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- PDB-7t8q: CRYSTAL STRUCTURE OF T151G CAO1 -

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Basic information

Entry
Database: PDB / ID: 7t8q
TitleCRYSTAL STRUCTURE OF T151G CAO1
ComponentsCarotenoid oxygenase 1
KeywordsOXIDOREDUCTASE / non-heme iron / beta propeller / stilbene / dioxygenase
Function / homologycarotenoid dioxygenase activity / 9-cis-epoxycarotenoid dioxygenase activity / carotene catabolic process / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / metal ion binding / : / Carotenoid cleavage oxygenase 1
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsDaruwalla, A. / Kiser, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2107713 United States
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF T151G CAO1
Authors: Daruwalla, A. / Kiser, P.D.
History
DepositionDec 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carotenoid oxygenase 1
B: Carotenoid oxygenase 1
C: Carotenoid oxygenase 1
D: Carotenoid oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,39318
Polymers237,8164
Non-polymers57814
Water22,2491235
1
A: Carotenoid oxygenase 1
D: Carotenoid oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,23210
Polymers118,9082
Non-polymers3248
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carotenoid oxygenase 1
C: Carotenoid oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,1618
Polymers118,9082
Non-polymers2546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.632, 100.632, 447.661
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA30 - 52630 - 526
21LEULEUBB30 - 52630 - 526
12PROPROAA30 - 52530 - 525
22PROPROCC30 - 52530 - 525
13LEULEUAA30 - 52630 - 526
23LEULEUDD30 - 52630 - 526
14PROPROBB30 - 52530 - 525
24PROPROCC30 - 52530 - 525
15LEULEUBB30 - 52630 - 526
25LEULEUDD30 - 52630 - 526
16PROPROCC30 - 52530 - 525
26PROPRODD30 - 52530 - 525

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Carotenoid oxygenase 1


Mass: 59453.887 Da / Num. of mol.: 4 / Mutation: T151G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: cao-1, NCU07008 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7S860
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1235 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES-NaOH pH 7 42% sodium polyacrylate 2100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 142491 / % possible obs: 99 % / Redundancy: 5.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Net I/σ(I): 13.8
Reflection shellResolution: 2.15→2.28 Å / Rmerge(I) obs: 1.475 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 22485 / CC1/2: 0.429

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5U8X

5u8x


Resolution: 2.15→49.09 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.106 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 6063 4.3 %RANDOM
Rwork0.1902 ---
obs0.1911 136427 99 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 122.13 Å2 / Biso mean: 45.495 Å2 / Biso min: 28.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.2 Å20 Å2
2--0.39 Å2-0 Å2
3----1.27 Å2
Refinement stepCycle: final / Resolution: 2.15→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15922 0 14 1235 17171
Biso mean--57.03 48.7 -
Num. residues----1991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01316444
X-RAY DIFFRACTIONr_bond_other_d0.0010.01514917
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.65222336
X-RAY DIFFRACTIONr_angle_other_deg1.0791.5834425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27951989
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85321.855949
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.533152534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.88315116
X-RAY DIFFRACTIONr_chiral_restr0.0410.21992
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218844
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023984
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A161960.06
12B161960.06
21A162920.05
22C162920.05
31A162700.06
32D162700.06
41B161750.06
42C161750.06
51B162530.06
52D162530.06
61C162750.05
62D162750.05
LS refinement shellResolution: 2.153→2.209 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 278 -
Rwork0.34 9802 -
all-10080 -
obs--96.06 %

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