PDB-5w6y: Physcomitrella patens Chorismate Mutase

ID or keywords:

Entry

Database: PDB / ID: 5w6y

Title

Physcomitrella patens Chorismate Mutase

Components

Chorismate mutase

Keywords

BIOSYNTHETIC PROTEIN / isomerase / chorismate mutase

Function / homology

Function and homology information

chorismate metabolic process / chorismate mutase / chorismate mutase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm
Similarity search - Function

Biological species

Physcomitrella patens (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.995 Å

Authors

Holland, C.K. / Kroll, K. / Jez, J.M.

Funding support

United States, 1items

Citation

Journal: Biochem. J. / Year: 2017
Title: Evolution of allosteric regulation in chorismate mutases from early plants.
Authors: Kroll, K. / Holland, C.K. / Starks, C.M. / Jez, J.M.

History

Deposition	Jun 18, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 11, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5w6y.cif.gz	220.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5w6y.ent.gz	176.4 KB	Display	PDB format
PDBx/mmJSON format	5w6y.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5w6y_validation.pdf.gz	466.1 KB	Display	wwPDB validaton report
Full document	5w6y_full_validation.pdf.gz	468.3 KB	Display
Data in XML	5w6y_validation.xml.gz	24.8 KB	Display
Data in CIF	5w6y_validation.cif.gz	36.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w6/5w6y ftp://data.pdbj.org/pub/pdb/validation_reports/w6/5w6y	HTTPS FTP

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Related structure data

Related structure data	4ppuS S: Starting model for refinement
Similar structure data	1csm-d 4ijv-1 4csm-2 3csm-2 6h3p-d 3pfe-d 3tfq-1 3k11-d 1np7-2 6lqo-1 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
Related items in Molecule of the Month	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Chorismate mutase

B: Chorismate mutase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	57.764, 78.408, 126.028
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	A-713- HOH

#1: Protein	Chorismate mutase Mass: 35232.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physcomitrella patens (plant) / Gene: PHYPADRAFT_181106 / Production host: Escherichia coli (E. coli) / References: UniProt: A9S498, chorismate mutase
#2: Chemical	ChemComp-TRP / TRYPTOPHAN Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂O₂
#3: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.03 Å³/Da / Density % sol: 39.26 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10 % w/v polyethylene glycol 4000, 20 % 2-Propanol (w/v), 100 mM HEPES, pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 28, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2→100 Å / Num. obs: 38350 / % possible obs: 96.6 % / Redundancy: 4.1 % / R_merge(I) obs: 0.082 / R_sym value: 0.059 / Net I/σ(I): 10.8
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.474 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1878 / R_sym value: 0.416 / % possible all: 97

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ppu

4ppu

Resolution: 1.995→37.419 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1963	1923	5.02 %
R_work	0.1546	-	-
obs	0.1567	38326	96.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.995→37.419 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3836	0	45	497	4378

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3997
X-RAY DIFFRACTION	f_angle_d	1.005	5421
X-RAY DIFFRACTION	f_dihedral_angle_d	14.717	1525
X-RAY DIFFRACTION	f_chiral_restr	0.039	585
X-RAY DIFFRACTION	f_plane_restr	0.006	709

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 (%)
1.9955-2.0454	0.217	134	0.1845	2464	X-RAY DIFFRACTION	94
2.0454-2.1007	0.2401	155	0.1796	2569	X-RAY DIFFRACTION	98
2.1007-2.1625	0.2203	154	0.1713	2606	X-RAY DIFFRACTION	98
2.1625-2.2323	0.2146	129	0.164	2609	X-RAY DIFFRACTION	98
2.2323-2.312	0.2065	143	0.1581	2616	X-RAY DIFFRACTION	98
2.312-2.4046	0.2099	135	0.1501	2603	X-RAY DIFFRACTION	98
2.4046-2.514	0.1911	128	0.1561	2643	X-RAY DIFFRACTION	98
2.514-2.6465	0.241	132	0.1544	2613	X-RAY DIFFRACTION	98
2.6465-2.8123	0.2116	121	0.1615	2628	X-RAY DIFFRACTION	98
2.8123-3.0293	0.2131	137	0.1598	2639	X-RAY DIFFRACTION	97
3.0293-3.334	0.2074	126	0.1586	2594	X-RAY DIFFRACTION	96
3.334-3.8161	0.1699	149	0.1403	2598	X-RAY DIFFRACTION	96
3.8161-4.8062	0.164	133	0.1322	2583	X-RAY DIFFRACTION	93
4.8062-37.4254	0.1805	147	0.1621	2638	X-RAY DIFFRACTION	92

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	2.3313	-0.1274	-0.1033	3.1415	-3.1963	4.1929	-0.108	-0.2027	-0.2472	0.3223	0.1294	0.0536	0.1999	0.0324	0.0297	0.2239	0.0238	0.0143	0.0942	-0.0038	0.1852	22.8984	22.1603	-22.7183
2	3.2648	0.5936	-1.2983	1.8493	0.8417	2.3727	0.2241	0.395	0.6445	-0.3801	-0.2641	0.2803	-0.8203	-0.1556	0.0872	0.3827	0.0209	-0.0217	0.1816	0.0732	0.3487	17.0392	46.1156	-34.4154
3	3.4098	0.8995	-0.2134	1.1933	-1.0614	5.1053	0.0419	-0.0821	0.0943	0.0243	-0.0932	0.1749	-0.2206	-0.2957	0.0308	0.1116	0.0248	-0.0068	0.0934	-0.043	0.1461	9.3263	34.9991	-21.551
4	4.6892	-0.7428	2.0189	1.6584	-1.9019	2.4384	-0.163	-0.5754	0.3748	0.5082	0.1765	-0.0249	-0.572	-0.6549	-0.1427	0.3314	0.0636	0.0241	0.3783	-0.056	0.2314	4.0902	31.5305	-12.303
5	1.0181	-0.1672	0.7841	0.9268	-0.7674	5.6052	-0.0225	-0.0368	0.0566	-0.0154	-0.0092	-0.0523	-0.1441	0.0963	0.0426	0.0961	-0.0059	-0.0158	0.0624	-0.0172	0.1567	21.9623	33.6843	-19.939
6	1.9055	-0.0148	1.3242	1.5423	0.1883	6.9796	-0.0145	-0.0297	0.1873	0.1467	0.0563	-0.3921	0.6012	0.6024	0.0469	0.2045	0.0642	-0.0526	0.2492	0.0091	0.2071	31.7877	27.3929	-0.8055
7	0.9809	-0.3965	1.0805	4.2451	0.1268	1.2275	0.0354	0.2499	0.0123	-0.2609	0.1107	-0.5463	0.2224	0.7138	-0.108	0.1304	0.0669	0.0398	0.2712	-0.0373	0.249	32.2245	18.2957	-33.787
8	1.457	-0.576	-1.9801	1.2568	1.2439	6.3299	0.0918	0.0614	0.0295	0.0002	-0.0143	-0.1601	-0.2123	0.2768	-0.1467	0.0922	-0.0022	-0.0289	0.1699	0.0002	0.1584	28.6203	31.383	-12.447
9	6.2498	6.8816	-6.5647	7.5805	-7.227	6.8949	0.0133	0.09	0.3003	0.1445	-0.1582	-0.1031	-0.4831	-0.3786	0.208	0.1711	0.0055	-0.0306	0.2052	0.0173	0.217	13.5833	34.5532	-40.8611
10	1.4783	-0.1052	-0.2359	1.5101	0.2143	2.2131	-0.0046	0.0984	0.0846	-0.0266	-0.082	0.2077	0.0895	-0.3269	0.1501	0.0877	-0.0166	-0.03	0.1202	-0.0384	0.1757	8.884	20.835	-34.902
11	0.4051	-0.7051	-0.6638	1.8561	0.7514	7.6677	0.0324	0.0934	0.1483	-0.2623	-0.0927	0.1816	-0.6074	-0.2527	0.0823	0.192	0.0405	-0.0778	0.1671	0	0.1742	4.1855	31.7522	-38.4471
12	0.9129	0.8787	-0.996	1.3309	-2.2695	4.7735	0.4071	0.1759	0.5488	0.0111	-0.2751	0.2425	-1.4939	-0.557	-0.0703	0.5951	0.1308	-0.1409	0.3921	0.0292	0.4826	3.3173	34.6655	-48.7001
13	2.4829	0.3158	-1.0447	2.4396	-2.3537	3.1141	0.1137	0.3767	-0.165	-0.3167	-0.0049	0.1681	0.2403	-0.7827	-0.322	0.2118	0.0222	-0.0583	0.3077	-0.0854	0.2068	1.0596	20.9174	-44.8568
14	1.2979	0.0207	-1.1238	0.744	0.2208	5.0869	0.0173	0.033	-0.0408	-0.0592	-0.0496	0.132	0.1391	-0.0648	0.0491	0.0752	0.0106	-0.0305	0.0843	-0.0127	0.1831	8.5818	19.0387	-38.8302
15	4.3814	5.7282	4.3434	9.3054	4.1925	7.8594	0.2802	1.1197	-0.5074	-0.8285	0.1205	-0.6299	0.3912	0.6264	-0.3422	0.3489	0.0879	0.0008	0.5635	-0.0811	0.2114	11.4869	17.914	-68.9938
16	2.4638	-1.52	1.838	1.5465	-1.3148	4.7961	0.2051	0.2397	-0.2726	-0.2759	-0.1321	0.156	0.5904	-0.1679	-0.0998	0.1941	-0.0018	-0.0132	0.1425	-0.0366	0.1919	15.7406	8.8041	-50.3873
17	6.6437	0.3352	1.9767	4.358	-0.1705	6.3348	0.2272	-0.5427	-0.6102	0.4263	-0.0209	0.0686	0.689	-0.3857	-0.1679	0.2568	-0.0133	0.0362	0.1153	0.0047	0.2092	14.1358	6.934	-34.1873
18	1.3253	-0.3412	0.9265	3.2221	-1.5763	4.4994	0.1307	0.3389	-0.0262	-0.43	-0.1495	0.2922	0.173	-0.4673	-0.0546	0.1871	0.0563	-0.0435	0.3156	-0.0853	0.176	6.9069	18.7103	-57.0807
19	3.0043	2.2699	2.6048	2.5107	1.5411	3.3232	0.1953	-0.2072	-0.2615	0.2289	0.0337	0.3033	0.1674	-0.8462	0.2236	0.3537	0.0252	0.0242	0.191	-0.0057	0.2178	7.188	25.2522	-19.262

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 73 through 96 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 97 through 117 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 118 through 145 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 146 through 163 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 164 through 228 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 229 through 257 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 258 through 287 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 288 through 316 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 401 through 401 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 69 through 117 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 118 through 145 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 146 through 164 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 165 through 182 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 183 through 228 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 229 through 238 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 239 through 269 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 270 through 298 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 299 through 316 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 401 through 401 )

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