PDB-8cq6: Bifunctional cyclohexadienyl dehydratase/chorismate mutase from D...

ID or keywords:

Entry

Database: PDB / ID: 8cq6

Title

Bifunctional cyclohexadienyl dehydratase/chorismate mutase from Duganella sacchari

Components

chorismate mutase

Keywords

UNKNOWN FUNCTION / chorismate mutase / cyclohexadienyl dehydratase / chorismate mutase/cyclohexadienyl dehydratase / cyclohexadienyl dehydratase/chorismate mutase / bifunctional chorismate mutase / bifunctional cyclohexadienyl dehydratase

Function / homology

Function and homology information

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

Biological species

Duganella sacchari (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.44 Å

Authors

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

Funding support

Switzerland, 1items

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: Novel exported fusion enzymes with chorismate mutase and cyclohexadienyl dehydratase activity: Shikimate pathway enzymes teamed up in no man's land.
Authors: Stocker, C. / Khatanbaatar, T. / Bressan, L. / Wurth-Roderer, K. / Cordara, G. / Krengel, U. / Kast, P.

History

Deposition	Mar 3, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 30, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8cq6.cif.gz	318 KB	Display	PDBx/mmCIF format
PDB format	pdb8cq6.ent.gz	249.6 KB	Display	PDB format
PDBx/mmJSON format	8cq6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cq6_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	8cq6_full_validation.pdf.gz	3.1 MB	Display
Data in XML	8cq6_validation.xml.gz	52.5 KB	Display
Data in CIF	8cq6_validation.cif.gz	72 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cq/8cq6 ftp://data.pdbj.org/pub/pdb/validation_reports/cq/8cq6	HTTPS FTP

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Related structure data

Related structure data	8cq3C 8cq4C 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

B: chorismate mutase

C: chorismate mutase

D: chorismate mutase

hetero molecules

185 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	92.108, 111.930, 221.386
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLY	GLY	SER	SER	A	A	20 - 401	20 - 401
2	1	1	GLY	GLY	SER	SER	B	B	20 - 401	20 - 401
3	2	2	ARG	ARG	SER	SER	A	A	21 - 401	21 - 401
4	2	2	ARG	ARG	SER	SER	C	C	21 - 401	21 - 401
5	3	3	ARG	ARG	SER	SER	A	A	21 - 401	21 - 401
6	3	3	ARG	ARG	SER	SER	D	D	21 - 401	21 - 401
7	4	4	ARG	ARG	VAL	VAL	B	B	21 - 405	21 - 405
8	4	4	ARG	ARG	VAL	VAL	C	C	21 - 405	21 - 405
9	5	5	ARG	ARG	VAL	VAL	B	B	21 - 405	21 - 405
10	5	5	ARG	ARG	VAL	VAL	D	D	21 - 405	21 - 405
11	6	6	ARG	ARG	LEU	LEU	C	C	21 - 409	21 - 409
12	6	6	ARG	ARG	LEU	LEU	D	D	21 - 409	21 - 409

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	chorismate mutase Mass: 46078.504 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Duganella sacchari (bacteria) / Gene: SAMN05192549_107367 / Production host: Escherichia coli (E. coli) / Strain (production host): KA29 / References: UniProt: A0A1M7QNQ8, chorismate mutase
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.17 Å³/Da / Density % sol: 61.2 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 3 M NaCl 0.1 M Bis-TRIS, pH 5.5 5.6 mg/mL protein in 20 mM TRIS-HCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.984 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 25, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.984 Å / Relative weight: 1
Reflection	Resolution: 2.44→99.9 Å / Num. obs: 51859 / % possible obs: 94 % / Redundancy: 13.2 % / CC_1/2: 0.994 / Net I/σ(I): 7.8
Reflection shell	Resolution: 2.44→2.66 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2594 / CC_1/2: 0.124

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0350	refinement
autoPROC		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.44→99.9 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.903 / SU B: 13.262 / SU ML: 0.271 / Cross valid method: FREE R-VALUE / ESU R: 3.908 / ESU R Free: 0.388

	R_factor	Num. reflection	% reflection
R_free	0.265	2573	4.962 %
R_work	0.2248	49285	-
all	0.227	-	-
obs	-	51858	60.296 %

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: 58.539 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.266 Å²	0 Å²	-0 Å²
2-	-	0.089 Å²	-0 Å²
3-	-	-	-0.355 Å²

Refinement step

Cycle: LAST / Resolution: 2.44→99.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12009	0	10	71	12090

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	12410
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	12003
X-RAY DIFFRACTION	r_angle_refined_deg	0.908	1.645	16908
X-RAY DIFFRACTION	r_angle_other_deg	0.311	1.568	27477
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	11.019	5	1561
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.795	5	117
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.632	10	2044
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	18.241	10	588
X-RAY DIFFRACTION	r_chiral_restr	0.041	0.2	1920
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	14974
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2946
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	2579
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.178	0.2	10637
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	5987
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	7434
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	219
X-RAY DIFFRACTION	r_metal_ion_refined	0.125	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.152	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.229	0.2	77
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.003	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	3.189	5.716	6235
X-RAY DIFFRACTION	r_mcbond_other	3.189	5.716	6235
X-RAY DIFFRACTION	r_mcangle_it	5.169	10.275	7799
X-RAY DIFFRACTION	r_mcangle_other	5.169	10.274	7800
X-RAY DIFFRACTION	r_scbond_it	3.48	6.141	6175
X-RAY DIFFRACTION	r_scbond_other	3.48	6.141	6176
X-RAY DIFFRACTION	r_scangle_it	5.923	11.116	9109
X-RAY DIFFRACTION	r_scangle_other	5.923	11.116	9110
X-RAY DIFFRACTION	r_lrange_it	8.538	53.96	13453
X-RAY DIFFRACTION	r_lrange_other	8.537	53.96	13454
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.061	0.05	12149
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.091	0.05	11649
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.086	0.05	11758
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.094	0.05	11865
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.081	0.05	12007
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.077	0.05	12448

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.06079	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06079	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09057	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.09057	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.08554	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.08554	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.0939	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.0939	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.08143	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.08143	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.07676	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.07676	0.0501

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 (%)
2.44-2.502	0.289	7	0.377	256	X-RAY DIFFRACTION	4.1812
2.502-2.571	0.479	32	0.368	774	X-RAY DIFFRACTION	13.2023
2.571-2.645	0.423	73	0.354	1230	X-RAY DIFFRACTION	21.8002
2.645-2.726	0.416	92	0.349	1765	X-RAY DIFFRACTION	32.1003
2.726-2.816	0.357	104	0.325	2052	X-RAY DIFFRACTION	38.5069
2.816-2.915	0.34	133	0.298	2367	X-RAY DIFFRACTION	45.8379
2.915-3.024	0.319	125	0.286	2695	X-RAY DIFFRACTION	53.5104
3.024-3.148	0.315	154	0.281	2854	X-RAY DIFFRACTION	59.5054
3.148-3.288	0.307	179	0.266	3067	X-RAY DIFFRACTION	66.5983
3.288-3.448	0.257	150	0.253	3371	X-RAY DIFFRACTION	75.9163
3.448-3.634	0.284	208	0.242	3696	X-RAY DIFFRACTION	87.7501
3.634-3.854	0.279	215	0.244	3982	X-RAY DIFFRACTION	99.8335
3.854-4.12	0.244	199	0.209	3748	X-RAY DIFFRACTION	99.8735
4.12-4.45	0.219	165	0.183	3524	X-RAY DIFFRACTION	99.8646
4.45-4.873	0.21	163	0.171	3284	X-RAY DIFFRACTION	100
4.873-5.447	0.26	163	0.189	2935	X-RAY DIFFRACTION	99.871
5.447-6.286	0.247	143	0.218	2624	X-RAY DIFFRACTION	100
6.286-7.692	0.242	125	0.191	2241	X-RAY DIFFRACTION	99.9577
7.692-10.846	0.192	79	0.191	1781	X-RAY DIFFRACTION	99.8926
10.846-99.9	0.375	64	0.292	1039	X-RAY DIFFRACTION	99.0126

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