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- PDB-5z45: Crystal structure of prenyltransferase AmbP1 pH6.5 complexed with... -

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Basic information

Entry
Database: PDB / ID: 5z45
TitleCrystal structure of prenyltransferase AmbP1 pH6.5 complexed with GSPP and cis-indolyl vinyl isonitrile
ComponentsAmbP1
KeywordsTRANSFERASE / Prenyltransferase / AmbP1 / indole
Function / homologyAromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metabolic process / 3-[(Z)-2-isocyanoethenyl]-1H-indole / GERANYL S-THIOLODIPHOSPHATE / AmbP1
Function and homology information
Biological speciesFischerella ambigua UTEX 1903 (Cyanobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsAwakawa, T. / Nakashima, Y. / Mori, T. / Abe, I.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Molecular Insight into the Mg2+-Dependent Allosteric Control of Indole Prenylation by Aromatic Prenyltransferase AmbP1
Authors: Awakawa, T. / Mori, T. / Nakashima, Y. / Zhai, R. / Wong, C.P. / Hillwig, M.L. / Liu, X. / Abe, I.
History
DepositionJan 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AmbP1
B: AmbP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1877
Polymers70,3092
Non-polymers8775
Water41423
1
A: AmbP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5093
Polymers35,1551
Non-polymers3552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-11 kcal/mol
Surface area12920 Å2
MethodPISA
2
B: AmbP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6774
Polymers35,1551
Non-polymers5233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-8 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.257, 116.257, 49.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein AmbP1 / Aromatic prenyltransferase / Orf2-1-related aromatic prenyltransferase


Mass: 35154.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella ambigua UTEX 1903 (Cyanobacteria)
Gene: ambP1, famD2 / Production host: Escherichia coli (E. coli) / References: UniProt: V5TDZ4
#2: Chemical ChemComp-GST / GERANYL S-THIOLODIPHOSPHATE / S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE


Mass: 330.275 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O6P2S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-8XL / 3-[(Z)-2-isocyanoethenyl]-1H-indole


Mass: 168.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM MES (pH6.5), 0.2M MgCl2, 22% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→29.55 Å / Num. obs: 20537 / % possible obs: 99 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.1
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2459 / CC1/2: 0.757 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z43
Resolution: 2.601→28.196 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.24
RfactorNum. reflection% reflection
Rfree0.2714 2015 9.82 %
Rwork0.1906 --
obs0.1985 20524 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.601→28.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4647 0 53 23 4723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084828
X-RAY DIFFRACTIONf_angle_d1.0686560
X-RAY DIFFRACTIONf_dihedral_angle_d17.6712834
X-RAY DIFFRACTIONf_chiral_restr0.053696
X-RAY DIFFRACTIONf_plane_restr0.007857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6012-2.66620.33151430.2331289X-RAY DIFFRACTION99
2.6662-2.73820.34551440.22811317X-RAY DIFFRACTION99
2.7382-2.81870.32191410.22391302X-RAY DIFFRACTION98
2.8187-2.90960.30471410.22021315X-RAY DIFFRACTION99
2.9096-3.01350.31521430.2211295X-RAY DIFFRACTION99
3.0135-3.1340.27651430.2071298X-RAY DIFFRACTION98
3.134-3.27650.29521410.20871321X-RAY DIFFRACTION100
3.2765-3.44890.30041410.19741322X-RAY DIFFRACTION99
3.4489-3.66460.26991460.19551323X-RAY DIFFRACTION99
3.6646-3.94680.28491440.19651327X-RAY DIFFRACTION99
3.9468-4.34270.23991410.17881336X-RAY DIFFRACTION99
4.3427-4.96820.26191510.16581329X-RAY DIFFRACTION99
4.9682-6.24810.25591470.18051346X-RAY DIFFRACTION99
6.2481-28.19810.22511490.17021389X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.03661.36623.9856.6892.19023.7334-0.3680.61870.6276-0.3411-0.077-0.5777-1.0171.09840.45970.5314-0.1730.00790.61060.15360.405116.8004164.1926-2.8217
24.4741-2.1640.59385.6671-1.06535.97490.3242-0.0944-0.18390.1498-0.20280.0359-0.1970.3261-0.12170.3912-0.1678-0.02650.43340.05620.297513.5161154.75781.4763
33.98535.1849-1.07896.90520.78347.08950.6938-0.8924-0.57991.5136-0.9694-0.164-0.54160.81520.32140.7704-0.2082-0.10640.7290.05360.458913.6771149.394416.6995
41.5966-0.43631.17553.38190.77882.97710.0611-0.3263-0.0390.8649-0.0436-0.43680.14920.4617-0.02030.4628-0.094-0.03130.53670.03690.35713.5889141.17388.4882
53.61222.6166-0.23477.52424.89136.57670.0459-0.51-0.14070.288-0.1216-0.0589-0.03030.30940.06380.2825-0.0233-0.040.37870.05510.22955.9295131.9214.5126
62.7839-6.9978-0.57499.6246-0.1916.77280.08060.9304-0.4141-0.8879-0.32150.4825-0.5662-0.01310.12940.4591-0.0799-0.0820.386-0.02080.40551.8215131.9068-13.4108
78.74744.4881-1.74927.7845-5.71355.3094-0.00970.31190.1758-0.4319-0.0976-0.04610.26770.04760.11720.34050.0334-0.07180.4118-0.02080.24183.0914137.7176-2.0641
86.00147.77491.1489.30410.07124.2244-0.94080.8256-0.0496-1.35890.80030.0013-0.35670.58450.12360.4824-0.0080.02130.48760.01760.40759.6371151.8056-15.2789
97.95946.75392.22949.63881.05174.1226-0.12810.6334-0.0408-0.50880.0519-0.3086-0.1790.16330.15990.3948-0.0024-0.01580.33280.01060.22428.6624147.5847-7.6452
109.67262.78172.39787.59364.12818.06030.00210.3710.47140.525-0.04431.32090.4712-2.14180.2670.41220.01080.05081.33770.09520.67588.4916179.9158-20.4719
117.665-2.6035-1.42836.9006-2.67359.1656-0.4185-0.07080.1067-0.95131.38491.73810.2587-2.429-0.80560.4655-0.1042-0.13721.17610.28550.816212.1721179.3111-29.4621
124.59246.51183.10439.52976.00419.1606-0.24240.12450.54960.00540.19340.6234-0.3151-0.5970.02090.29130.0072-0.08450.62080.12640.514421.1113181.0378-20.2436
136.6589-1.84780.85115.09151.0483.10410.24680.981-0.1971-0.9303-0.01350.50250.12-0.4377-0.22390.5113-0.1253-0.13550.68130.07620.349526.4732172.4333-33.9024
142.8550.53431.98312.698-1.57667.8465-0.0123-0.0212-0.228-0.27130.0288-0.23020.4496-0.0444-0.04970.22160.01030.04210.23290.02120.383842.6305175.1963-22.0816
154.05540.1868-0.94623.00980.01128.118-0.0588-0.41060.2260.0702-0.02450.00890.0751-0.4020.0560.23070.01540.02420.32050.03790.416939.4825182.4257-15.2649
168.41583.3931-1.2513.50880.9506-0.07280.2468-0.44410.59950.6115-0.18080.7292-0.0207-0.8861-0.0610.4190.0090.0880.80450.07050.490923.0155179.6185-9.4361
175.01851.0217-0.36365.3064-1.34586.9361-0.0564-0.1749-0.2115-0.1842-0.0839-0.64620.2728-0.74440.14680.37160.07250.0520.51640.12540.486527.2135178.636-14.4966
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 127 )
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 172 )
6X-RAY DIFFRACTION6chain 'A' and (resid 173 through 206 )
7X-RAY DIFFRACTION7chain 'A' and (resid 207 through 230 )
8X-RAY DIFFRACTION8chain 'A' and (resid 231 through 268 )
9X-RAY DIFFRACTION9chain 'A' and (resid 269 through 289 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 18 )
11X-RAY DIFFRACTION11chain 'B' and (resid 19 through 40 )
12X-RAY DIFFRACTION12chain 'B' and (resid 41 through 63 )
13X-RAY DIFFRACTION13chain 'B' and (resid 64 through 122 )
14X-RAY DIFFRACTION14chain 'B' and (resid 123 through 190 )
15X-RAY DIFFRACTION15chain 'B' and (resid 191 through 220 )
16X-RAY DIFFRACTION16chain 'B' and (resid 221 through 260 )
17X-RAY DIFFRACTION17chain 'B' and (resid 261 through 291 )

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