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- PDB-5xk7: Crystal structure of Isosesquilavandulyl Diphosphate Synthase fro... -

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Basic information

Entry
Database: PDB / ID: 5xk7
TitleCrystal structure of Isosesquilavandulyl Diphosphate Synthase from Streptomyces sp. strain CNH-189 in complex with DMAPP
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 / DIMETHYLALLYL DIPHOSPHATE / PYROPHOSPHATE 2- / Undecaprenyl diphosphate synthase
Function and homology information
Biological speciesStreptomyces sp. CNH189 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.911 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.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)109,52122
Polymers106,8334
Non-polymers2,68818
Water16,286904
1
A: Undecaprenyl diphosphate synthase
B: Undecaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,72611
Polymers53,4162
Non-polymers1,3099
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-53 kcal/mol
Surface area17240 Å2
MethodPISA
2
C: Undecaprenyl diphosphate synthase
D: Undecaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,79611
Polymers53,4162
Non-polymers1,3799
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-53 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.924, 120.653, 126.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 6 types, 922 molecules

#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- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-DMA / DIMETHYLALLYL DIPHOSPHATE / Dimethylallyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12O7P2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 904 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
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 DMAPP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 17, 2017
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→25 Å / Num. obs: 79758 / % possible obs: 98.5 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Net I/σ(I): 27.8
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7741 / CC1/2: 0.958 / % possible all: 97.1

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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: 1.911→24.729 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.97
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 1999 2.51 %RANDOM
Rwork0.1688 ---
obs0.1694 79708 98.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.911→24.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6842 0 149 904 7895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047218
X-RAY DIFFRACTIONf_angle_d0.7549821
X-RAY DIFFRACTIONf_dihedral_angle_d21.0074328
X-RAY DIFFRACTIONf_chiral_restr0.0461058
X-RAY DIFFRACTIONf_plane_restr0.0051250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.911-1.95880.30911350.25445278X-RAY DIFFRACTION95
1.9588-2.01180.26671410.22545429X-RAY DIFFRACTION97
2.0118-2.07090.25391450.21255428X-RAY DIFFRACTION97
2.0709-2.13770.24591400.1925447X-RAY DIFFRACTION98
2.1377-2.21410.22441320.1775506X-RAY DIFFRACTION99
2.2141-2.30270.19021520.17485504X-RAY DIFFRACTION99
2.3027-2.40740.22311370.18085540X-RAY DIFFRACTION99
2.4074-2.53420.22391430.18145582X-RAY DIFFRACTION99
2.5342-2.69280.21081470.18565584X-RAY DIFFRACTION99
2.6928-2.90040.20931410.18265610X-RAY DIFFRACTION100
2.9004-3.19170.19571480.18455656X-RAY DIFFRACTION100
3.1917-3.65230.19841440.16145650X-RAY DIFFRACTION99
3.6523-4.59670.14051440.14135692X-RAY DIFFRACTION99
4.5967-24.73110.16181500.14635803X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 7.9075 Å / Origin y: 73.7212 Å / Origin z: 44.5425 Å
111213212223313233
T0.2363 Å2-0.0318 Å20.0389 Å2-0.2536 Å2-0.0111 Å2--0.2607 Å2
L0.2004 °2-0.1551 °20.2039 °2-0.5858 °2-0.2363 °2--0.8355 °2
S0.04 Å °-0.0344 Å °0.0219 Å °-0.0347 Å °-0.047 Å °-0.0071 Å °0.058 Å °0.0362 Å °0.0059 Å °
Refinement TLS groupSelection details: all

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