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- PDB-5xk8: Crystal structure of Isosesquilavandulyl Diphosphate Synthase fro... -

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Basic information

Entry
Database: PDB / ID: 5xk8
TitleCrystal structure of Isosesquilavandulyl Diphosphate Synthase from Streptomyces sp. strain CNH-189 in complex with GPP
ComponentsUndecaprenyl diphosphate synthase
KeywordsTRANSFERASE / prenyltransferase / antibiotic biosynthesis
Function / homologyDecaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / transferase activity, transferring alkyl or aryl (other than methyl) groups / GERANYL DIPHOSPHATE / Undecaprenyl diphosphate synthase
Function and homology information
Biological speciesStreptomyces sp. CNH189 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 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 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Nov 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.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)108,1149
Polymers106,8334
Non-polymers1,2815
Water8,611478
1
A: Undecaprenyl diphosphate synthase
B: Undecaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0695
Polymers53,4162
Non-polymers6533
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-31 kcal/mol
Surface area17600 Å2
MethodPISA
2
C: Undecaprenyl diphosphate synthase
D: Undecaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0454
Polymers53,4162
Non-polymers6282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-17 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.342, 121.151, 121.246
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-GPP / GERANYL DIPHOSPHATE / Geranyl pyrophosphate


Mass: 314.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H20O7P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: PROTEIN: 10 mg/mL in 25 mM Tris-Cl (pH 7.5) and 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 GPP

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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: 2.3→25 Å / Num. obs: 42982 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 24.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4245 / CC1/2: 0.961 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XK3
Resolution: 2.304→24.867 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.86
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 2122 4.94 %RANDOM
Rwork0.1854 ---
obs0.1869 42934 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.304→24.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6808 0 77 478 7363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037039
X-RAY DIFFRACTIONf_angle_d0.6119543
X-RAY DIFFRACTIONf_dihedral_angle_d19.1744192
X-RAY DIFFRACTIONf_chiral_restr0.0411038
X-RAY DIFFRACTIONf_plane_restr0.0041233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3042-2.35770.36091310.26342623X-RAY DIFFRACTION98
2.3577-2.41660.28641520.25842710X-RAY DIFFRACTION99
2.4166-2.48190.28861370.24242673X-RAY DIFFRACTION99
2.4819-2.55490.28931230.22842686X-RAY DIFFRACTION99
2.5549-2.63730.28211460.22622679X-RAY DIFFRACTION99
2.6373-2.73140.27261390.22442706X-RAY DIFFRACTION99
2.7314-2.84060.26571420.21732698X-RAY DIFFRACTION99
2.8406-2.96970.25391660.22482700X-RAY DIFFRACTION100
2.9697-3.1260.23391300.21632745X-RAY DIFFRACTION100
3.126-3.32140.22791340.2022698X-RAY DIFFRACTION100
3.3214-3.57720.21831230.17972775X-RAY DIFFRACTION100
3.5772-3.93590.18591290.16032768X-RAY DIFFRACTION100
3.9359-4.50250.17411910.15722722X-RAY DIFFRACTION100
4.5025-5.66160.17771320.13922787X-RAY DIFFRACTION99
5.6616-24.8680.17711470.16782842X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 9.3458 Å / Origin y: 11.7008 Å / Origin z: -10.47 Å
111213212223313233
T0.233 Å2-0.0187 Å20.0041 Å2-0.2392 Å2-0.0227 Å2--0.2664 Å2
L0.164 °2-0.243 °20.3372 °2-0.4749 °2-0.3022 °2--0.8575 °2
S-0.0308 Å °-0.0478 Å °0.0084 Å °-0.0231 Å °-0.022 Å °0.0126 Å °-0.0498 Å °0.0068 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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