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- PDB-5y72: DMSPP Bound AmbP3 -

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Basic information

Entry
Database: PDB / ID: 5y72
TitleDMSPP Bound AmbP3
ComponentsAmbP3
KeywordsTRANSFERASE / Prenyltransferase
Function / homologyhapalindole G dimethylallyltransferase / Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / DIMETHYLALLYL S-THIOLODIPHOSPHATE / Hapalindole dimethylallyltransferase
Function and homology information
Biological speciesFischerella ambigua UTEX 1903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWong, C.P. / Awakawa, T. / Nakashima, Y.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Two Distinct Substrate Binding Modes for the Normal and Reverse Prenylation of Hapalindoles by the Prenyltransferase AmbP3
Authors: Wong, C.P. / Awakawa, T. / Nakashima, Y. / Mori, T. / Zhu, Q. / Liu, X. / Abe, I.
History
DepositionAug 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 2.0Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AmbP3
B: AmbP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6134
Polymers76,0882
Non-polymers5242
Water7,692427
1
A: AmbP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3062
Polymers38,0441
Non-polymers2621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-3 kcal/mol
Surface area11910 Å2
MethodPISA
2
B: AmbP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3062
Polymers38,0441
Non-polymers2621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-3 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.394, 55.080, 77.668
Angle α, β, γ (deg.)105.41, 106.02, 98.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein AmbP3


Mass: 38044.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella ambigua UTEX 1903 (bacteria)
Gene: ambP3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: V5TDY7
#2: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O6P2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, PEG 8000, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→44 Å / Num. obs: 79907 / % possible obs: 96.1 % / Redundancy: 3.7 % / Net I/σ(I): 13
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.506 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata processing
Aimlessdata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y4G

5y4g


Resolution: 1.65→43.953 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23
RfactorNum. reflection% reflection
Rfree0.2033 3948 4.94 %
Rwork0.1814 --
obs0.1825 79907 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→43.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4557 0 28 427 5012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064742
X-RAY DIFFRACTIONf_angle_d0.8736484
X-RAY DIFFRACTIONf_dihedral_angle_d7.2173751
X-RAY DIFFRACTIONf_chiral_restr0.053718
X-RAY DIFFRACTIONf_plane_restr0.006839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.67010.2991240.26472675X-RAY DIFFRACTION94
1.6701-1.69130.28481370.2552618X-RAY DIFFRACTION94
1.6913-1.71350.25621590.2262729X-RAY DIFFRACTION94
1.7135-1.7370.27641350.22182585X-RAY DIFFRACTION94
1.737-1.76180.2451470.21112664X-RAY DIFFRACTION95
1.7618-1.78810.25691330.20352755X-RAY DIFFRACTION95
1.7881-1.81610.24861100.22052633X-RAY DIFFRACTION95
1.8161-1.84580.27481260.21282748X-RAY DIFFRACTION95
1.8458-1.87770.23641530.21832666X-RAY DIFFRACTION95
1.8777-1.91180.23581290.20692730X-RAY DIFFRACTION95
1.9118-1.94860.25541580.20142653X-RAY DIFFRACTION96
1.9486-1.98830.21141830.19982645X-RAY DIFFRACTION96
1.9883-2.03160.24141360.19652732X-RAY DIFFRACTION96
2.0316-2.07880.20581260.18822729X-RAY DIFFRACTION96
2.0788-2.13080.24951230.20022758X-RAY DIFFRACTION96
2.1308-2.18840.23781320.18922710X-RAY DIFFRACTION96
2.1884-2.25280.26231390.19012708X-RAY DIFFRACTION96
2.2528-2.32550.22471600.19562714X-RAY DIFFRACTION97
2.3255-2.40860.21831600.18932741X-RAY DIFFRACTION97
2.4086-2.50510.24261420.18862701X-RAY DIFFRACTION96
2.5051-2.61910.22761350.19692736X-RAY DIFFRACTION96
2.6191-2.75710.2421390.19552713X-RAY DIFFRACTION96
2.7571-2.92980.20751290.19452753X-RAY DIFFRACTION97
2.9298-3.1560.2071470.19022779X-RAY DIFFRACTION98
3.156-3.47350.18661410.17722774X-RAY DIFFRACTION98
3.4735-3.97580.18271510.14932761X-RAY DIFFRACTION98
3.9758-5.0080.13651520.13482782X-RAY DIFFRACTION99
5.008-43.96830.15111420.16532767X-RAY DIFFRACTION98

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