[English] 日本語
Yorodumi
- PDB-3aeu: Structure of the light-independent protochlorophyllide reductase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3aeu
TitleStructure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark
Components
  • Light-independent protochlorophyllide reductase subunit B
  • Light-independent protochlorophyllide reductase subunit N
KeywordsOXIDOREDUCTASE / Iron/sulfur cluster / Bacteriochlorophyll biosynthesis / Chlorophyll biosynthesis / Photosynthesis
Function / homology
Function and homology information


ferredoxin:protochlorophyllide reductase (ATP-dependent) / photosynthesis, dark reaction / light-independent bacteriochlorophyll biosynthetic process / oxidoreductase activity, acting on iron-sulfur proteins as donors / oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 - #20 / Light-independent protochlorophyllide reductase, N subunit / : / Light-independent protochlorophyllide reductase, B subunit / Protochlorophyllide reductase, ChlB, light independent / Light-independent protochlorophyllide reductase subunit B-like, C-terminal / Proto-chlorophyllide reductase, C-terminal / Proto-chlorophyllide reductase 57 kD subunit / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / Nitrogenase/oxidoreductase, component 1 ...Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 - #20 / Light-independent protochlorophyllide reductase, N subunit / : / Light-independent protochlorophyllide reductase, B subunit / Protochlorophyllide reductase, ChlB, light independent / Light-independent protochlorophyllide reductase subunit B-like, C-terminal / Proto-chlorophyllide reductase, C-terminal / Proto-chlorophyllide reductase 57 kD subunit / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / Nitrogenase/oxidoreductase, component 1 / : / Nitrogenase component 1 type Oxidoreductase / Nitrogenase molybdenum iron protein domain / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Light-independent protochlorophyllide reductase subunit B / Light-independent protochlorophyllide reductase subunit N
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMuraki, N. / Nomata, J. / Shiba, T. / Fujita, Y. / Kurisu, G.
CitationJournal: Nature / Year: 2010
Title: X-ray crystal structure of the light-independent protochlorophyllide reductase
Authors: Muraki, N. / Nomata, J. / Ebata, K. / Mizoguchi, T. / Shiba, T. / Tamiaki, H. / Kurisu, G. / Fujita, Y.
History
DepositionFeb 10, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Light-independent protochlorophyllide reductase subunit N
B: Light-independent protochlorophyllide reductase subunit B
C: Light-independent protochlorophyllide reductase subunit N
D: Light-independent protochlorophyllide reductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,5626
Polymers208,8594
Non-polymers7032
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16160 Å2
ΔGint-81 kcal/mol
Surface area57580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.354, 80.615, 176.220
Angle α, β, γ (deg.)90.00, 101.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRASNASNAA7 - 42019 - 432
21THRTHRASNASNCC7 - 42019 - 432
12METMETARGARGBB1 - 4191 - 419
22METMETARGARGDD1 - 4191 - 419

NCS ensembles :
ID
1
2

-
Components

#1: Protein Light-independent protochlorophyllide reductase subunit N / LI-POR subunit N / DPOR subunit N / dark-operative protochlorophyllide oxidoreductase N-protein


Mass: 47212.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: bchN / Plasmid: PASK-IBA5PLUS / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P26164, EC: 1.18.-.-
#2: Protein Light-independent protochlorophyllide reductase subunit B / LI-POR subunit B / DPOR subunit B / dark-operative protochlorophyllide oxidoreductase B-protein


Mass: 57217.520 Da / Num. of mol.: 2 / Mutation: D36A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: bchB, bchK / Plasmid: PASK-IBA5PLUS / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P26163, EC: 1.18.-.-
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350, 0.2M SODIUM CLORIDE, 0.1M MOPS-NAOH(PH7.0), pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 48730 / % possible obs: 97.9 % / Observed criterion σ(I): -2 / Biso Wilson estimate: 63.03 Å2 / Rmerge(I) obs: 0.141

-
Processing

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

2zmp
PDB Unreleased entry


Resolution: 2.9→39.9 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.876 / SU B: 32.579 / SU ML: 0.285 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2467 5.1 %RANDOM
Rwork0.205 ---
obs0.208 46241 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20.89 Å2
2--1.64 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12721 0 16 15 12752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02213016
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.9817709
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25651660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13423.047535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.529152138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.88915108
X-RAY DIFFRACTIONr_chiral_restr0.1120.22055
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029794
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.26297
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.28936
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2377
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4921.58471
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.904213335
X-RAY DIFFRACTIONr_scbond_it1.4634999
X-RAY DIFFRACTIONr_scangle_it2.4744.54350
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1656tight positional0.060.05
2B1668tight positional0.050.05
1A1512loose positional0.55
2B1525loose positional0.445
1A1656tight thermal0.070.5
2B1668tight thermal0.080.5
1A1512loose thermal1.2510
2B1525loose thermal1.1410
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 151 -
Rwork0.361 2831 -
obs--81.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2966-0.0666-0.02860.43580.11290.55890.00010.04120.00330.0084-0.0404-0.00780.0361-0.01540.0403-0.0277-0.00440.02560.0207-0.0033-0.058455.176436.6971100.832
20.3976-0.0707-0.28180.2318-0.02170.60570.0132-0.10440.0586-0.0269-0.0028-0.0012-0.04460.1046-0.0104-0.0547-0.0450.0010.0123-0.0202-0.007257.105461.1821128.2383
30.35880.06240.05330.5025-0.18740.45140.0097-0.1246-0.01590.0206-0.0310.01470.02790.0110.0213-0.04410.0150.01860.1003-0.0121-0.048216.392540.951158.4472
40.5042-0.0375-0.41290.27750.15670.63020.0330.07580.0987-0.0171-0.0150.0374-0.0596-0.1123-0.018-0.03280.0455-0.00550.02740.00540.014417.52263.8656129.8817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 420
2X-RAY DIFFRACTION2B1 - 419
3X-RAY DIFFRACTION3C7 - 420
4X-RAY DIFFRACTION4D1 - 419

+
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