PDB-8pnj: Chorismate mutase

ID or keywords:

Entry

Database: PDB / ID: 8pnj

Title

Chorismate mutase

Components

chorismate mutase

Keywords

UNKNOWN FUNCTION / chorismate mutase / cyclohexadienyl dehydratase / chorismate mutase/cyclohexadienyl dehydratase / cyclohexadienyl dehydratase/chorismate mutase / bifunctional chorismate mutase / bifunctional cyclohexadienyl dehydratase / bifunctional enzyme / shikimate pathway enzymes / metabolic enzymes / aromatic amino acid synthesis / protein crystal structure

Function / homology

Function and homology information

chorismate metabolic process / chorismate mutase / chorismate mutase activity
Similarity search - Function

Biological species

Aequoribacter fuscus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.355 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. / Cordara, G. / Krengel, U.

History

Deposition	Jun 30, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 10, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8pnj.cif.gz	102.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8pnj.ent.gz	73.5 KB	Display	PDB format
PDBx/mmJSON format	8pnj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8pnj_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	8pnj_full_validation.pdf.gz	2.4 MB	Display
Data in XML	8pnj_validation.xml.gz	17.4 KB	Display
Data in CIF	8pnj_validation.cif.gz	23.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pn/8pnj ftp://data.pdbj.org/pub/pdb/validation_reports/pn/8pnj	HTTPS FTP

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Related structure data

Related structure data	9rvgC 8cq4 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: chorismate mutase

hetero molecules

48.5 kDa, 1 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)	48.608, 105.344, 55.776
Angle α, β, γ (deg.)	90.000, 112.484, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 1 molecules A

#1: Protein	chorismate mutase Mass: 47854.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequoribacter fuscus (bacteria) / Gene: EYZ66_08225 / Production host: Escherichia coli (E. coli) / Strain (production host): KA29 / References: UniProt: A0A7Z2NRM1

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Non-polymers , 5 types, 48 molecules

#2: Chemical	ChemComp-TSA / 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID Mass: 228.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.01 Å³/Da / Density % sol: 59.13 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1:1 volume ratio of 5 mg/ml protein in 20 mM TRIS-HCl, pH=8, 150 uM NaCl buffer and 0.1M BTP, pH=8.5 0.2M KSCN 20% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 11, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.35→46.336 Å / Num. obs: 20939 / % possible obs: 97.3 % / Redundancy: 3.1 % / B_iso Wilson estimate: 34.2 Å² / CC_1/2: 0.959 / Net I/σ(I): 4.1
Reflection shell	Resolution: 2.35→2.44 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1801 / CC_1/2: 0.475 / % possible all: 85

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.355→46.336 Å / Cor.coef. F_o:F_c: 0.929 / Cor.coef. F_o:F_c free: 0.876 / WR_factor R_free: 0.284 / WR_factor R_work: 0.215 / SU B: 9.888 / SU ML: 0.228 / Average fsc free: 0.9393 / Average fsc work: 0.9666 / Cross valid method: FREE R-VALUE / ESU R: 0.377 / ESU R Free: 0.283
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2842	979	4.68 %
R_work	0.2148	19940	-
all	0.218	-	-
obs	-	20919	97.234 %

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: 38.122 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.155 Å²	-0 Å²	-0.058 Å²
2-	-	2.847 Å²	0 Å²
3-	-	-	-1.969 Å²

Refinement step

Cycle: LAST / Resolution: 2.355→46.336 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3087	0	44	41	3172

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	3422
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3112
X-RAY DIFFRACTION	r_angle_refined_deg	1.451	1.644	4675
X-RAY DIFFRACTION	r_angle_other_deg	0.511	1.556	7286
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.206	5	436
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	17.852	9.828	29
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.804	10	592
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.974	10	163
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	532
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4008
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	668
X-RAY DIFFRACTION	r_nbd_refined	0.226	0.2	707
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	2991
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	1640
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	1870
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.174	0.2	126
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.416	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.326	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.273	0.2	89
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.267	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	2.975	3.902	1678
X-RAY DIFFRACTION	r_mcbond_other	2.97	3.902	1678
X-RAY DIFFRACTION	r_mcangle_it	4.416	5.841	2136
X-RAY DIFFRACTION	r_mcangle_other	4.416	5.844	2137
X-RAY DIFFRACTION	r_scbond_it	3.003	4.114	1744
X-RAY DIFFRACTION	r_scbond_other	3.003	4.113	1745
X-RAY DIFFRACTION	r_scangle_it	4.466	6.095	2539
X-RAY DIFFRACTION	r_scangle_other	4.465	6.094	2540
X-RAY DIFFRACTION	r_lrange_it	6.884	54.052	3770
X-RAY DIFFRACTION	r_lrange_other	6.883	54.045	3770

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
2.355-2.416	0.344	65	0.346	1256	0.346	1597	0.922	0.919	82.7176	0.346
2.416-2.482	0.354	80	0.31	1379	0.312	1502	0.91	0.939	97.1372	0.31
2.482-2.554	0.364	89	0.288	1408	0.293	1534	0.91	0.951	97.588	0.288
2.554-2.632	0.353	58	0.273	1383	0.277	1455	0.927	0.96	99.0378	0.273
2.632-2.718	0.289	65	0.205	1310	0.209	1396	0.946	0.974	98.4957	0.205
2.718-2.813	0.256	50	0.183	1313	0.186	1371	0.961	0.98	99.4165	0.183
2.813-2.919	0.282	63	0.174	1247	0.179	1326	0.951	0.982	98.7934	0.174
2.919-3.038	0.264	58	0.183	1203	0.187	1268	0.958	0.98	99.4479	0.183
3.038-3.172	0.267	62	0.187	1146	0.191	1208	0.955	0.98	100	0.187
3.172-3.326	0.271	43	0.202	1113	0.205	1165	0.958	0.977	99.2275	0.202
3.326-3.505	0.318	65	0.241	1044	0.246	1123	0.92	0.967	98.7533	0.241
3.505-3.716	0.301	50	0.215	985	0.219	1046	0.942	0.974	98.9484	0.215
3.716-3.971	0.302	36	0.226	938	0.23	990	0.933	0.966	98.3838	0.226
3.971-4.287	0.3	37	0.194	869	0.198	921	0.923	0.974	98.3713	0.194
4.287-4.692	0.253	38	0.166	779	0.17	839	0.962	0.981	97.3778	0.166
4.692-5.239	0.245	35	0.195	711	0.198	778	0.958	0.977	95.8869	0.195
5.239-6.036	0.259	26	0.244	643	0.244	684	0.948	0.966	97.807	0.244
6.036-7.362	0.3	30	0.221	536	0.226	579	0.957	0.973	97.7547	0.221
7.362-10.282	0.213	14	0.178	427	0.179	458	0.987	0.977	96.2882	0.178
10.282-46.336	0.159	15	0.258	250	0.252	272	0.986	0.959	97.4265	0.258

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