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- PDB-6acs: poly-cis-prenyltransferase -

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Basic information

Entry
Database: PDB / ID: 6acs
Titlepoly-cis-prenyltransferase
ComponentsDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
KeywordsTRANSFERASE / citrate / complex / undecaprenyl pyrophosphate / synthase / UPPS
Function / homology
Function and homology information


ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / 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
CITRIC ACID / ISOPROPYL ALCOHOL / Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsKo, T.-P. / Chen, Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Taiwan
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Structure of undecaprenyl pyrophosphate synthase from Acinetobacter baumannii
Authors: Ko, T.P. / Huang, C.H. / Lai, S.J. / Chen, Y.
History
DepositionJul 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
B: Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2108
Polymers59,5212
Non-polymers6896
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-24 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.222, 121.501, 45.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) / Ditrans / polycis-undecaprenylcistransferase / Undecaprenyl diphosphate synthase / UDS / ...Ditrans / polycis-undecaprenylcistransferase / Undecaprenyl diphosphate synthase / UDS / Undecaprenyl pyrophosphate synthase / UPP synthase


Mass: 29760.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: WP_000132222 / Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: uppS, ispU, ABUW_1737, AM462_03305, CBI29_02230 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D5YHU7, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: Protein: Tris-HCl, NaCl, glycerol Reservoir: PEG 20000, isopropanol, citric acid Cryoprotectant: glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→30 Å / Num. obs: 47890 / % possible obs: 99.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 33.1
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 4726 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JP3

1jp3


Resolution: 1.81→28.881 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.31
RfactorNum. reflection% reflection
Rfree0.1818 2000 4.18 %
Rwork0.1598 --
obs0.1608 47814 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.81→28.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3638 0 46 466 4150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073819
X-RAY DIFFRACTIONf_angle_d0.95161
X-RAY DIFFRACTIONf_dihedral_angle_d14.2552282
X-RAY DIFFRACTIONf_chiral_restr0.061564
X-RAY DIFFRACTIONf_plane_restr0.005670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.8550.26791380.2313149X-RAY DIFFRACTION97
1.8548-1.90490.22211420.20143268X-RAY DIFFRACTION100
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)
10.4308-0.39780.14840.46920.21080.51050.05490.07040.0921-0.1122-0.0220.31160.0971-0.0408-00.2321-0.0093-0.03440.21510.0090.223824.719230.859831.0382
20.3123-0.2585-0.08870.49140.19320.0833-0.0136-0.0135-0.14940.0222-0.0426-0.05710.24850.1911-00.247-0.0025-0.01270.20420.00820.182128.944224.535935.5992
30.21-0.0111-0.03930.41380.25540.1353-0.05960.1765-0.655-0.0396-0.0901-0.08580.2706-0.13660.00020.32980.0117-0.0210.2881-0.01010.420532.423112.459838.7146
40.474-0.25470.19410.739-0.08040.03690.06980.0558-0.15430.0423-0.0377-0.0665-0.0270.2735-00.23510.0248-0.01060.24640.00010.232439.905321.362239.3802
50.2224-0.28370.03310.36330.33331.1291-0.03770.06620.1149-0.0320.0432-0.0114-0.04830.07380.00060.1982-0.01380.00380.20270.00910.194132.955635.714945.03
60.184-0.0711-0.00170.3454-0.1310.1405-0.17820.26520.01170.16040.32210.0004-0.10570.05670.00780.3481-0.0018-0.01740.34370.06380.254824.137541.387328.6224
70.5011-0.01260.14470.23780.25960.39270.0779-0.08740.1171-0.0998-0.15060.07650.0322-0.077200.18470.01110.00550.1977-0.01370.29889.531748.668552.7948
80.36160.02820.33360.120.21350.4941-0.08-0.13210.294-0.40990.1527-0.19630.049-0.0106-0.030.2934-0.02110.08490.18870.01230.379321.003752.95650.4286
90.1558-0.22420.14030.2949-0.17110.2067-0.19310.05620.19730.0318-0.1964-0.16820.0106-0.3362-0.00230.51540.11470.01330.4518-0.05410.580219.152264.728356.4306
100.26740.01420.18070.22480.12690.19650.0033-0.63290.30670.4264-0.0235-0.3972-0.24810.1871-0.0020.3479-0.0081-0.03920.313-0.11750.426725.236358.27862.8023
111.2132-0.1918-0.04680.48640.12110.48790.0131-0.07190.13670.0162-0.0140.01720.0064-0.023900.20150.00140.00650.17530.00420.205422.578943.121653.2883
12-0.0228-0.0111-0.00482.19870.2620.0366-0.0969-0.08660.3122-0.10340.1673-0.376-0.05860.20710.01810.34510.0049-0.04871.0058-0.02780.307711.988431.147563.7272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1( chain 'A' and resid 3 through 41 )
2X-RAY DIFFRACTION2( chain 'A' and resid 42 through 70 )
3X-RAY DIFFRACTION3( chain 'A' and resid 71 through 94 )
4X-RAY DIFFRACTION4( chain 'A' and resid 95 through 138 )
5X-RAY DIFFRACTION5( chain 'A' and resid 139 through 217 )
6X-RAY DIFFRACTION6( chain 'A' and resid 218 through 240 )
7X-RAY DIFFRACTION7( chain 'B' and resid 6 through 52 )
8X-RAY DIFFRACTION8( chain 'B' and resid 53 through 70 )
9X-RAY DIFFRACTION9( chain 'B' and resid 71 through 95 )
10X-RAY DIFFRACTION10( chain 'B' and resid 96 through 123 )
11X-RAY DIFFRACTION11( chain 'B' and resid 124 through 235 )
12X-RAY DIFFRACTION12( chain 'B' and resid 236 through 253 )

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