PDB-8pni: Chorismate mutase

ID or keywords:

Entry

Database: PDB / ID: 8pni

Title

Chorismate mutase

Components

Monofunctional chorismate mutase

Keywords

ISOMERASE / chorismate mutase / Pseudomonas aeruginosa / periplasmic enzyme

Function / homology

Function and homology information

salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / L-phenylalanine biosynthetic process / periplasmic space / protein homodimerization activity
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.21 Å

Authors

Khatanbaatar, T. / Cordara, G. / Krengel, U.

Funding support

Switzerland, 1items

Citation

Journal: To Be Published
Title: Structural analysis of chorismate mutase and cyclohexadienyl dehydratase from Pseudomonas aeruginosa
Authors: Khatanbaatar, T. / Bressan, L. / Wurth-Roderer, K. / Gabriele, C. / Kast, P. / Krengel, U.

History

Deposition	Jun 30, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 10, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8pni.cif.gz	198.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8pni.ent.gz	124 KB	Display	PDB format
PDBx/mmJSON format	8pni.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8pni_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	8pni_full_validation.pdf.gz	1.2 MB	Display
Data in XML	8pni_validation.xml.gz	16.7 KB	Display
Data in CIF	8pni_validation.cif.gz	23.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pn/8pni ftp://data.pdbj.org/pub/pdb/validation_reports/pn/8pni	HTTPS FTP

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Related structure data

Related structure data	8pnjC C: citing same article (ref.)
Similar structure data	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)

Deposited unit

A: Monofunctional chorismate mutase

B: Monofunctional chorismate mutase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS

Unit cell

Length a, b, c (Å)	48.445, 48.445, 113.364
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Monofunctional chorismate mutase Mass: 21398.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: aroQ, PA5184 / Production host: Escherichia coli (E. coli) / Strain (production host): KA12 / References: UniProt: Q9HU05, chorismate mutase
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.4 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1:3 volume ratio of 8 mg/mL protein in 20 mM Bis-Tris, pH 6.5 storage buffer and 0.2 M ammonium citrate dibasic 20% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 17, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.873 Å / Relative weight: 1
Reflection	Resolution: 1.21→39.35 Å / Num. obs: 88399 / % possible obs: 97.4 % / Redundancy: 9.8 % / CC_1/2: 0.999 / Net I/σ(I): 15
Reflection shell	Resolution: 1.21→1.23 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3688 / CC_1/2: 0.507 / % possible all: 79.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0350	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.21→39.35 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.975 / SU B: 1.496 / SU ML: 0.031 / Cross valid method: FREE R-VALUE / ESU R: 0.041 / ESU R Free: 0.04

	R_factor	Num. reflection	% reflection
R_free	0.1706	4283	4.847 %
R_work	0.1429	84084	-
all	0.144	-	-
obs	-	88367	97.353 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 20.706 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.135 Å²	0.067 Å²	0 Å²
2-	-	0.135 Å²	-0 Å²
3-	-	-	-0.437 Å²

Refinement step

Cycle: LAST / Resolution: 1.21→39.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2442	0	26	200	2668

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	2919
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2656
X-RAY DIFFRACTION	r_angle_refined_deg	1.472	1.632	3995
X-RAY DIFFRACTION	r_angle_other_deg	0.559	1.549	6246
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.62	5	393
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	13.036	10	41
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.381	10	540
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.322	10	154
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	433
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3660
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	552
X-RAY DIFFRACTION	r_nbd_refined	0.251	0.2	705
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.173	0.2	2370
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	1431
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.066	0.2	1493
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.177	0.2	133
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.064	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.22	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.207	0.2	47
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.223	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	6.818	1.984	1472
X-RAY DIFFRACTION	r_mcbond_other	6.811	273.814	1472
X-RAY DIFFRACTION	r_mcangle_it	7.406	2.935	1899
X-RAY DIFFRACTION	r_mcangle_other	7.404	3.155	1900
X-RAY DIFFRACTION	r_scbond_it	10.383	2.654	1447
X-RAY DIFFRACTION	r_scbond_other	10.39	2.652	1444
X-RAY DIFFRACTION	r_scangle_it	11.408	3.782	2096
X-RAY DIFFRACTION	r_scangle_other	11.406	3.783	2097
X-RAY DIFFRACTION	r_lrange_it	9.465		3409
X-RAY DIFFRACTION	r_lrange_other	9.475		3371
X-RAY DIFFRACTION	r_rigid_bond_restr	22.211	3	2895

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 (%)
1.21-1.241	0.256	288	0.263	5163	X-RAY DIFFRACTION	81.0196
1.241-1.275	0.26	294	0.244	5943	X-RAY DIFFRACTION	95.4399
1.275-1.312	0.231	284	0.21	5931	X-RAY DIFFRACTION	97.6894
1.312-1.353	0.221	338	0.184	5701	X-RAY DIFFRACTION	97.9086
1.353-1.397	0.218	284	0.171	5604	X-RAY DIFFRACTION	98.1497
1.397-1.446	0.21	252	0.155	5416	X-RAY DIFFRACTION	98.3515
1.446-1.5	0.179	246	0.128	5280	X-RAY DIFFRACTION	98.4851
1.5-1.562	0.166	216	0.11	5115	X-RAY DIFFRACTION	98.7405
1.562-1.631	0.151	262	0.105	4815	X-RAY DIFFRACTION	99.0248
1.631-1.71	0.152	240	0.107	4672	X-RAY DIFFRACTION	99.0722
1.71-1.803	0.139	218	0.104	4411	X-RAY DIFFRACTION	99.2921
1.803-1.912	0.164	210	0.118	4199	X-RAY DIFFRACTION	99.481
1.912-2.044	0.174	200	0.131	3977	X-RAY DIFFRACTION	99.6184
2.044-2.207	0.163	191	0.136	3687	X-RAY DIFFRACTION	99.7172
2.207-2.417	0.172	160	0.125	3413	X-RAY DIFFRACTION	99.8603
2.417-2.701	0.169	186	0.129	3030	X-RAY DIFFRACTION	99.9379
2.701-3.116	0.154	132	0.141	2702	X-RAY DIFFRACTION	99.9295
3.116-3.81	0.158	132	0.142	2277	X-RAY DIFFRACTION	99.9585
3.81-5.363	0.15	98	0.149	1770	X-RAY DIFFRACTION	100
5.363-39.35	0.206	52	0.225	978	X-RAY DIFFRACTION	99.7096

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