[English] 日本語
Yorodumi
- PDB-2zxk: Crystal structure of SeMet-Red chlorophyll catabolite reductase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zxk
TitleCrystal structure of SeMet-Red chlorophyll catabolite reductase
ComponentsRed chlorophyll catabolite reductase, chloroplastic
KeywordsOXIDOREDUCTASE / ALPHA-BETA-ALPHA SANDWICH / Chlorophyll catabolism / Chloroplast / Coiled coil / NADP / Plastid / 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 / cytosol / cytoplasm
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
Red chlorophyll catabolite reductase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsSugishima, M. / Kitamori, Y. / Fukuyama, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of red chlorophyll catabolite reductase: enlargement of the ferredoxin-dependent bilin reductase family
Authors: Sugishima, M. / Kitamori, Y. / Noguchi, M. / Kohchi, T. / Fukuyama, K.
History
DepositionDec 29, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,6584
Polymers65,6122
Non-polymers462
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-33 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.978, 83.539, 120.404
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 32806.172 Da / Num. of mol.: 2 / Fragment: truncated the chloroplast transit peptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RCCR / 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-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 22% PEG 4000, 0.1M ammonium sulfate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97912, 0.97940, 0.96406, 0.99500
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 19, 2008
RadiationMonochromator: Si(111) double monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979121
20.97941
30.964061
40.9951
ReflectionResolution: 2.5→50 Å / Num. all: 19469 / Num. obs: 19469 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 11 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 8.5 / Num. unique all: 1768 / % possible all: 91.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→19.48 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.863 / SU B: 24.391 / SU ML: 0.263 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.018 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29085 963 5.2 %RANDOM
Rwork0.21542 ---
all0.21929 17640 --
obs0.21929 17640 100 %-
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: 28.762 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4065 0 2 44 4111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224148
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9795624
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3815514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15524.194186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.89915720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8791529
X-RAY DIFFRACTIONr_chiral_restr0.1260.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023129
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.21993
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22838
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2660.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7891.52610
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.524225
X-RAY DIFFRACTIONr_scbond_it2.55631568
X-RAY DIFFRACTIONr_scangle_it3.9864.51399
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 47 -
Rwork0.241 1110 -
obs--100 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more