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- PDB-5y4g: Apo Structure of AmbP3 -

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Basic information

Entry
Database: PDB / ID: 5y4g
TitleApo Structure of AmbP3
ComponentsAmbP3
KeywordsTRANSFERASE / Prenyltransferase
Function / homologyhapalindole G dimethylallyltransferase / Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / Hapalindole dimethylallyltransferase
Function and homology information
Biological speciesFischerella ambigua UTEX 1903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AmbP3
B: AmbP3


Theoretical massNumber of molelcules
Total (without water)76,0882
Polymers76,0882
Non-polymers00
Water7,242402
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, homology, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-0 kcal/mol
Surface area23660 Å2
Unit cell
Length a, b, c (Å)46.150, 55.781, 77.841
Angle α, β, γ (deg.)105.28, 106.59, 99.32
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 (E. coli) / References: UniProt: V5TDY7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, magnesium chloride, PEG 8000

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→43.9 Å / Num. obs: 45559 / % possible obs: 97.5 % / Redundancy: 3.5 % / Net I/σ(I): 20.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.159 / % 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 / Resolution: 2→31.987 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.16
RfactorNum. reflection% reflection
Rfree0.2427 2004 4.4 %
Rwork0.1987 --
obs0.2006 45559 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→31.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 0 0 402 5044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074797
X-RAY DIFFRACTIONf_angle_d0.886541
X-RAY DIFFRACTIONf_dihedral_angle_d6.9583876
X-RAY DIFFRACTIONf_chiral_restr0.055718
X-RAY DIFFRACTIONf_plane_restr0.007854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05010.27391390.21642998X-RAY DIFFRACTION95
2.0501-2.10560.28431410.23383074X-RAY DIFFRACTION95
2.1056-2.16750.24731460.2073100X-RAY DIFFRACTION97
2.1675-2.23740.27821420.21093106X-RAY DIFFRACTION97
2.2374-2.31740.29511520.23893037X-RAY DIFFRACTION95
2.3174-2.41010.24541250.20113109X-RAY DIFFRACTION97
2.4101-2.51980.26761510.21453126X-RAY DIFFRACTION98
2.5198-2.65260.29321430.22263131X-RAY DIFFRACTION98
2.6526-2.81870.26431420.21583116X-RAY DIFFRACTION98
2.8187-3.03620.30341420.22253151X-RAY DIFFRACTION98
3.0362-3.34140.26351430.21063143X-RAY DIFFRACTION98
3.3414-3.82420.21421420.18363150X-RAY DIFFRACTION98
3.8242-4.81550.19191470.15793153X-RAY DIFFRACTION99
4.8155-31.99110.18771490.17613161X-RAY DIFFRACTION99

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