PDB-5a3k: Chorismatase mechanisms reveal fundamentally different types of r...

ID or keywords:

Entry

Database: PDB / ID: 5a3k

Title

Chorismatase mechanisms reveal fundamentally different types of reaction in a single conserved protein fold

Components

PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE

Keywords

OXIDOREDUCTASE

Function / homology

3-hydroxybenzoate synthase / Chorismatase, FkbO/Hyg5 family / oxo-acid-lyase activity / RutC-like superfamily /

3-HYDROXYBENZOIC ACID / 3-hydroxybenzoate synthase

Function and homology information

Biological species

STREPTOMYCES HYGROSCOPICUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.753 Å

Authors

Hubrich, F. / Juneja, P. / Mueller, M. / Diederichs, K. / Welte, W. / Andexer, J.N.

Citation

Journal: J.Am.Chem.Soc. / Year: 2015
Title: Chorismatase Mechanisms Reveal Fundamentally Different Types of Reaction in a Single Conserved Protein Fold.
Authors: Hubrich, F. / Juneja, P. / Meuller, M. / Diederichs, K. / Welte, W. / Andexer, J.N.

History

Deposition	Jun 1, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 19, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2015	Group: Database references
Revision 1.2	Aug 23, 2017	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3	May 22, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5a3k.cif.gz	402.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5a3k.ent.gz	336.7 KB	Display	PDB format
PDBx/mmJSON format	5a3k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a3/5a3k ftp://data.pdbj.org/pub/pdb/validation_reports/a3/5a3k	HTTPS FTP

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Related structure data

Related structure data	5ag3SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1t1g-d 5ag3-1 1vit-1 1hag-d 1t1i-d 1is9-d 5mt2-d 1ga1-d 6trh-4 3vh0-3 Search similar-shape structures by Omokage search (details) 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

Related structure data

5ag3SC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (1)

Deposited unit

A: PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE

B: PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE

C: PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE

hetero molecules

113 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE

hetero molecules

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

2

B: PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE

hetero molecules

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

3

C: PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.772, 127.214, 81.890
Angle α, β, γ (deg.)	90.00, 104.85, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE / HYG5-CHORISMATASE Mass: 37453.980 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES HYGROSCOPICUS (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RP-PL1SL2 / References: UniProt: O30478
#2: Chemical	ChemComp-3HB / 3-HYDROXYBENZOIC ACID / 3-Hydroxybenzoic acid Mass: 138.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₇H₆O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.8 Å³/Da / Density % sol: 56.1 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop / pH: 6.5 Details: C327S HYG5 WAS CONCENTRATED TO 2MG/ML AND AFTERWARDS SUPPLEMENTED WITH 15 MM 3-HBA. C327S WAS CRYSTALLISED USING THE HANGING-DROP DIFFUSION METHOD IN 0.1 M MES PH6.5-7,0.2 M AMMONIUM SULPHATE,PH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2014
Radiation	Monochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99987 Å / Relative weight: 1
Reflection	Resolution: 2.75→44.27 Å / Num. obs: 30925 / % possible obs: 94.5 % / Observed criterion σ(I): 0.64 / Redundancy: 3.2 % / B_iso Wilson estimate: 57.52 Å² / R_merge(I) obs: 0.28 / Net I/σ(I): 5.15
Reflection shell	Resolution: 2.75→2.85 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.2 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AG3

5ag3

Resolution: 2.753→44.266 Å / SU ML: 0.56 / σ(F): 1.1 / Phase error: 35.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3019	2842	4.8 %
R_work	0.2489	-	-
obs	0.2515	30908	91.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.753→44.266 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7766	0	45	92	7903

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7997
X-RAY DIFFRACTION	f_angle_d	0.723	10864
X-RAY DIFFRACTION	f_dihedral_angle_d	10.45	2875
X-RAY DIFFRACTION	f_chiral_restr	0.026	1147
X-RAY DIFFRACTION	f_plane_restr	0.003	1459

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 (%)
2.7529-2.8004	0.3985	118	0.3691	2928	X-RAY DIFFRACTION	95
2.8004-2.8513	0.407	141	0.362	2945	X-RAY DIFFRACTION	96
2.8513-2.9061	0.4278	170	0.3523	2932	X-RAY DIFFRACTION	94
2.9061-2.9655	0.367	127	0.3377	2905	X-RAY DIFFRACTION	96
2.9655-3.0299	0.3665	138	0.3178	3027	X-RAY DIFFRACTION	97
3.0299-3.1004	0.3614	157	0.3048	2950	X-RAY DIFFRACTION	98
3.1004-3.1779	0.3854	157	0.2984	2990	X-RAY DIFFRACTION	97
3.1779-3.2638	0.3661	128	0.2973	2938	X-RAY DIFFRACTION	97
3.2638-3.3598	0.3215	173	0.2707	2976	X-RAY DIFFRACTION	97
3.3598-3.4682	0.3208	148	0.2568	2925	X-RAY DIFFRACTION	95
3.4682-3.5921	0.3451	144	0.28	2851	X-RAY DIFFRACTION	92
3.5921-3.7359	0.4335	45	0.4257	1027	X-RAY DIFFRACTION	33
3.7359-3.9058	0.4545	154	0.3694	2679	X-RAY DIFFRACTION	87
3.9058-4.1116	0.3856	139	0.2734	2387	X-RAY DIFFRACTION	80
4.1116-4.369	0.2237	153	0.2081	2908	X-RAY DIFFRACTION	96
4.369-4.706	0.2608	133	0.1891	2879	X-RAY DIFFRACTION	92
4.706-5.1789	0.2564	186	0.183	2884	X-RAY DIFFRACTION	96
5.1789-5.9268	0.259	141	0.1974	2991	X-RAY DIFFRACTION	97
5.9268-7.4613	0.2213	135	0.2041	2937	X-RAY DIFFRACTION	95
7.4613-44.2713	0.197	155	0.1691	2950	X-RAY DIFFRACTION	96

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	1.6706	-0.0819	-0.6789	2.279	-3.473	7.2112	-0.5735	0.0922	0.5858	-0.3651	0.0471	0.1163	-0.1372	-1.3014	0.2048	0.3975	0.0183	-0.1247	0.5523	0.1846	0.7689	2.9136	17.9783	22.2176
2	2.4896	0.3931	0.8392	5.1863	-1.3672	3.2209	0.0429	0.1273	0.3948	-0.4194	0.0483	0.2448	0.0142	-0.1322	-0.1231	0.3393	0.0579	0.0098	0.3275	-0.0982	0.5822	17.0079	13.9391	19.6548
3	2.6558	-1.5639	1.6283	0.9528	0.6305	3.5143	-0.0704	0.0772	0.0568	0.1272	-0.2239	0.0891	-0.417	0.1839	0.3635	0.4005	-0.0715	-0.0739	0.4374	0.0554	0.9033	25.6488	19.3016	32.3163
4	5.7367	0.8323	1.418	6.6296	-1.8681	3.0704	-0.0349	-0.2409	0.3921	0.3514	0.2372	-0.2994	-0.2591	-0.1288	-0.155	0.3862	0.0202	0.0544	0.2756	-0.0741	0.2892	11.4065	19.9439	42.4263
5	9.5857	-2.9855	-6.0932	4.1258	-0.6137	6.8789	0.2421	-0.1363	-0.131	0.3804	0.1733	-0.1335	-0.2531	0.8939	-0.4757	0.4801	-0.0085	-0.1394	0.5222	-0.0554	0.4459	60.8034	52.6333	41.6419
6	0.332	0.0974	-1.3043	0.9637	-2.5535	8.558	-0.1972	-0.1329	-0.1963	0.4305	-0.6512	-0.1029	-0.8386	0.5365	0.8554	0.5395	-0.0322	-0.1061	0.3568	-0.0548	0.8756	52.4161	58.3606	51.3361
7	6.0199	-1.3423	-3.5523	1.0432	0.3917	6.2215	0.3015	0.6791	0.1808	-0.2584	-0.4824	0.4865	-0.6359	-0.1956	0.1371	0.5351	0.0154	-0.0888	0.2765	-0.0569	0.6697	47.1512	54.9704	40.2925
8	4.129	-2.2462	-3.9582	5.3335	-0.1515	5.0381	0.1923	1.2221	0.4053	-0.8215	-0.6286	0.9711	0.6027	-1.3136	0.1861	0.4612	-0.1136	-0.1157	0.7664	-0.0446	0.7594	35.6521	52.4588	39.2122
9	2.4617	0.1631	-2.1444	1.3515	-0.8606	2.9494	0.316	0.0527	-0.2457	0.0077	-0.0413	0.4182	-0.1495	-0.8354	-0.3078	0.3807	0.0663	-0.085	0.5598	-0.0108	0.9035	39.6335	46.3555	50.8902
10	2.0016	-1.5175	0.0666	5.0092	0.0695	5.6726	-0.1818	0.0766	0.103	-0.4373	-0.9792	1.0591	-0.1542	-0.6838	0.9461	0.4922	0.0195	-0.2467	0.5446	0.0083	0.9988	35.9983	43.6338	46.4778
11	4.2664	-1.8747	-2.5408	8.1799	1.2829	3.613	0.469	0.8565	-0.0093	-1.6367	0.4342	0.1083	-0.0111	-1.4168	0.3877	0.3027	0.3306	-0.0771	0.5816	-0.0116	0.8288	45.6582	44.1879	37.2812
12	1.4965	-0.1991	-0.7291	3.9707	-0.7026	6.1666	0.0571	0.0888	-1.3803	0.2453	0.0456	1.1614	1.0217	-0.5139	-0.092	0.4503	-0.0938	-0.0156	0.3633	0.0118	1.0796	36.5957	32.2965	48.8282
13	2.4256	0.2684	-3.5832	4.2366	-3.99	8.0253	0.3104	0.342	-0.4115	-0.1916	0.03	0.6869	0.3043	-0.5096	-0.2943	0.4066	0.1147	-0.2464	0.6268	-0.2067	0.7738	49.7239	33.0424	44.6971
14	2.4005	-2.2809	-1.7662	3.5119	2.1472	5.5109	0.0788	-0.1821	-0.7684	0.0788	0.0053	0.0568	0.4422	0.8518	-0.1058	0.4567	0.0062	-0.2255	0.5943	-0.0024	0.9716	56.3913	32.706	52.122
15	2.3108	-1.917	-0.8345	1.8821	-0.0266	1.7506	0.1239	-0.0402	-0.8847	-0.0158	-0.1846	0.5313	0.0917	-0.2736	0.1665	0.4303	-0.0818	-0.1664	0.3821	-0.0088	0.6377	50.9271	39.2916	55.6303
16	4.1804	-0.971	-5.2462	5.5816	0.2952	6.6124	-0.7102	0.2678	0.7014	0.001	-0.7481	-0.1909	0.7951	0.1546	0.7829	0.6164	-0.0377	-0.0657	0.7779	0.0257	0.668	40.6729	53.128	-3.4294
17	7.7221	-1.2469	1.9357	5.789	-0.3691	1.078	0.1293	0.7027	-0.7866	-1.4227	0.0838	0.5165	0.1838	0.1583	-0.1186	0.5542	-0.0779	0.0398	0.2926	-0.0711	0.2911	30.9522	54.2984	-11.6002
18	2.9584	0.9463	-0.9168	4.4915	-1.9515	3.1301	0.1729	0.0174	-0.5477	-0.688	-0.3298	0.7316	0.5742	-0.2251	0.1321	0.4276	0.0505	-0.0862	0.4203	-0.1486	0.6086	23.4955	54.1606	-6.6386
19	5.332	-1.0419	0.5308	8.4509	-2.224	5.3542	0.0248	-0.3487	0.7236	-0.209	0.0907	0.7062	-0.1659	-0.8119	-0.1031	0.348	-0.0526	-0.1362	0.5596	-0.1376	0.7115	15.6092	63.8569	-1.6766
20	2.2205	-1.6657	0.3249	3.858	0.5885	7.2907	-0.1522	-0.2561	-0.1057	0.0606	-0.1191	0.6606	-0.4109	-0.5906	0.1025	0.3348	-0.0881	0.0668	0.2797	-0.0375	0.3533	17.349	64.6827	7.3978
21	5.76	2.6236	-0.3359	6.5838	-0.356	6.3029	-0.3771	-0.9295	0.6798	1.242	-0.1594	0.9562	-0.1099	-0.203	0.4298	0.3961	-0.0695	-0.0663	0.6461	-0.0844	0.2086	27.0973	66.0819	11.1199
22	1.6418	-1.2999	0.5923	5.2524	-1.9269	6.6849	-0.3098	-0.23	0.8669	0.9039	-0.5037	-0.5376	-0.8446	0.5021	0.5511	0.466	-0.1311	0.0395	0.3289	-0.106	0.5078	31.1854	71.0885	11.0704
23	2.0349	0.3183	0.4111	4.8369	-1.5492	3.6506	0.7713	0.6274	1.7575	0.5476	0.3709	-0.5667	-0.5123	0.9436	-1.0852	0.7124	0.132	0.0422	0.5942	-0.3349	0.4685	39.4216	75.2832	1.2667
24	8.5066	-6.8417	5.6977	6.1116	-4.5442	6.7453	0.6247	0.4341	-2.1236	-0.7325	0.0224	2.2934	-0.2539	-0.0374	-0.563	0.4893	0.0128	-0.0288	0.4405	-0.0764	0.7092	26.9367	72.803	1.7527

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 6 THROUGH 37 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 38 THROUGH 121 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 122 THROUGH 220 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 221 THROUGH 340 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 8 THROUGH 37 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 38 THROUGH 63 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 64 THROUGH 103 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 104 THROUGH 121 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 122 THROUGH 145 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 146 THROUGH 180 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 181 THROUGH 196 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 197 THROUGH 220 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 221 THROUGH 254 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 255 THROUGH 318 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 319 THROUGH 340 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 9 THROUGH 28 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 29 THROUGH 50 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 51 THROUGH 121 )
19	X-RAY DIFFRACTION	19	CHAIN 'C' AND (RESID 122 THROUGH 180 )
20	X-RAY DIFFRACTION	20	CHAIN 'C' AND (RESID 181 THROUGH 220 )
21	X-RAY DIFFRACTION	21	CHAIN 'C' AND (RESID 221 THROUGH 254 )
22	X-RAY DIFFRACTION	22	CHAIN 'C' AND (RESID 255 THROUGH 298 )
23	X-RAY DIFFRACTION	23	CHAIN 'C' AND (RESID 299 THROUGH 323 )
24	X-RAY DIFFRACTION	24	CHAIN 'C' AND (RESID 324 THROUGH 340 )

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi