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- PDB-5z44: Crystal structure of prenyltransferase AmbP1 complexed with GSPP -

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Basic information

Entry
Database: PDB / ID: 5z44
TitleCrystal structure of prenyltransferase AmbP1 complexed with GSPP
ComponentsAmbP1
KeywordsTRANSFERASE / Prenyltransferase / AmbP1 / indole
Function / homologyAromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metal ion binding / GERANYL S-THIOLODIPHOSPHATE / AmbP1
Function and homology information
Biological speciesFischerella ambigua UTEX 1903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.458 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.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)71,0196
Polymers70,3092
Non-polymers7094
Water73941
1
A: AmbP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5093
Polymers35,1551
Non-polymers3552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area13070 Å2
MethodPISA
2
B: AmbP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5093
Polymers35,1551
Non-polymers3552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-13 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.717, 115.717, 48.431
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-GST / GERANYL S-THIOLODIPHOSPHATE / S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE


Mass: 330.275 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O6P2S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM MES (pH6.5), 0.2M MgCl2, 22% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.458→48.4 Å / Num. obs: 23647 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Net I/σ(I): 17.3
Reflection shellResolution: 2.46→2.56 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2713 / CC1/2: 0.867 / % possible all: 99.8

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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: 2.458→44.676 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.07
RfactorNum. reflection% reflection
Rfree0.2455 1986 8.41 %
Rwork0.1855 --
obs0.1905 23619 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.458→44.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4676 0 40 41 4757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084843
X-RAY DIFFRACTIONf_angle_d0.9686582
X-RAY DIFFRACTIONf_dihedral_angle_d21.0921766
X-RAY DIFFRACTIONf_chiral_restr0.051700
X-RAY DIFFRACTIONf_plane_restr0.006862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4577-2.51920.40791430.28831551X-RAY DIFFRACTION99
2.5192-2.58730.37081400.26111519X-RAY DIFFRACTION100
2.5873-2.66340.29491420.24941541X-RAY DIFFRACTION100
2.6634-2.74940.31341360.22121528X-RAY DIFFRACTION99
2.7494-2.84760.27551470.20011560X-RAY DIFFRACTION100
2.8476-2.96160.25061400.20381517X-RAY DIFFRACTION100
2.9616-3.09640.28251400.20691534X-RAY DIFFRACTION100
3.0964-3.25960.27941420.20681545X-RAY DIFFRACTION100
3.2596-3.46370.24071440.18271536X-RAY DIFFRACTION100
3.4637-3.7310.22761430.18211552X-RAY DIFFRACTION99
3.731-4.10630.24261360.16921516X-RAY DIFFRACTION98
4.1063-4.69990.19941440.16161551X-RAY DIFFRACTION99
4.6999-5.91920.21531420.17511569X-RAY DIFFRACTION99
5.9192-44.68330.24531470.17141614X-RAY DIFFRACTION99
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)
18.00790.7777-0.37495.7403-0.20947.0684-0.468-0.142-0.07820.02170.06170.5342-0.4177-0.81130.35620.43960.1714-0.11010.6335-0.17650.540815.6446-44.8808-0.842
26.292-2.1035-0.17481.81270.64233.8785-0.5095-0.88020.6290.58810.095-0.0193-0.7085-0.37180.36360.67290.1596-0.1150.552-0.21890.556530.606-42.98729.5945
33.59210.0698-3.02772.2959-1.80678.6797-0.098-0.10550.03610.2052-0.1146-0.1482-0.4817-0.00310.22090.3043-0.0026-0.05680.271-0.07860.458443.2848-52.6569-1.9396
45.8523-2.90620.93573.6105-0.57853.48560.03930.63760.0665-0.4594-0.19360.0902-0.1278-0.35160.14430.4059-0.04230.00120.4677-0.10420.394429.0377-51.2961-11.4628
53.26971.10750.19286.2592-0.14654.52580.31820.4232-1.0386-0.49610.22450.08781.16070.2414-0.46790.79610.1463-0.27820.4783-0.15630.7099-2.5839-37.1083-28.2243
65.5116-0.47151.21195.19751.95286.38160.09290.3463-0.1516-0.120.1185-0.07840.29360.2065-0.21050.2327-0.0129-0.02230.21680.02160.224-1.8673-15.2117-21.2261
72.8345-0.5151.61858.2552-1.83687.05220.3578-0.3633-0.81270.42420.13050.2631.14830.1639-0.4210.46460.017-0.09110.41810.08180.4778-6.7614-28.9896-12.3151
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 190 )
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 290 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 127 )
6X-RAY DIFFRACTION6chain 'B' and (resid 128 through 190 )
7X-RAY DIFFRACTION7chain 'B' and (resid 191 through 290 )

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