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

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Basic information

Entry
Database: PDB / ID: 6vcg
TitleCrystal structure of Nitrosotalea devanaterra carotenoid cleavage dioxygenase, cobalt form
Componentscarotenoid cleavage dioxygenase
KeywordsOXIDOREDUCTASE / non-heme iron enzyme / carotenoid / apocarotenoid / mononuclear iron / beta propeller / RPE65 / dioxygenase / cobalt OXIDOREDUCTASE
Function / homologybeta-carotene 15,15'-dioxygenase activity / carotenoid dioxygenase activity / carotene catabolic process / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / retinal metabolic process / metal ion binding / : / Putative dioxygenase
Function and homology information
Biological speciesCandidatus Nitrosotalea devanaterra (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsDaruwalla, A. / Shi, W. / Kiser, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY009339 United States
CitationJournal: 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
DepositionDec 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: 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 1.2Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Sep 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 11, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)323,76116
Polymers323,2916
Non-polymers47010
Water8,287460
1
A: carotenoid cleavage dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9412
Polymers53,8821
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: carotenoid cleavage dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9643
Polymers53,8821
Non-polymers822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: carotenoid cleavage dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9994
Polymers53,8821
Non-polymers1173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: carotenoid cleavage dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9412
Polymers53,8821
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: carotenoid cleavage dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9763
Polymers53,8821
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: carotenoid cleavage dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9412
Polymers53,8821
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.010, 108.010, 491.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA7 - 4727 - 472
21ASNASNBB7 - 4727 - 472
12ASNASNAA7 - 4727 - 472
22ASNASNCC7 - 4727 - 472
13ASNASNAA7 - 4727 - 472
23ASNASNDD7 - 4727 - 472
14LYSLYSAA8 - 4728 - 472
24LYSLYSEE8 - 4728 - 472
15GLNGLNAA10 - 47210 - 472
25GLNGLNFF10 - 47210 - 472
16ASNASNBB7 - 4727 - 472
26ASNASNCC7 - 4727 - 472
17ASNASNBB7 - 4727 - 472
27ASNASNDD7 - 4727 - 472
18LYSLYSBB8 - 4728 - 472
28LYSLYSEE8 - 4728 - 472
19GLNGLNBB10 - 47210 - 472
29GLNGLNFF10 - 47210 - 472
110ASNASNCC7 - 4727 - 472
210ASNASNDD7 - 4727 - 472
111LYSLYSCC8 - 4728 - 472
211LYSLYSEE8 - 4728 - 472
112GLNGLNCC10 - 47210 - 472
212GLNGLNFF10 - 47210 - 472
113LYSLYSDD8 - 4728 - 472
213LYSLYSEE8 - 4728 - 472
114GLNGLNDD10 - 47210 - 472
214GLNGLNFF10 - 47210 - 472
115GLNGLNEE10 - 47210 - 472
215GLNGLNFF10 - 47210 - 472

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#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
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.96 % / Description: rod
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 22% Sokalan PA 25 CL 0.1 M MES-NaOH pH 6 0.1 M NaCl 10% xylitol 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979364 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979364 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 142530 / % possible obs: 99.8 % / Redundancy: 8.8 % / Biso Wilson estimate: 61 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.143 / Net I/σ(I): 10.59
Reflection shellResolution: 2.3→2.44 Å / Rmerge(I) obs: 2.173 / Mean I/σ(I) obs: 0.79 / Num. unique obs: 22771 / CC1/2: 0.44 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6VCF

6vcf


Resolution: 2.3→49.44 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU B: 30.105 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.371 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 7076 5 %RANDOM
Rwork0.2376 ---
obs0.2384 135427 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 211.68 Å2 / Biso mean: 69.28 Å2 / Biso min: 28.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.32 Å2-0 Å2
2---0.65 Å20 Å2
3---2.09 Å2
Refinement stepCycle: final / Resolution: 2.3→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21144 0 10 460 21614
Biso mean--59.93 54.69 -
Num. residues----2665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01321756
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719478
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.64429513
X-RAY DIFFRACTIONr_angle_other_deg1.1531.57245137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.02252652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.01323.2131133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.039153455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2211588
X-RAY DIFFRACTIONr_chiral_restr0.0520.22863
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0224468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024764
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A147520.07
12B147520.07
21A147120.07
22C147120.07
31A149910.04
32D149910.04
41A130700.06
42E130700.06
51A133500.04
52F133500.04
61B150270.03
62C150270.03
71B147620.06
72D147620.06
81B131230.05
82E131230.05
91B133370.04
92F133370.04
101C146910.06
102D146910.06
111C130600.04
112E130600.04
121C132930.04
122F132930.04
131D130200.06
132E130200.06
141D132860.04
142F132860.04
151E128960.04
152F128960.04
LS refinement shellResolution: 2.301→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 514 -
Rwork0.428 9765 -
all-10279 -
obs--97.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.69960.37590.12564.1592-1.16692.5606-0.0718-0.1286-0.03950.54760.17230.1138-0.63080.1745-0.10050.5287-0.03980.08220.35810.01750.26616.28225.06621.756
21.62730.0066-0.13892.8699-0.09872.43030.0123-0.03970.06090.09870.02920.09930.69050.3404-0.04150.59710.157-0.04420.3177-0.02590.010860.74762.09923.008
31.7060.60330.5113.0765-0.13992.8344-0.14970.2520.098-0.60890.1835-0.2371-0.41590.5006-0.03380.8026-0.25760.08020.5382-0.01290.114416.39729.654-20.71
41.9792-0.31990.35892.26690.16842.3601-0.14860.3098-0.138-0.34240.1576-0.13130.42430.551-0.0090.78940.0471-0.03550.5974-0.03430.030763.64266.067-19.055
52.8113-0.95780.7926.2749-2.12993.4337-0.0261-0.1285-0.3756-0.45140.36120.93240.2196-0.9643-0.33510.49180.0779-0.0760.71980.07190.440571.715.69622.908
63.0718-0.1946-0.27113.2450.76111.9868-0.0487-0.02060.34120.4824-0.25060.6999-0.1338-0.62680.29930.7905-0.01840.05330.7346-0.14540.399773.4787.091-21.359
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 472
2X-RAY DIFFRACTION1A1000
3X-RAY DIFFRACTION1A1122 - 1192
4X-RAY DIFFRACTION2B7 - 472
5X-RAY DIFFRACTION2B501 - 502
6X-RAY DIFFRACTION2B646 - 711
7X-RAY DIFFRACTION3C7 - 472
8X-RAY DIFFRACTION3C501 - 502
9X-RAY DIFFRACTION3C619
10X-RAY DIFFRACTION4D6 - 472
11X-RAY DIFFRACTION4D1000
12X-RAY DIFFRACTION4D1125 - 1133
13X-RAY DIFFRACTION5E8 - 472
14X-RAY DIFFRACTION5E501
15X-RAY DIFFRACTION5E601
16X-RAY DIFFRACTION6F10 - 472
17X-RAY DIFFRACTION6F1000

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