PDB-9rvg: Chorismate mutase

ID or keywords:

Entry

Database: PDB / ID: 9rvg

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: 1.109 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	Jul 8, 2025	Deposition site: PDBE / Processing site: PDBE
Supersession	Jul 23, 2025	ID: 8PNI
Revision 1.0	Jul 23, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9rvg.cif.gz	198.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9rvg.ent.gz	123.2 KB	Display	PDB format
PDBx/mmJSON format	9rvg.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/rv/9rvg ftp://data.pdbj.org/pub/pdb/validation_reports/rv/9rvg	HTTPS FTP

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Related structure data

Related structure data	8pnjC 6cnz 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
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) / 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.: 207 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.1 Å³/Da / Density % sol: 31.46 % / Description: P32 dimer in assymmetric unit
Crystal grow	Temperature: 298.5 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M ammonium citrate dibasic 20% w/v PEG 3350 (JCSG+ crystallization screen; Molecular Dimensions Ltd., condition A3).

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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: 0.87313 Å
Detector	Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 17, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 1.1→39.4 Å / Num. obs: 103362 / % possible obs: 97.4 % / Redundancy: 9.8 % / B_iso Wilson estimate: 14.6 Å² / CC_1/2: 0.999 / Net I/σ(I): 15
Reflection shell	Resolution: 1.11→1.23 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2907 / CC_1/2: 0.143 / % possible all: 49.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
XDS		data reduction
XDS		data scaling
PHASER	7.0.078	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.109→39.377 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.975 / SU B: 2.041 / SU ML: 0.043 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.039

	R_factor	Num. reflection	% reflection
R_free	0.1854	5228	5.06 %
R_work	0.1653	98100	-
all	0.166	-	-
obs	-	103328	87.663 %

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: 18.466 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.749 Å²	-0.375 Å²	0 Å²
2-	-	-0.749 Å²	-0 Å²
3-	-	-	2.43 Å²

Refinement step

Cycle: LAST / Resolution: 1.109→39.377 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2442	0	26	207	2675

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	2940
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2875
X-RAY DIFFRACTION	r_angle_refined_deg	1.856	1.837	4028
X-RAY DIFFRACTION	r_angle_other_deg	0.707	1.784	6599
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.818	5	398
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.044	5	40
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.631	10	543
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.899	10	154
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	438
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	3891
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	749
X-RAY DIFFRACTION	r_nbd_refined	0.254	0.2	728
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.173	0.2	2540
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	1432
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.07	0.2	1585
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.196	0.2	148
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.068	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.274	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.206	0.2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.29	0.2	20
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.044	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	5.04	1.734	1483
X-RAY DIFFRACTION	r_mcbond_other	5.024	1.733	1483
X-RAY DIFFRACTION	r_mcangle_it	7.015	3.101	1915
X-RAY DIFFRACTION	r_mcangle_other	7.016	3.101	1916
X-RAY DIFFRACTION	r_scbond_it	7.046	2.114	1457
X-RAY DIFFRACTION	r_scbond_other	7.048	2.111	1454
X-RAY DIFFRACTION	r_scangle_it	10.099	3.753	2112
X-RAY DIFFRACTION	r_scangle_other	10.097	3.754	2113
X-RAY DIFFRACTION	r_lrange_it	11.601	1391.845	3442
X-RAY DIFFRACTION	r_lrange_other	11.637	1407.179	3403
X-RAY DIFFRACTION	r_rigid_bond_restr	5.066	3	5783

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.109-1.138	0.353	214	0.334	4278	0.335	8708	0.918	0.931	51.5848	0.329
1.138-1.169	0.324	284	0.305	4789	0.306	8471	0.95	0.948	59.8867	0.295
1.169-1.203	0.282	274	0.303	4104	0.302	8282	0.967	0.959	52.8616	0.279
1.203-1.24	0.286	304	0.266	5948	0.267	8077	0.969	0.977	77.405	0.234
1.24-1.281	0.297	333	0.244	7029	0.246	7733	0.967	0.982	95.2024	0.212
1.281-1.326	0.254	431	0.225	6937	0.226	7534	0.971	0.986	97.7967	0.193
1.326-1.376	0.243	344	0.214	6757	0.216	7239	0.973	0.985	98.0937	0.185
1.376-1.432	0.217	392	0.193	6460	0.195	6979	0.978	0.987	98.1803	0.163
1.432-1.495	0.228	277	0.178	6305	0.18	6682	0.974	0.988	98.5034	0.152
1.495-1.568	0.171	310	0.15	6056	0.151	6448	0.983	0.991	98.7283	0.129
1.568-1.653	0.188	214	0.143	5769	0.145	6042	0.986	0.992	99.0235	0.126
1.653-1.753	0.189	256	0.144	5455	0.146	5758	0.983	0.991	99.1837	0.131
1.753-1.874	0.191	278	0.151	5128	0.153	5439	0.977	0.989	99.3933	0.141
1.874-2.023	0.198	252	0.151	4762	0.153	5037	0.977	0.989	99.5434	0.146
2.023-2.216	0.169	222	0.148	4417	0.149	4650	0.985	0.989	99.7634	0.149
2.216-2.477	0.16	238	0.14	3926	0.141	4169	0.986	0.99	99.8801	0.148
2.477-2.858	0.182	250	0.15	3473	0.152	3725	0.981	0.987	99.9463	0.163
2.858-3.496	0.181	170	0.15	2942	0.151	3115	0.981	0.987	99.9037	0.168
3.496-4.924	0.138	134	0.141	2277	0.141	2411	0.989	0.989	100	0.168
4.924-39.377	0.164	51	0.219	1288	0.217	1342	0.979	0.977	99.7765	0.332

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