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- PDB-5z46: Crystal structure of prenyltransferase AmbP1 pH8 complexed with G... -

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Basic information

Entry
Database: PDB / ID: 5z46
TitleCrystal structure of prenyltransferase AmbP1 pH8 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 / metal ion binding / 3-[(Z)-2-isocyanoethenyl]-1H-indole / GERANYL S-THIOLODIPHOSPHATE / AmbP1
Function and homology information
Biological speciesFischerella ambigua UTEX 1903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 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
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AmbP1
B: AmbP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9058
Polymers70,3092
Non-polymers5966
Water3,207178
1
A: AmbP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2033
Polymers35,1551
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area13060 Å2
MethodPISA
2
B: AmbP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7025
Polymers35,1551
Non-polymers5474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-8 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.267, 117.267, 49.324
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 (bacteria)
Gene: ambP1, famD2 / Production host: Escherichia coli (E. coli) / References: UniProt: V5TDZ4
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GST / GERANYL S-THIOLODIPHOSPHATE / S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE


Mass: 330.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O6P2S
#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


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM MES, 0.2M MgCl2, 22% PEG8000, ligands were soaked at pH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.999→49.3 Å / Num. obs: 45762 / % possible obs: 99.7 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 19.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 7 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3359 / % possible all: 98.1

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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

5z43


Resolution: 1.999→37.745 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.33
RfactorNum. reflection% reflection
Rfree0.2352 2016 4.41 %
Rwork0.1889 --
obs0.1909 45733 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.999→37.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4687 0 36 178 4901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074857
X-RAY DIFFRACTIONf_angle_d0.9116602
X-RAY DIFFRACTIONf_dihedral_angle_d15.8392858
X-RAY DIFFRACTIONf_chiral_restr0.055702
X-RAY DIFFRACTIONf_plane_restr0.007866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9992-2.04910.31771430.25153096X-RAY DIFFRACTION98
2.0491-2.10450.29871370.22693057X-RAY DIFFRACTION100
2.1045-2.16650.25611420.21793121X-RAY DIFFRACTION100
2.1665-2.23640.28251430.21323096X-RAY DIFFRACTION100
2.2364-2.31630.23931430.20973086X-RAY DIFFRACTION100
2.3163-2.4090.25791430.21053102X-RAY DIFFRACTION100
2.409-2.51860.26491420.20863128X-RAY DIFFRACTION100
2.5186-2.65140.29641440.21773115X-RAY DIFFRACTION100
2.6514-2.81750.29661400.20923121X-RAY DIFFRACTION100
2.8175-3.03490.241470.2073122X-RAY DIFFRACTION100
3.0349-3.34020.25831480.19593132X-RAY DIFFRACTION100
3.3402-3.82310.21051430.17573146X-RAY DIFFRACTION100
3.8231-4.81510.1791440.16263155X-RAY DIFFRACTION100
4.8151-37.75150.22761570.17263240X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.1473-2.1456-0.42157.71810.68938.83260.2580.0674-0.3413-0.0156-0.35520.10050.5557-0.22740.07690.3203-0.10210.00280.2482-0.0510.273145.652316.223610.7398
21.4615-0.1167-0.47487.49040.17721.86140.0869-0.3141-0.01760.7011-0.22630.42880.0936-0.41060.13120.362-0.08840.07810.452-0.06260.301943.49830.873221.5598
31.62331.09220.0764.92930.41152.1222-0.04250.1938-0.0985-0.418-0.0125-0.01110.2116-0.10380.06170.23840.00810.02090.2911-0.00280.223952.623235.52294.6635
48.2824-3.0771-2.73312.0605-2.42029.22240.08160.2105-0.64210.27720.0432-1.69970.12671.88410.02950.33220.101-0.03970.9807-0.22470.766348.9886-8.1007-10.081
58.7208-7.1629-1.63357.04221.64947.63980.11970.7910.1237-0.6310.0493-1.4109-0.40341.8-0.21240.3169-0.0980.09660.9481-0.19330.654446.6637-2.1423-19.6308
69.00955.8923-3.49492.2076-7.25569.7709-0.1187-0.3068-1.2207-0.3614-0.0251-0.21020.50340.59320.12360.28590.06910.03210.4547-0.10740.519337.3472-6.8033-9.0819
79.6454-3.5583-0.82356.3558-1.14884.58480.03110.7862-0.2976-0.77450.1862-0.2091-0.12110.3802-0.2320.3721-0.14160.08950.4498-0.09480.326331.89821.2562-23.272
88.11452.4753-3.22354.4128-0.63387.09820.09070.25470.1817-0.34360.15770.0365-0.42590.17-0.24650.2206-0.0024-0.00880.1945-0.01530.190616.9149-0.2647-16.1807
94.1286-1.6031-1.31226.32542.15263.3298-0.0209-0.5665-0.24770.53940.2863-0.29270.38520.3526-0.31810.2720.0165-0.03530.29280.03240.292216.3362-5.2414-2.3919
103.77460.62251.32683.50121.46645.12170.0145-0.5211-0.36040.36590.0348-0.52370.13730.8986-0.11540.30850.0574-0.03870.5661-0.0040.408233.429-4.5937-0.7449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 127 )
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 290 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 23 )
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 40 )
6X-RAY DIFFRACTION6chain 'B' and (resid 41 through 63 )
7X-RAY DIFFRACTION7chain 'B' and (resid 64 through 122 )
8X-RAY DIFFRACTION8chain 'B' and (resid 123 through 172 )
9X-RAY DIFFRACTION9chain 'B' and (resid 173 through 220 )
10X-RAY DIFFRACTION10chain 'B' and (resid 221 through 292 )

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