PDB-6vcf: Crystal structure of Nitrosotalea devanaterra carotenoid cleavage...

ID or keywords:

Entry

Database: PDB / ID: 6vcf

Title

Crystal structure of Nitrosotalea devanaterra carotenoid cleavage dioxygenase, iron form

Components

carotenoid cleavage dioxygenase

Keywords

OXIDOREDUCTASE / non-heme iron enzyme / carotenoid / apocarotenoid / mononuclear iron / beta propeller / RPE65 / dioxygenase

Function / homology

carotenoid dioxygenase activity / carotene catabolic process / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / metal ion binding / BICARBONATE ION / : / Putative dioxygenase

Function and homology information

Biological species

Candidatus Nitrosotalea devanaterra (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.687 Å

Authors

Daruwalla, A. / Shi, W. / Kiser, P.D.

Funding support

United States, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis for carotenoid cleavage by an archaeal carotenoid dioxygenase.
Authors: Daruwalla, A. / Zhang, J. / Lee, H.J. / Khadka, N. / Farquhar, E.R. / Shi, W. / von Lintig, J. / Kiser, P.D.

History

Deposition	Dec 20, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	Aug 5, 2020	Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _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
Revision 1.2	Aug 19, 2020	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3	Sep 2, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6vcf.cif.gz	1023.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6vcf.ent.gz	844.2 KB	Display	PDB format
PDBx/mmJSON format	6vcf.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6vcf_validation.pdf.gz	266.9 KB	Display	wwPDB validaton report
Full document	6vcf_full_validation.pdf.gz	266.8 KB	Display
Data in XML	6vcf_validation.xml.gz	1.3 KB	Display
Data in CIF	6vcf_validation.cif.gz	24.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vc/6vcf ftp://data.pdbj.org/pub/pdb/validation_reports/vc/6vcf	HTTPS FTP

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Related structure data

Related structure data	6vcgC 6vchC 3kvcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6vcg-4 6vcg-1 6vch-1 6vch-4 6vcg-2 6vch-3 6n64-3 5v2d-4 1rgu-1 6vcg-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6vcgC

6vchC

3kvcS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#147 - Mar 2012 Rhodopsin similarity (3) #66 - Jun 2005 Carotenoid Oxygenase similarity (2) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (2) #111 - Mar 2009 Hydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #59 - Nov 2004 Photosystem II similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#147 - Mar 2012
Rhodopsin
similarity (3)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (2)
#244 - Apr 2020
Photosynthetic Supercomplexes
similarity (2)
#111 - Mar 2009
Hydrogenase
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#49 - Jan 2004
Carbonic Anhydrase
similarity (1)
#59 - Nov 2004
Photosystem II
similarity (1)
#61 - Jan 2005
Phenylalanine Hydroxylase
similarity (1)

Deposited unit

A: carotenoid cleavage dioxygenase

B: carotenoid cleavage dioxygenase

C: carotenoid cleavage dioxygenase

D: carotenoid cleavage dioxygenase

E: carotenoid cleavage dioxygenase

F: carotenoid cleavage dioxygenase

hetero molecules

324 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: carotenoid cleavage dioxygenase

hetero molecules

defined by author
54 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: carotenoid cleavage dioxygenase

hetero molecules

defined by author
54 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: carotenoid cleavage dioxygenase

hetero molecules

defined by author
54 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: carotenoid cleavage dioxygenase

hetero molecules

defined by author
53.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: carotenoid cleavage dioxygenase

hetero molecules

defined by author
53.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: carotenoid cleavage dioxygenase

hetero molecules

defined by author
53.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	107.267, 107.267, 491.109
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains A B
2	1	Chains A C
3	1	Chains A D
4	1	Chains A E
5	1	Chains A F
6	1	Chains B C
7	1	Chains B D
8	1	Chains B E
9	1	Chains B F
10	1	Chains C D
11	1	Chains C E
12	1	Chains C F
13	1	Chains D E
14	1	Chains D F
15	1	Chains E F

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	carotenoid cleavage dioxygenase Mass: 53881.797 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Nitrosotalea devanaterra (archaea) Gene: NDEV_1113 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A128A3G4

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Non-polymers , 5 types, 255 molecules

#2: Chemical	ChemComp-FE2 / FE (II) ION Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-BCT / BICARBONATE ION Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.52 Å³/Da / Density % sol: 51.25 % / Description: rod
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 22% Sokalan PA 25 CL 0.1 M MES-NaOH pH 6 0.1 M NaCl 22% Xylitol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979354 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979354 Å / Relative weight: 1
Reflection	Resolution: 2.68→50 Å / Num. obs: 88233 / % possible obs: 99.5 % / Redundancy: 10.5 % / B_iso Wilson estimate: 66 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.185 / Net I/σ(I): 11.77
Reflection shell	Resolution: 2.68→2.85 Å / Redundancy: 10.1 % / R_merge(I) obs: 1.954 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 13897 / CC_1/2: 0.373 / % possible all: 97.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KVC

3kvc

Resolution: 2.687→49.149 Å / Cor.coef. F_o:F_c: 0.925 / Cor.coef. F_o:F_c free: 0.912 / WR_factor R_free: 0.248 / WR_factor R_work: 0.229 / SU B: 49.825 / SU ML: 0.406 / Average fsc free: 0.8241 / Average fsc work: 0.8318 / Cross valid method: FREE R-VALUE / ESU R Free: 0.377
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2714	4373	4.961 %
R_work	0.2516	83770	-
all	0.253	-	-
obs	-	88143	99.741 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 83.729 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.846 Å²	-0.423 Å²	-0 Å²
2-	-	-0.846 Å²	0 Å²
3-	-	-	2.744 Å²

Refinement step

Cycle: LAST / Resolution: 2.687→49.149 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21385	0	17	244	21646

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.013	21961
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	19798
X-RAY DIFFRACTION	r_angle_refined_deg	1.198	1.644	29764
X-RAY DIFFRACTION	r_angle_other_deg	1.051	1.573	45924
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.075	5	2660
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.277	23.157	1153
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.868	15	3571
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.863	15	93
X-RAY DIFFRACTION	r_chiral_restr	0.036	0.2	2876
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	24601
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4790
X-RAY DIFFRACTION	r_nbd_refined	0.17	0.2	3394
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.153	0.2	18360
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	10286
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.067	0.2	10026
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.131	0.2	663
X-RAY DIFFRACTION	r_metal_ion_refined	0.162	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.11	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.157	0.2	125
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.211	0.2	9
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.032	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.45	3.097	10700
X-RAY DIFFRACTION	r_mcbond_other	0.45	3.096	10699
X-RAY DIFFRACTION	r_mcangle_it	0.831	4.642	13340
X-RAY DIFFRACTION	r_mcangle_other	0.831	4.642	13341
X-RAY DIFFRACTION	r_scbond_it	0.267	3.092	11261
X-RAY DIFFRACTION	r_scbond_other	0.267	3.091	11258
X-RAY DIFFRACTION	r_scangle_it	0.493	4.627	16424
X-RAY DIFFRACTION	r_scangle_other	0.493	4.627	16423
X-RAY DIFFRACTION	r_lrange_it	2.077	34.341	22859
X-RAY DIFFRACTION	r_lrange_other	2.066	34.346	22829
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.068	0.05	14667
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.071	0.05	14601
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.052	0.05	14780
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.06	0.05	13294
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.053	0.05	13486
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.044	0.05	14873
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.062	0.05	14663
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.044	0.05	13350
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.048	0.05	13521
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.066	0.05	14592
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.04	0.05	13292
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.041	0.05	13479
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.059	0.05	13263
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.051	0.05	13473
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.037	0.05	13019

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
2.687-2.757	0.435	299	0.49	6054	0.488	6500	0.511	0.518	97.7385	0.519
2.757-2.832	0.422	316	0.395	6021	0.396	6337	0.601	0.61	100	0.393
2.832-2.914	0.355	305	0.363	5856	0.363	6161	0.708	0.729	100	0.353
2.914-3.003	0.386	297	0.333	5718	0.336	6015	0.753	0.776	100	0.317
3.003-3.101	0.33	290	0.301	5502	0.303	5792	0.827	0.834	100	0.279
3.101-3.21	0.334	277	0.283	5349	0.286	5627	0.837	0.853	99.9822	0.26
3.21-3.33	0.293	275	0.283	5177	0.283	5452	0.895	0.888	100	0.262
3.33-3.466	0.34	265	0.297	4970	0.299	5241	0.84	0.859	99.8855	0.277
3.466-3.619	0.286	249	0.283	4743	0.284	4992	0.889	0.884	100	0.269
3.619-3.794	0.303	233	0.266	4558	0.268	4801	0.883	0.901	99.7917	0.246
3.794-3.998	0.284	223	0.263	4307	0.264	4578	0.886	0.895	98.9515	0.238
3.998-4.239	0.236	218	0.224	4095	0.225	4313	0.925	0.928	100	0.21
4.239-4.529	0.232	205	0.2	3852	0.201	4057	0.935	0.946	100	0.191
4.529-4.889	0.206	189	0.193	3635	0.194	3824	0.942	0.947	100	0.188
4.889-5.35	0.2	175	0.194	3274	0.194	3449	0.949	0.95	100	0.192
5.35-5.973	0.228	156	0.197	3008	0.198	3164	0.943	0.949	100	0.193
5.973-6.88	0.271	138	0.238	2626	0.24	2765	0.916	0.927	99.9638	0.235
6.88-8.385	0.262	119	0.224	2258	0.226	2378	0.921	0.923	99.9579	0.229
8.385-11.69	0.177	91	0.185	1751	0.184	1842	0.961	0.962	100	0.203
11.69-49.149	0.267	53	0.262	1015	0.262	1069	0.923	0.916	99.9065	0.296

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	2.5569	0.2508	0.1747	4.055	-0.6816	2.3733	-0.0514	-0.0903	0.0454	0.6203	0.093	0.0224	-0.6581	0.3123	-0.0417	0.5795	-0.1159	0.0888	0.2344	-0.0334	0.0739	16.4103	24.6674	21.7207
2	2.1938	0.1053	-0.0427	4.2312	0.0345	3.6832	0.076	-0.0893	0.0598	0.2444	0.0293	0.0785	0.8943	0.497	-0.1053	0.5545	0.1885	-0.074	0.1474	-0.0362	0.0165	60.4343	61.1861	23.0808
3	1.8838	0.4628	0.1544	3.9988	-0.3508	3.6142	0.0352	0.233	0.179	-0.3719	0.0787	-0.094	-0.4819	0.5109	-0.1139	0.5549	-0.2246	0.0154	0.3909	-0.0053	0.069	15.7773	29.522	-20.8248
4	3.2331	0.6011	0.4046	3.3675	0.1337	3.0663	-0.3015	0.4422	-0.4278	-0.523	0.3561	-0.3304	0.6826	0.7454	-0.0546	0.7812	0.0385	-0.0748	0.4901	-0.0674	0.1209	63.3872	65.2733	-19.1907
5	3.6176	-0.3832	0.4173	8.8441	-1.6552	3.4773	0.051	-0.1039	-0.0612	-1.0038	0.2857	1.8034	0.268	-0.8779	-0.3367	0.5407	0.1041	-0.2319	0.5067	0.1256	0.5665	70.9691	5.1029	22.8193
6	4.1312	1.9844	-0.5072	7.5859	-1.491	2.3835	0.5691	-0.0405	0.7162	1.5808	-0.2249	1.8887	-0.7084	-0.6091	-0.3442	0.9995	-0.0384	0.4303	0.6359	-0.0422	0.6434	71.4742	6.7354	-21.0815

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	7 - 503
2	X-RAY DIFFRACTION	2	ALL	B	7 - 503
3	X-RAY DIFFRACTION	3	ALL	C	7 - 502
4	X-RAY DIFFRACTION	4	ALL	D	7 - 1000
5	X-RAY DIFFRACTION	5	ALL	E	7 - 1000
6	X-RAY DIFFRACTION	6	ALL	F	10 - 1000

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Protein , 1 types, 6 molecules ABCDEF

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Non-polymers , 5 types, 255 molecules

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