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- PDB-5xk6: Structure of a prenyltransferase soaked with IPP -

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Basic information

Entry
Database: PDB / ID: 5xk6
TitleStructure of a prenyltransferase soaked with IPP
ComponentsUndecaprenyl diphosphate synthase
KeywordsTRANSFERASE / prenyltransferase / antibiotic biosynthesis
Function / homologyditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / polyprenol biosynthetic process / Decaprenyl diphosphate synthase-like superfamily / metal ion binding / PYROPHOSPHATE 2- / Undecaprenyl diphosphate synthase
Function and homology information
Biological speciesStreptomyces sp. CNH189 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsKo, T.P. / Guo, R.T. / Liu, W. / Chen, C.C. / Gao, J.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: "Head-to-Middle" and "Head-to-Tail" cis-Prenyl Transferases: Structure of Isosesquilavandulyl Diphosphate Synthase.
Authors: Gao, J. / Ko, T.P. / Chen, L. / Malwal, S.R. / Zhang, J. / Hu, X. / Qu, F. / Liu, W. / Huang, J.W. / Cheng, Y.S. / Chen, C.C. / Yang, Y. / Zhang, Y. / Oldfield, E. / Guo, R.T.
History
DepositionMay 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Undecaprenyl diphosphate synthase
B: Undecaprenyl diphosphate synthase
C: Undecaprenyl diphosphate synthase
D: Undecaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,37018
Polymers106,8334
Non-polymers1,53714
Water24,6451368
1
A: Undecaprenyl diphosphate synthase
B: Undecaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1859
Polymers53,4162
Non-polymers7697
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-70 kcal/mol
Surface area17490 Å2
MethodPISA
2
C: Undecaprenyl diphosphate synthase
D: Undecaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1859
Polymers53,4162
Non-polymers7697
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-71 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.552, 120.634, 130.077
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 diphosphate synthase


Mass: 26708.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CNH189 (bacteria) / Gene: mcl22 / Plasmid: pET46Ek/LIC
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: M4T4U9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1368 / 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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: PROTEIN: 10 mg/mL in 25 mM Tris-Cl (pH 7.5) 150 mM NaCl RESERVOIR: 0.2 M (NH4)2SO4, 0.1 M MES pH 6.5, 30% PEG 5000MME SOAK: 5 mM MgCl2, 5 mM (NH4)4P2O7, 0.1 M MES pH 6.5, 30% PEG 5000MME, 10 mM IPP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 28, 2017
RadiationMonochromator: LN2 cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.58→25 Å / Num. obs: 147602 / % possible obs: 99.9 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/σ(I): 43.8
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 14590 / CC1/2: 0.987 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XK3

5xk3


Resolution: 1.58→24.559 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.91
RfactorNum. reflection% reflectionSelection details
Rfree0.173 2006 1.36 %RANDOM
Rwork0.1527 ---
obs0.1529 147507 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.58→24.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6866 0 78 1368 8312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127299
X-RAY DIFFRACTIONf_angle_d1.2359957
X-RAY DIFFRACTIONf_dihedral_angle_d20.7384431
X-RAY DIFFRACTIONf_chiral_restr0.0741083
X-RAY DIFFRACTIONf_plane_restr0.0091286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5803-1.61980.19761420.170810140X-RAY DIFFRACTION99
1.6198-1.66360.21681490.16210289X-RAY DIFFRACTION100
1.6636-1.71260.18951390.15710368X-RAY DIFFRACTION100
1.7126-1.76780.19991360.155710272X-RAY DIFFRACTION100
1.7678-1.8310.17581520.157810341X-RAY DIFFRACTION100
1.831-1.90430.19391390.163410349X-RAY DIFFRACTION100
1.9043-1.99090.21081420.157910311X-RAY DIFFRACTION100
1.9909-2.09580.17041340.155210378X-RAY DIFFRACTION100
2.0958-2.2270.15191430.147310381X-RAY DIFFRACTION100
2.227-2.39890.17821470.14910378X-RAY DIFFRACTION100
2.3989-2.640.15721420.156310449X-RAY DIFFRACTION100
2.64-3.02140.19991450.16110448X-RAY DIFFRACTION100
3.0214-3.80440.16071490.14710571X-RAY DIFFRACTION100
3.8044-24.56210.15381470.144510826X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.8072 Å / Origin y: 72.4984 Å / Origin z: 45.2408 Å
111213212223313233
T0.0822 Å2-0.0038 Å20.0159 Å2-0.0895 Å2-0.0005 Å2--0.0949 Å2
L0.0914 °2-0.0451 °20.1312 °2-0.1957 °2-0.1316 °2--0.3609 °2
S0.0039 Å °-0.0069 Å °0.0117 Å °-0.0163 Å °-0.0179 Å °-0.0093 Å °-0.0016 Å °0.0211 Å °-0.0023 Å °
Refinement TLS groupSelection details: all

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