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- PDB-5yk9: Crystal structure of selenomethionine-labelled indole prenyltrans... -

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Basic information

Entry
Database: PDB / ID: 5yk9
TitleCrystal structure of selenomethionine-labelled indole prenyltransferase AmbP1
ComponentsAmbP1
KeywordsTRANSFERASE / cyanobacteria
Function / homologyAromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metal ion binding / AmbP1
Function and homology information
Biological speciesFischerella ambigua UTEX 1903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.001 Å
AuthorsAwakawa, T. / Nakashima, Y. / Liu, X. / Abe, I.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPSJP15H01836 Japan
JSPSJP16H06443 Japan
JSPSJP17H04763 Japan
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Crystal structure of selenomethionine-labelled indole prenyltransferase AmbP1 at 3.00 Angstroms resolution.
Authors: Awakawa, T. / Nakashima, Y. / Liu, X. / Abe, I.
History
DepositionOct 12, 2017Deposition 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
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: AmbP1
B: AmbP1


Theoretical massNumber of molelcules
Total (without water)70,6852
Polymers70,6852
Non-polymers00
Water00
1
A: AmbP1


Theoretical massNumber of molelcules
Total (without water)35,3421
Polymers35,3421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AmbP1


Theoretical massNumber of molelcules
Total (without water)35,3421
Polymers35,3421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.259, 142.350, 157.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35342.262 Da / Num. of mol.: 2 / Fragment: UNP residues 2-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella ambigua UTEX 1903 (bacteria)
Gene: ambP1, famD2 / Production host: Escherichia coli (E. coli) / References: UniProt: V5TDZ4
Has protein modificationY

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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: 3.83 Å3/Da / Density % sol: 67.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG8000, MES, magnesium chloride

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 3→49.16 Å / Num. obs: 21912 / % possible obs: 99.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 17.6
Reflection shellResolution: 3→3.18 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.513 / Num. unique obs: 2545 / Rpim(I) all: 0.213 / Rrim(I) all: 0.556 / Rsym value: 0.513 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
SHELXDEphasing
Aimlessdata scaling
XDSdata processing
RefinementMethod to determine structure: SAD / Resolution: 3.001→49.16 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 26.51
RfactorNum. reflection% reflection
Rfree0.2647 1122 5.14 %
Rwork0.2387 --
obs0.2401 21844 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.001→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4474 0 0 0 4474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014599
X-RAY DIFFRACTIONf_angle_d1.176282
X-RAY DIFFRACTIONf_dihedral_angle_d4.8382689
X-RAY DIFFRACTIONf_chiral_restr0.068695
X-RAY DIFFRACTIONf_plane_restr0.007834
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0006-3.1371133254299
3.1371-3.3024109254699
3.3024-3.5093148252099
3.5093-3.7802154254299
3.7802-4.16040.21711330.2148258799
4.1604-4.7620.22731440.2143259799
4.762-5.99791412638100
5.9979160275099

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