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- PDB-5y7c: Hapalindole A and DMSPP Bound AmbP3 -

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Basic information

Entry
Database: PDB / ID: 5y7c
TitleHapalindole A and DMSPP Bound AmbP3
ComponentsAmbP3
KeywordsTRANSFERASE / Prenyltransferase
Function / homologyhapalindole G dimethylallyltransferase / Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / Hapalindole A / DIMETHYLALLYL S-THIOLODIPHOSPHATE / Hapalindole dimethylallyltransferase
Function and homology information
Biological speciesFischerella ambigua UTEX 1903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 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 2.0Oct 16, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AmbP3
B: AmbP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2906
Polymers76,0882
Non-polymers1,2024
Water4,216234
1
A: AmbP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6453
Polymers38,0441
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-2 kcal/mol
Surface area11450 Å2
MethodPISA
2
B: AmbP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6453
Polymers38,0441
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-1 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.465, 54.724, 77.991
Angle α, β, γ (deg.)105.23, 106.60, 98.51
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: Chemical ChemComp-8O0 / Hapalindole A


Mass: 338.874 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23ClN2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 47.41 %
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-17A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→44.2 Å / Num. obs: 45052 / % possible obs: 97.2 % / Redundancy: 3.5 % / Net I/σ(I): 8.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.476 / % possible all: 95.4

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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: 2.003→37.837 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.49
RfactorNum. reflection% reflection
Rfree0.2427 2224 4.94 %
Rwork0.1953 --
obs0.1977 45052 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.003→37.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 76 234 4824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074731
X-RAY DIFFRACTIONf_angle_d0.8416480
X-RAY DIFFRACTIONf_dihedral_angle_d7.8453188
X-RAY DIFFRACTIONf_chiral_restr0.05721
X-RAY DIFFRACTIONf_plane_restr0.005827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0031-2.04660.32031410.25832630X-RAY DIFFRACTION95
2.0466-2.09430.25661470.23832638X-RAY DIFFRACTION97
2.0943-2.14660.26271530.22042611X-RAY DIFFRACTION96
2.1466-2.20470.27181580.2172713X-RAY DIFFRACTION97
2.2047-2.26950.28981360.2122609X-RAY DIFFRACTION97
2.2695-2.34280.28531400.2212711X-RAY DIFFRACTION97
2.3428-2.42650.31161670.21272642X-RAY DIFFRACTION97
2.4265-2.52360.25381460.21132678X-RAY DIFFRACTION97
2.5236-2.63840.2922880.21382738X-RAY DIFFRACTION98
2.6384-2.77750.27431080.21272758X-RAY DIFFRACTION98
2.7775-2.95150.26991400.21382672X-RAY DIFFRACTION98
2.9515-3.17920.23971290.20762707X-RAY DIFFRACTION98
3.1792-3.4990.25891400.19592685X-RAY DIFFRACTION98
3.499-4.00480.21361260.17222682X-RAY DIFFRACTION97
4.0048-5.04370.18751430.1562698X-RAY DIFFRACTION97
5.0437-37.8440.20861620.17762656X-RAY DIFFRACTION97

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