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / SU B: 9.259 / SU ML: 0.213 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.585 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25262 890 5.2 %RANDOM
Rwork0.2022 ---
all0.21 17182 --
obs0.20686 16292 93.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.119 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2--0.37 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.457→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 40 70 3370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193349
X-RAY DIFFRACTIONr_bond_other_d0.0030.022296
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9864505
X-RAY DIFFRACTIONr_angle_other_deg2.40935594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6485409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02524.494158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.0415627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0241526
X-RAY DIFFRACTIONr_chiral_restr0.0780.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023676
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02674
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.457→2.521 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 42 -
Rwork0.215 614 -
obs--49.89 %

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