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- PDB-5kh2: Crystal Structure of Steptococcus pneumoniae Undecaprenyl pyropho... -

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Basic information

Entry
Database: PDB / ID: 5kh2
TitleCrystal Structure of Steptococcus pneumoniae Undecaprenyl pyrophosphate Synthase (UPPS)
ComponentsIsoprenyl transferase
KeywordsTRANSFERASE / UPPS / native / bacterial / undecaprenyl S. pneumoniae
Function / homology
Function and homology information


di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / manganese ion binding / magnesium ion binding / plasma membrane / cytosol
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
Isoprenyl transferase
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsConcha, N.O.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Discovery and Characterization of a Class of Pyrazole Inhibitors of Bacterial Undecaprenyl Pyrophosphate Synthase.
Authors: Concha, N. / Huang, J. / Bai, X. / Benowitz, A. / Brady, P. / Grady, L.C. / Kryn, L.H. / Holmes, D. / Ingraham, K. / Jin, Q. / Pothier Kaushansky, L. / McCloskey, L. / Messer, J.A. / ...Authors: Concha, N. / Huang, J. / Bai, X. / Benowitz, A. / Brady, P. / Grady, L.C. / Kryn, L.H. / Holmes, D. / Ingraham, K. / Jin, Q. / Pothier Kaushansky, L. / McCloskey, L. / Messer, J.A. / O'Keefe, H. / Patel, A. / Satz, A.L. / Sinnamon, R.H. / Schneck, J. / Skinner, S.R. / Summerfield, J. / Taylor, A. / Taylor, J.D. / Evindar, G. / Stavenger, R.A.
History
DepositionJun 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Derived calculations
Category: citation / diffrn ...citation / diffrn / diffrn_radiation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn.pdbx_serial_crystal_experiment ..._citation.journal_id_CSD / _diffrn.pdbx_serial_crystal_experiment / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_source.pdbx_wavelength_list / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoprenyl transferase
B: Isoprenyl transferase
C: Isoprenyl transferase
D: Isoprenyl transferase


Theoretical massNumber of molelcules
Total (without water)123,6454
Polymers123,6454
Non-polymers00
Water6,143341
1
A: Isoprenyl transferase
B: Isoprenyl transferase


Theoretical massNumber of molelcules
Total (without water)61,8222
Polymers61,8222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Isoprenyl transferase
D: Isoprenyl transferase


Theoretical massNumber of molelcules
Total (without water)61,8222
Polymers61,8222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.687, 118.029, 178.326
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A18 - 248
2115C18 - 248
1125B18 - 246
2125D18 - 246

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.997161, -0.065885, 0.036454), (-0.066315, -0.997741, 0.010704), (0.035666, -0.013092, -0.999278)-1.28828, 0.2683, 88.728302
3given(1), (1), (1)
4given(0.996737, -0.069861, 0.040427), (-0.070586, -0.997365, 0.016771), (0.039149, -0.01957, -0.999042)-1.63486, -0.11934, 88.61512

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Components

#1: Protein
Isoprenyl transferase


Mass: 30911.205 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: uppS, SP_0261 / Production host: Escherichia coli (E. coli)
References: UniProt: Q97SR4, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 ul protein (9.5mg/ml in 50mM Tris-HCl, pH 7.5, 0.2M NaCl, 1mM EDTA) mixed with 2ul reservoir solution containing either 10-20% ethanol, 0.1M Tris-Hcl, pH 8.5 or 4-5% PEG 6000, 0.1M HEPES, pH 7.5
PH range: 7.5 - 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.987,1.000
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 17, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9871
211
ReflectionResolution: 2.3→20 Å / Num. obs: 53529 / % possible obs: 94.3 % / Redundancy: 5 % / Net I/σ(I): 15

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementResolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / SU B: 12.447 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.216 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24491 2792 5.1 %RANDOM
Rwork0.21255 ---
obs0.21418 52056 91.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--0.38 Å2-0 Å2
3----1.3 Å2
Refinement stepCycle: 1 / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6856 0 0 341 7197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197003
X-RAY DIFFRACTIONr_bond_other_d0.0010.026668
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.9639522
X-RAY DIFFRACTIONr_angle_other_deg0.857315270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3045880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4724.984311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.295151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5441530
X-RAY DIFFRACTIONr_chiral_restr0.0570.21088
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021576
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_it0.5682.283539
X-RAY DIFFRACTIONr_mcbond_other0.5682.2793538
X-RAY DIFFRACTIONr_mcangle_it1.0693.4094409
X-RAY DIFFRACTIONr_mcangle_other1.0693.414410
X-RAY DIFFRACTIONr_scbond_it0.2922.2763464
X-RAY DIFFRACTIONr_scbond_other0.2922.2763464
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5973.4065111
X-RAY DIFFRACTIONr_long_range_B_refined4.57918.2247963
X-RAY DIFFRACTIONr_long_range_B_other4.45117.9667866
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1306MEDIUM POSITIONAL0.130.5
1A1984LOOSE POSITIONAL0.325
1A1306MEDIUM THERMAL2.212
1A1984LOOSE THERMAL1.9610
2B1275MEDIUM POSITIONAL0.150.5
2B2029LOOSE POSITIONAL0.445
2B1275MEDIUM THERMAL2.32
2B2029LOOSE THERMAL2.3210
LS refinement shellResolution: 2.261→2.32 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 123 -
Rwork0.257 2385 -
obs--57.22 %
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)
11.56860.14560.0981.1765-0.11523.17190.0781-0.11820.0324-0.05720.07020.07780.68260.2809-0.14830.25980.0995-0.00160.0631-0.01210.250515.992-14.30931.564
20.9366-0.5790.37941.0975-0.00911.56380.0258-0.01070.0571-0.03130.03390.0241-0.04130.0086-0.05970.04390.018-0.0050.0099-0.00630.26515.1419.88316.03
31.51080.1673-0.49211.4156-0.04112.82830.13480.1260.0199-0.10460.0612-0.0193-0.69180.1769-0.19610.2427-0.07240.03640.0411-0.0070.273216.13113.99257.201
41.32650.4286-0.25711.41130.09211.43520.01970.0032-0.0430.05560.06260.0190.0293-0.0202-0.08230.025-0.0206-0.00960.028-0.01030.28073.093-9.00972.559
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 246
2X-RAY DIFFRACTION2B17 - 246
3X-RAY DIFFRACTION3C18 - 248
4X-RAY DIFFRACTION4D18 - 246

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