PDB-5z45: Crystal structure of prenyltransferase AmbP1 pH6.5 complexed with...

ID or keywords:

Entry

Database: PDB / ID: 5z45

Title

Crystal structure of prenyltransferase AmbP1 pH6.5 complexed with GSPP and cis-indolyl vinyl isonitrile

Components

AmbP1

Keywords

TRANSFERASE / Prenyltransferase / AmbP1 / indole

Function / homology

Aromatic 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 species

Fischerella ambigua UTEX 1903 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.601 Å

Authors

Awakawa, T. / Nakashima, Y. / Mori, T. / Abe, I.

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.

History

Deposition	Jan 10, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 6, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 13, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 22, 2023	Group: 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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5z45.cif.gz	250.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5z45.ent.gz	203.3 KB	Display	PDB format
PDBx/mmJSON format	5z45.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5z45_validation.pdf.gz	891.7 KB	Display	wwPDB validaton report
Full document	5z45_full_validation.pdf.gz	899.7 KB	Display
Data in XML	5z45_validation.xml.gz	22.8 KB	Display
Data in CIF	5z45_validation.cif.gz	30.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z4/5z45 ftp://data.pdbj.org/pub/pdb/validation_reports/z4/5z45	HTTPS FTP

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Related structure data

Related structure data	5yk9C 5z43SC 5z44C 5z46C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5z46-2 5z44-2 5z44-1 1zb6-d 3ror-d 5z43-2 3qr3-2 5y84-2 5y7c-2 1y1n-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: AmbP1

B: AmbP1

hetero molecules

71.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: AmbP1

hetero molecules

defined by author&software
Evidence: gel filtration
35.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: AmbP1

hetero molecules

defined by author&software
35.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	116.257, 116.257, 49.687
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

#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: 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.: 23 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.49 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM MES (pH6.5), 0.2M MgCl2, 22% PEG8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 7, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.6→29.55 Å / Num. obs: 20537 / % possible obs: 99 % / Redundancy: 3.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.059 / Net I/σ(I): 14.1
Reflection shell	Resolution: 2.6→2.72 Å / R_merge(I) obs: 0.479 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2459 / CC_1/2: 0.757 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5Z43

5z43

Resolution: 2.601→28.196 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.24

	R_factor	Num. reflection	% reflection
R_free	0.2714	2015	9.82 %
R_work	0.1906	-	-
obs	0.1985	20524	98.98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.601→28.196 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4647	0	53	23	4723

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4828
X-RAY DIFFRACTION	f_angle_d	1.068	6560
X-RAY DIFFRACTION	f_dihedral_angle_d	17.671	2834
X-RAY DIFFRACTION	f_chiral_restr	0.053	696
X-RAY DIFFRACTION	f_plane_restr	0.007	857

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6012-2.6662	0.3315	143	0.233	1289	X-RAY DIFFRACTION	99
2.6662-2.7382	0.3455	144	0.2281	1317	X-RAY DIFFRACTION	99
2.7382-2.8187	0.3219	141	0.2239	1302	X-RAY DIFFRACTION	98
2.8187-2.9096	0.3047	141	0.2202	1315	X-RAY DIFFRACTION	99
2.9096-3.0135	0.3152	143	0.221	1295	X-RAY DIFFRACTION	99
3.0135-3.134	0.2765	143	0.207	1298	X-RAY DIFFRACTION	98
3.134-3.2765	0.2952	141	0.2087	1321	X-RAY DIFFRACTION	100
3.2765-3.4489	0.3004	141	0.1974	1322	X-RAY DIFFRACTION	99
3.4489-3.6646	0.2699	146	0.1955	1323	X-RAY DIFFRACTION	99
3.6646-3.9468	0.2849	144	0.1965	1327	X-RAY DIFFRACTION	99
3.9468-4.3427	0.2399	141	0.1788	1336	X-RAY DIFFRACTION	99
4.3427-4.9682	0.2619	151	0.1658	1329	X-RAY DIFFRACTION	99
4.9682-6.2481	0.2559	147	0.1805	1346	X-RAY DIFFRACTION	99
6.2481-28.1981	0.2251	149	0.1702	1389	X-RAY DIFFRACTION	99

Refinement TLS params.

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

ID	L11 (°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)
1	8.0366	1.3662	3.985	6.689	2.1902	3.7334	-0.368	0.6187	0.6276	-0.3411	-0.077	-0.5777	-1.017	1.0984	0.4597	0.5314	-0.173	0.0079	0.6106	0.1536	0.4051	16.8004	164.1926	-2.8217
2	4.4741	-2.164	0.5938	5.6671	-1.0653	5.9749	0.3242	-0.0944	-0.1839	0.1498	-0.2028	0.0359	-0.197	0.3261	-0.1217	0.3912	-0.1678	-0.0265	0.4334	0.0562	0.2975	13.5161	154.7578	1.4763
3	3.9853	5.1849	-1.0789	6.9052	0.7834	7.0895	0.6938	-0.8924	-0.5799	1.5136	-0.9694	-0.164	-0.5416	0.8152	0.3214	0.7704	-0.2082	-0.1064	0.729	0.0536	0.4589	13.6771	149.3944	16.6995
4	1.5966	-0.4363	1.1755	3.3819	0.7788	2.9771	0.0611	-0.3263	-0.039	0.8649	-0.0436	-0.4368	0.1492	0.4617	-0.0203	0.4628	-0.094	-0.0313	0.5367	0.0369	0.357	13.5889	141.1738	8.4882
5	3.6122	2.6166	-0.2347	7.5242	4.8913	6.5767	0.0459	-0.51	-0.1407	0.288	-0.1216	-0.0589	-0.0303	0.3094	0.0638	0.2825	-0.0233	-0.04	0.3787	0.0551	0.2295	5.9295	131.921	4.5126
6	2.7839	-6.9978	-0.5749	9.6246	-0.191	6.7728	0.0806	0.9304	-0.4141	-0.8879	-0.3215	0.4825	-0.5662	-0.0131	0.1294	0.4591	-0.0799	-0.082	0.386	-0.0208	0.4055	1.8215	131.9068	-13.4108
7	8.7474	4.4881	-1.7492	7.7845	-5.7135	5.3094	-0.0097	0.3119	0.1758	-0.4319	-0.0976	-0.0461	0.2677	0.0476	0.1172	0.3405	0.0334	-0.0718	0.4118	-0.0208	0.2418	3.0914	137.7176	-2.0641
8	6.0014	7.7749	1.148	9.3041	0.0712	4.2244	-0.9408	0.8256	-0.0496	-1.3589	0.8003	0.0013	-0.3567	0.5845	0.1236	0.4824	-0.008	0.0213	0.4876	0.0176	0.4075	9.6371	151.8056	-15.2789
9	7.9594	6.7539	2.2294	9.6388	1.0517	4.1226	-0.1281	0.6334	-0.0408	-0.5088	0.0519	-0.3086	-0.179	0.1633	0.1599	0.3948	-0.0024	-0.0158	0.3328	0.0106	0.2242	8.6624	147.5847	-7.6452
10	9.6726	2.7817	2.3978	7.5936	4.1281	8.0603	0.0021	0.371	0.4714	0.525	-0.0443	1.3209	0.4712	-2.1418	0.267	0.4122	0.0108	0.0508	1.3377	0.0952	0.6758	8.4916	179.9158	-20.4719
11	7.665	-2.6035	-1.4283	6.9006	-2.6735	9.1656	-0.4185	-0.0708	0.1067	-0.9513	1.3849	1.7381	0.2587	-2.429	-0.8056	0.4655	-0.1042	-0.1372	1.1761	0.2855	0.8162	12.1721	179.3111	-29.4621
12	4.5924	6.5118	3.1043	9.5297	6.0041	9.1606	-0.2424	0.1245	0.5496	0.0054	0.1934	0.6234	-0.3151	-0.597	0.0209	0.2913	0.0072	-0.0845	0.6208	0.1264	0.5144	21.1113	181.0378	-20.2436
13	6.6589	-1.8478	0.8511	5.0915	1.048	3.1041	0.2468	0.981	-0.1971	-0.9303	-0.0135	0.5025	0.12	-0.4377	-0.2239	0.5113	-0.1253	-0.1355	0.6813	0.0762	0.3495	26.4732	172.4333	-33.9024
14	2.855	0.5343	1.9831	2.698	-1.5766	7.8465	-0.0123	-0.0212	-0.228	-0.2713	0.0288	-0.2302	0.4496	-0.0444	-0.0497	0.2216	0.0103	0.0421	0.2329	0.0212	0.3838	42.6305	175.1963	-22.0816
15	4.0554	0.1868	-0.9462	3.0098	0.0112	8.118	-0.0588	-0.4106	0.226	0.0702	-0.0245	0.0089	0.0751	-0.402	0.056	0.2307	0.0154	0.0242	0.3205	0.0379	0.4169	39.4825	182.4257	-15.2649
16	8.4158	3.3931	-1.251	3.5088	0.9506	-0.0728	0.2468	-0.4441	0.5995	0.6115	-0.1808	0.7292	-0.0207	-0.8861	-0.061	0.419	0.009	0.088	0.8045	0.0705	0.4909	23.0155	179.6185	-9.4361
17	5.0185	1.0217	-0.3636	5.3064	-1.3458	6.9361	-0.0564	-0.1749	-0.2115	-0.1842	-0.0839	-0.6462	0.2728	-0.7444	0.1468	0.3716	0.0725	0.052	0.5164	0.1254	0.4865	27.2135	178.636	-14.4966

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 70 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 71 through 87 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 88 through 127 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 128 through 172 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 173 through 206 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 207 through 230 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 231 through 268 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 269 through 289 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2 through 18 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 19 through 40 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 41 through 63 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 64 through 122 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 123 through 190 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 191 through 220 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 221 through 260 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 261 through 291 )

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