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- PDB-6l8h: Crystal structure of CYP97C1 -

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Basic information

Entry
Database: PDB / ID: 6l8h
TitleCrystal structure of CYP97C1
ComponentsCarotene epsilon-monooxygenase, chloroplastic
KeywordsOXIDOREDUCTASE / lutein biosynthesis / photosynthesis / monooxygenase / carotenoid / P450
Function / homology
Function and homology information


carotenoid epsilon hydroxylase / : / carotenoid biosynthetic process / chloroplast envelope / chloroplast / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Carotene epsilon-monooxygenase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNiu, G. / Guo, Q. / Liu, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis for plant lutein biosynthesis from alpha-carotene.
Authors: Niu, G. / Guo, Q. / Wang, J. / Zhao, S. / He, Y. / Liu, L.
History
DepositionNov 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carotene epsilon-monooxygenase, chloroplastic
B: Carotene epsilon-monooxygenase, chloroplastic
C: Carotene epsilon-monooxygenase, chloroplastic
D: Carotene epsilon-monooxygenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,41922
Polymers211,7984
Non-polymers4,62118
Water34,3011904
1
A: Carotene epsilon-monooxygenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0595
Polymers52,9501
Non-polymers1,1094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carotene epsilon-monooxygenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0595
Polymers52,9501
Non-polymers1,1094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carotene epsilon-monooxygenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1516
Polymers52,9501
Non-polymers1,2015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Carotene epsilon-monooxygenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1516
Polymers52,9501
Non-polymers1,2015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.749, 127.322, 143.671
Angle α, β, γ (deg.)90.000, 92.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Carotene epsilon-monooxygenase, chloroplastic / Cytochrome P450 97C1 / Protein LUTEIN DEFICIENT 1


Mass: 52949.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYP97C1, LUT1, At3g53130, T4D2.60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6TBX7, carotenoid epsilon hydroxylase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar
ChemComp-SOG / octyl 1-thio-beta-D-glucopyranoside / 2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / 1-S-OCTYL-BETA-D-THIOGLUCOSIDE / octyl 1-thio-beta-D-glucoside / octyl 1-thio-D-glucoside / octyl 1-thio-glucoside


Type: D-saccharide / Mass: 308.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O5S / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1904 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Ammonium citrate, PEG 3350, OTG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.995→50 Å / Num. obs: 148875 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 13.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 2 / Num. unique obs: 14803 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KF2

4kf2


Resolution: 2→40.7 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 6849 5.1 %
Rwork0.172 127486 -
obs0.175 134335 89.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.86 Å2 / Biso mean: 30.47 Å2 / Biso min: 7.86 Å2
Refinement stepCycle: final / Resolution: 2→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14602 0 312 1904 16818
Biso mean--32.7 36.95 -
Num. residues----1862
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.001-2.01720.2799960.2362206544
2.0172-2.04090.30551340.2267277458
2.0409-2.06580.34511680.2179295262
2.0658-2.0920.25461800.209310067
2.092-2.11950.28731770.2074330969
2.1195-2.14850.2721810.1979345173
2.1485-2.17920.29082000.1906361176
2.1792-2.21170.23381960.1976381979
2.2117-2.24630.26141820.1974395183
2.2463-2.28310.25492360.1997411086
2.2831-2.32250.27072100.2038425890
2.3225-2.36470.24112380.1933451294
2.3647-2.41020.25522530.1878454897
2.4102-2.45940.2532810.1943469599
2.4594-2.51290.23442390.19964717100
2.5129-2.57130.27782380.19484856100
2.5713-2.63560.25092510.19044659100
2.6356-2.70680.25692740.194816100
2.7068-2.78650.25892750.1954718100
2.7865-2.87640.24192400.19064751100
2.8764-2.97920.28622670.18984762100
2.9792-3.09840.26092500.18454799100
3.0984-3.23940.23982450.17834770100
3.2394-3.41010.21082730.17084750100
3.4101-3.62360.23262540.16074802100
3.6236-3.90320.19952750.14854720100
3.9032-4.29560.17192410.13534800100
4.2956-4.91630.16322660.12644784100
4.9163-6.19050.17232630.15034827100
6.1905-40.6990.17992660.1583480099

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