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- PDB-6j94: Crystal structure of CYP97A3 -

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Basic information

Entry
Database: PDB / ID: 6j94
TitleCrystal structure of CYP97A3
ComponentsProtein LUTEIN DEFICIENT 5, chloroplastic
KeywordsOXIDOREDUCTASE / lutein biosynthesis / photosynthesis / monooxygenase / carotenoid / P450
Function / homology
Function and homology information


beta-carotene 3-hydroxylase activity / xanthophyll biosynthetic process / carotenoid biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / chloroplast envelope / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / chloroplast / iron ion binding / heme binding
Similarity search - Function
: / Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Protein LUTEIN DEFICIENT 5, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsNiu, G. / Guo, Q. / Wang, J. / Zhao, S.
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
DepositionJan 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
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
Revision 1.2Jun 24, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein LUTEIN DEFICIENT 5, chloroplastic
B: Protein LUTEIN DEFICIENT 5, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1614
Polymers116,9282
Non-polymers1,2332
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-74 kcal/mol
Surface area40330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.006, 70.414, 133.168
Angle α, β, γ (deg.)90.000, 124.620, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein LUTEIN DEFICIENT 5, chloroplastic / Cytochrome P450 97A3


Mass: 58463.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYP97A3, LUT5, At1g31800, F5M6.19 / Production host: Escherichia coli (E. coli)
References: UniProt: Q93VK5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 59.69 %
Crystal growTemperature: 289 K / Method: liquid diffusion / pH: 6.5 / Details: 0.1 M MES, 12% (w/v) PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 48368 / % possible obs: 98.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 35.23 Å2 / CC1/2: 0.937 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.054 / Rrim(I) all: 0.105 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2 / Num. unique obs: 4769 / CC1/2: 0.752 / Rpim(I) all: 0.409 / Rrim(I) all: 0.807 / % possible all: 97.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KF2

4kf2


Resolution: 2.401→41.963 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.74
RfactorNum. reflection% reflection
Rfree0.2133 2354 5.05 %
Rwork0.1831 --
obs0.1846 46652 94.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.94 Å2 / Biso mean: 20.87 Å2 / Biso min: 2.59 Å2
Refinement stepCycle: final / Resolution: 2.401→41.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7241 0 86 648 7975
Biso mean--6.64 23.73 -
Num. residues----914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057553
X-RAY DIFFRACTIONf_angle_d0.94710299
X-RAY DIFFRACTIONf_chiral_restr0.0631151
X-RAY DIFFRACTIONf_plane_restr0.0041314
X-RAY DIFFRACTIONf_dihedral_angle_d13.9662811
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4007-2.44970.3109910.24261891198270
2.4497-2.5030.26391330.23992157229079
2.503-2.56120.26431390.24212415255488
2.5612-2.62520.27371280.23042648277696
2.6252-2.69620.28611490.23322636278598
2.6962-2.77550.28581320.21992686281898
2.7755-2.86510.24091570.21612655281298
2.8651-2.96740.25481330.21182720285399
2.9674-3.08620.21541310.20372704283598
3.0862-3.22660.24731490.19912656280599
3.2266-3.39670.21541520.19272702285499
3.3967-3.60940.24471510.1752710286199
3.6094-3.88790.18531450.15692725287099
3.8879-4.27880.17361330.1522724285799
4.2788-4.89710.15491540.14152718287299
4.8971-6.16670.20081600.17562738289899
6.1667-41.9690.17011170.16182813293097

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