PDB-6hqv: Pentafunctional AROM Complex from Chaetomium thermophilum

ID or keywords:

Entry

Database: PDB / ID: 6hqv

Title

Pentafunctional AROM Complex from Chaetomium thermophilum

Components

Pentafunctional AROM polypeptide

Keywords

BIOSYNTHETIC PROTEIN / Multifunctional Enzyme /

Shikimate Pathway / Aromatic Amino Acid Biosynthesis /

3-Dehydroquinate Synthase /

3-Dehydroquinate Dehydratase /

Shikimate Dehydrogenase /

Shikimate Kinase /

3-Phosphoshikimate 1-Carboxyvinyltransferase / 5-Enolpyruvylshikimate-3-Phosphate Synthase

Function / homology

Function and homology information

3-dehydroquinate synthase /

3-dehydroquinate synthase activity /

shikimate kinase / shikimate dehydrogenase (NADP+) /

3-phosphoshikimate 1-carboxyvinyltransferase /

3-phosphoshikimate 1-carboxyvinyltransferase activity /

shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity /

3-dehydroquinate dehydratase /

3-dehydroquinate dehydratase activity ...
Similarity search - Function

Biological species

Chaetomium thermophilum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3 Å

Authors

Arora Verasto, H. / Hartmann, M.D.

Citation

Journal: Nat.Chem.Biol. / Year: 2020
Title: Architecture and functional dynamics of the pentafunctional AROM complex.
Authors: Arora Veraszto, H. / Logotheti, M. / Albrecht, R. / Leitner, A. / Zhu, H. / Hartmann, M.D.

History

Deposition	Sep 25, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 6, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 22, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Aug 26, 2020	Group: Database references / Derived calculations / Category: citation / struct_conn Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6hqv.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb6hqv.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	6hqv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hq/6hqv ftp://data.pdbj.org/pub/pdb/validation_reports/hq/6hqv	HTTPS FTP

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Related structure data

Similar structure data	21948 4u1w-d 21945 5ctq-d 21944 21943 4u1y-d 21941 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	SASBDB: SASDHP8associated SAS data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#218 - Feb 2018 EPSP Synthase and Weedkillers similarity (9) #124 - Apr 2010 Concanavalin A and Circular Permutation similarity (1) #235 - Jul 2019 AMPA Receptor similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: Pentafunctional AROM polypeptide

B: Pentafunctional AROM polypeptide

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	153.943, 377.616, 70.882
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	0	1	0	A	15 - 1581
2	0	1	0	B	15 - 1581

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Protein , 1 types, 2 molecules AB

#1: Protein	Pentafunctional AROM polypeptide Mass: 174663.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: C-terminal hexa-His tag Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0008860 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: G0S061, 3-dehydroquinate dehydratase, shikimate kinase, 3-dehydroquinate synthase, 3-phosphoshikimate 1-carboxyvinyltransferase, shikimate dehydrogenase (NADP+)

#1: Protein

Pentafunctional AROM polypeptide

Mass: 174663.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal hexa-His tag
Source: (gene. exp.)

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0008860 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: G0S061,

3-dehydroquinate dehydratase,

shikimate kinase,

3-dehydroquinate synthase,

3-phosphoshikimate 1-carboxyvinyltransferase, shikimate dehydrogenase (NADP+)

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Non-polymers , 6 types, 19 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GLU / GLUTAMIC ACID / Glutamic acid Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₉NO₄
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-3DS / (4S,5R)-4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylic acid / 3-dehydroshikimate / 3-Dehydroshikimic acid Mass: 172.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₈O₅ / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-SKM / (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID / SHIKIMATE / Shikimic acid Mass: 174.151 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₇H₁₀O₅ / Feature type: SUBJECT OF INVESTIGATION

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.98 Å³/Da / Density % sol: 58.73 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 61 mM MES and 39 mM imidazole pH 6.5, 24% (v/v) ethylene glycol, 12% (w/v) PEG 8000, 30 mM sodium L-glutamate, 30 mM DL-alanine, 30 mM glycine, 30 mM DL-lysine HCl, 30 mM DL-serine

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.978 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 3→39.8 Å / Num. obs: 84026 / % possible obs: 99.7 % / Redundancy: 7.02 % / CC_1/2: 1 / R_merge(I) obs: 0.104 / Net I/σ(I): 13.67
Reflection shell	Resolution: 3→3.18 Å / Redundancy: 6.96 % / R_merge(I) obs: 1.34 / Mean I/σ(I) obs: 1.28 / CC_1/2: 0.54 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
XDS		data reduction
XDS		data scaling
SHELXDE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3→39.8 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.936 / SU B: 39.509 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R Free: 0.387 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23292	4170	5 %	RANDOM
R_work	0.20928	-	-	-
obs	0.21049	79855	99.71 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 108.917 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.62 Å²	0 Å²	-0 Å²
2-	-	4.36 Å²	-0 Å²
3-	-	-	-1.75 Å²

Refinement step

Cycle: 1 / Resolution: 3→39.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23389	0	229	0	23618

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.019	24106
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	23112
X-RAY DIFFRACTION	r_angle_refined_deg	1.048	1.99	32846
X-RAY DIFFRACTION	r_angle_other_deg	0.743	3	53168
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.967	5	3086
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.397	23.718	944
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.086	15	3656
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.27	15	156
X-RAY DIFFRACTION	r_chiral_restr	0.053	0.2	3828
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	27157
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5183
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.78	7.224	12365
X-RAY DIFFRACTION	r_mcbond_other	1.78	7.224	12364
X-RAY DIFFRACTION	r_mcangle_it	2.993	10.837	15444
X-RAY DIFFRACTION	r_mcangle_other	2.993	10.837	15445
X-RAY DIFFRACTION	r_scbond_it	1.69	7.324	11741
X-RAY DIFFRACTION	r_scbond_other	1.69	7.324	11737
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.85	10.937	17397
X-RAY DIFFRACTION	r_long_range_B_refined	4.676	57.059	26001
X-RAY DIFFRACTION	r_long_range_B_other	4.676	57.057	26000
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 95743 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 2.998→3.075 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.346	284	-
R_work	0.337	5867	-
obs	-	-	99.07 %

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	2.5632	1.2621	-0.108	2.2602	0.0621	0.9361	0.0657	-0.1383	0.0052	0.2503	0.0913	-0.1924	0.024	0.0379	-0.1569	0.1514	0.0941	-0.0642	0.0716	-0.0456	0.0566	83.5916	171.593	32.5318
2	2.415	0.3505	-0.0731	2.4834	1.1338	2.5609	0.0111	-0.6618	-0.0639	0.4842	0.0644	-0.7047	0.0773	0.8075	-0.0755	0.2962	0.0004	-0.095	0.6577	-0.1762	0.5641	122.4014	190.4928	32.0702
3	3.3914	0.193	2.9694	0.3477	0.1802	5.3354	0.0323	-0.5388	-0.0586	0.2491	-0.3677	-0.3399	0.3162	0.3871	0.3354	0.3948	-0.0201	-0.223	0.9666	0.1499	0.9584	133.4868	144.412	46.5331
4	2.9087	-0.3564	0.1357	1.9074	0.591	2.5799	-0.1347	-0.4769	0.0529	0.1262	0.0311	-0.131	0.1755	0.0224	0.1036	0.2258	0.1546	-0.0997	0.1694	-0.042	0.1714	102.4657	137.0197	33.7669
5	6.5587	-2.17	-0.2052	1.7639	-0.0179	1.0607	-0.1414	0.0901	-0.1625	0.0767	0.0819	-0.1599	0.0691	0.2482	0.0595	0.3422	0.0958	-0.0116	0.11	-0.0844	0.3586	127.9415	118.6233	9.511
6	3.4926	1.0489	-0.3247	1.2073	0.0524	0.7631	-0.0469	0.2862	0.0126	-0.1578	0.1401	0.1784	-0.0211	-0.1512	-0.0932	0.1652	0.0625	-0.0743	0.0915	0.0101	0.0702	56.896	159.1159	7.3433
7	2.0539	-0.2057	1.5837	1.3229	-0.3699	3.794	0.1327	0.0898	-0.1678	-0.0724	-0.0951	0.0873	0.4461	-0.2179	-0.0376	0.2123	-0.0008	-0.0312	0.2988	0.0783	0.3474	19.475	138.1841	8.1798
8	0.5775	0.3885	0.6313	1.9767	0.8567	3.9323	-0.0656	0.4125	-0.13	-0.553	-0.0115	0.6082	0.3466	-0.7037	0.0771	0.5802	-0.1515	-0.207	0.7431	-0.1117	0.8024	51.7769	104.6147	-12.8619
9	1.8489	-0.1323	1.2352	2.8658	-0.0177	1.7058	-0.1032	0.1968	0.0117	-0.189	0.0186	0.0274	0.0849	0.0007	0.0846	0.2344	0.0399	-0.0266	0.0736	-0.0344	0.0993	75.0179	124.5985	0.8921
10	1.0807	1.4275	0.2039	6.3215	1.6376	0.909	0.0152	-0.2537	-0.414	1.0758	-0.0261	-0.1355	0.4157	-0.1186	0.0109	0.5542	0.0789	0.0449	0.3127	0.0865	0.4624	78.0855	90.9391	22.4449

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	15 - 398
2	X-RAY DIFFRACTION	1	A	1601 - 1604
3	X-RAY DIFFRACTION	2	A	399 - 850
4	X-RAY DIFFRACTION	2	A	1609 - 1610
5	X-RAY DIFFRACTION	3	A	851 - 1040
6	X-RAY DIFFRACTION	3	A	1607 - 1608
7	X-RAY DIFFRACTION	4	A	1041 - 1285
8	X-RAY DIFFRACTION	4	A	1605
9	X-RAY DIFFRACTION	5	A	1286 - 1581
10	X-RAY DIFFRACTION	5	A	1606
11	X-RAY DIFFRACTION	6	B	15 - 398
12	X-RAY DIFFRACTION	6	B	1601 - 1604
13	X-RAY DIFFRACTION	7	B	399 - 850
14	X-RAY DIFFRACTION	7	B	1608 - 1609
15	X-RAY DIFFRACTION	8	B	851 - 1040
16	X-RAY DIFFRACTION	8	B	1607 - 1608
17	X-RAY DIFFRACTION	9	B	1041 - 1285
18	X-RAY DIFFRACTION	9	B	1605
19	X-RAY DIFFRACTION	10	B	1286 - 1581
20	X-RAY DIFFRACTION	10	B	1606

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