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- PDB-3agc: F218V mutant of the substrate-bound red chlorophyll catabolite re... -

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Basic information

Entry
Database: PDB / ID: 3agc
TitleF218V mutant of the substrate-bound red chlorophyll catabolite reductase from Arabidopsis thaliana
ComponentsRed chlorophyll catabolite reductase, chloroplastic
KeywordsOXIDOREDUCTASE / chlorophyll degradation / substrate-bound enzyme / Chlorophyll catabolism / Chloroplast / NADP / Transit peptide
Function / homology
Function and homology information


red chlorophyll catabolite reductase / red chlorophyll catabolite reductase activity / chlorophyll catabolic process / regulation of plant-type hypersensitive response / defense response to other organism / regulation of programmed cell death / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / chloroplast ...red chlorophyll catabolite reductase / red chlorophyll catabolite reductase activity / chlorophyll catabolic process / regulation of plant-type hypersensitive response / defense response to other organism / regulation of programmed cell death / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / mitochondrion / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Red chlorophyll catabolite reductase / Red chlorophyll catabolite reductase (RCC reductase) / oxygen-dependent coproporphyrinogen oxidase - #20 / oxygen-dependent coproporphyrinogen oxidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-RCC / Red chlorophyll catabolite reductase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSugishima, M. / Fukuyama, K.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structures of the substrate-bound forms of red chlorophyll catabolite reductase: implications for site-specific and stereospecific reaction
Authors: Sugishima, M. / Okamoto, Y. / Noguchi, M. / Kohchi, T. / Tamiaki, H. / Fukuyama, K.
History
DepositionMar 30, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Red chlorophyll catabolite reductase, chloroplastic
B: Red chlorophyll catabolite reductase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3685
Polymers62,6962
Non-polymers6733
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-15 kcal/mol
Surface area23810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.089, 84.321, 131.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Red chlorophyll catabolite reductase, chloroplastic / RCC reductase / AtRCCR / Accelerated cell death protein 2


Mass: 31347.766 Da / Num. of mol.: 2 / Fragment: UNP residues 49-319 / Mutation: F218V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RCCR, ACD2, At4g37000, C7A10_360 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q8LDU4, EC: 1.3.1.80
#2: Chemical ChemComp-RCC / 3-{(2Z,3S,4S)-5-[(Z)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-2-[(5R)-2-[(3-ethyl-5-formyl-4-methyl-1H-pyrrol-2-yl)methyl]-5-(methoxycarbonyl)-3-methyl-4-oxo-4,5-dihydrocyclopenta[b]pyrrol-6(1H)-ylidene]-4-methyl-3,4-dihydro-2H-pyrrol-3-yl}propanoic acid / Red chlorophyll catabolite


Mass: 626.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H38N4O7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 1.99 Å3/Da / Density % sol: 38.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 35% PEG 2000 monomethyl ether, 0.1M ammonium acetate, 3% dioxane, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 13, 2009
RadiationMonochromator: Si(111) double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 34491 / Num. obs: 34491 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rsym value: 0.059 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 6 % / Mean I/σ(I) obs: 8 / Num. unique all: 3425 / Rsym value: 0.356 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZXL

2zxl


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.907 / SU B: 9.357 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.242 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26992 1735 5 %RANDOM
Rwork0.20885 ---
all0.21181 32702 --
obs0.21181 32702 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.784 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4225 0 48 315 4588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224371
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9965926
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4575527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59124.171199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73615791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2591534
X-RAY DIFFRACTIONr_chiral_restr0.0760.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023278
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.22111
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22980
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2346
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4281.52675
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82824367
X-RAY DIFFRACTIONr_scbond_it1.16631782
X-RAY DIFFRACTIONr_scangle_it1.9654.51559
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 130 -
Rwork0.226 2339 -
obs--97.98 %

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