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- PDB-3aga: Crystal structure of RCC-bound red chlorophyll catabolite reducta... -

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Basic information

Entry
Database: PDB / ID: 3aga
TitleCrystal structure of RCC-bound red chlorophyll catabolite reductase from Arabidopsis thaliana
ComponentsRed chlorophyll catabolite reductase, chloroplastic
KeywordsOXIDOREDUCTASE / chlorophyll degradation / enzyme-substrate complex / 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: 2.6 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_asym_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_asym_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)64,0916
Polymers62,7922
Non-polymers1,2994
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-16 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.500, 85.640, 133.300
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: 31395.805 Da / Num. of mol.: 2 / Fragment: UNP residues 49-319
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.: 2 / 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.: 27 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% 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: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 28, 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: 2.6→50 Å / Num. all: 16060 / Num. obs: 16060 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.086 / Net I/σ(I): 12.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 763 / Rsym value: 0.373 / % possible all: 91.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZXL

2zxl


Resolution: 2.6→19.96 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 738 -random
Rwork0.228 ---
all0.23 16060 --
obs0.23 15088 90.4 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-20.024 Å20 Å20 Å2
2---2.044 Å20 Å2
3----17.98 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4247 0 94 27 4368
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5361.5
X-RAY DIFFRACTIONc_scbond_it1.8752
X-RAY DIFFRACTIONc_mcangle_it2.6922
X-RAY DIFFRACTIONc_scangle_it2.8772.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4RCC.param

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