[English] 日本語
Yorodumi
- PDB-5zf0: X-ray Structure of the Electron Transfer Complex between Ferredox... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zf0
TitleX-ray Structure of the Electron Transfer Complex between Ferredoxin and Photosystem I
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Ferredoxin-1
  • Photosystem I iron-sulfur center
  • PsaX
KeywordsPHOTOSYNTHESIS/ELECTRON TRANSPORT / Photosystem I / Ferredoxin / PHOTOSYNTHESIS-ELECTRON TRANSPORT complex
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Ferredoxin [2Fe-2S], plant / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK ...Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Ferredoxin [2Fe-2S], plant / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Ferredoxin-1 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII ...BETA-CAROTENE / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Ferredoxin-1 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XI
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
Thermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsKubota-Kawai, H. / Mutoh, R. / Shinmura, K. / Setif, P. / Nowaczyk, M. / Roegner, M. / Ikegami, T. / Tanaka, T. / Kurisu, G.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceGS016 Japan
Japan science and technology agency Japan
Japan Society for the Promotion of Science13J03550 Japan
Citation
Journal: Nat Plants / Year: 2018
Title: X-ray structure of an asymmetrical trimeric ferredoxin-photosystem I complex
Authors: Kubota-Kawai, H. / Mutoh, R. / Shinmura, K. / Setif, P. / Nowaczyk, M.M. / Rogner, M. / Ikegami, T. / Tanaka, H. / Kurisu, G.
#1: Journal: Biochemistry / Year: 2015
Title: X-ray Structure and Nuclear Magnetic Resonance Analysis of the Interaction Sites of the Ga-Substituted Cyanobacterial Ferredoxin
Authors: Mutoh, R. / Muraki, N. / Shinmura, K. / Kubota-Kawai, H. / Lee, Y.H. / Nowaczyk, M.M. / Roegner, M. / Hase, T. / Ikegami, T. / Kurisu, G.
History
DepositionMar 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_conn_type
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn_type.id
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A1: Photosystem I P700 chlorophyll a apoprotein A1
B1: Photosystem I P700 chlorophyll a apoprotein A2
C1: Photosystem I iron-sulfur center
D1: Photosystem I reaction center subunit II
E1: Photosystem I reaction center subunit IV
F1: Photosystem I reaction center subunit III
I1: Photosystem I reaction center subunit VIII
J1: Photosystem I reaction center subunit IX
K1: Photosystem I reaction center subunit PsaK
L1: Photosystem I reaction center subunit XI
M1: Photosystem I reaction center subunit XII
X1: PsaX
A2: Photosystem I P700 chlorophyll a apoprotein A1
B2: Photosystem I P700 chlorophyll a apoprotein A2
C2: Photosystem I iron-sulfur center
D2: Photosystem I reaction center subunit II
E2: Photosystem I reaction center subunit IV
F2: Photosystem I reaction center subunit III
I2: Photosystem I reaction center subunit VIII
J2: Photosystem I reaction center subunit IX
K2: Photosystem I reaction center subunit PsaK
L2: Photosystem I reaction center subunit XI
M2: Photosystem I reaction center subunit XII
X2: PsaX
A3: Photosystem I P700 chlorophyll a apoprotein A1
B3: Photosystem I P700 chlorophyll a apoprotein A2
C3: Photosystem I iron-sulfur center
D3: Photosystem I reaction center subunit II
E3: Photosystem I reaction center subunit IV
F3: Photosystem I reaction center subunit III
I3: Photosystem I reaction center subunit VIII
J3: Photosystem I reaction center subunit IX
K3: Photosystem I reaction center subunit PsaK
L3: Photosystem I reaction center subunit XI
M3: Photosystem I reaction center subunit XII
X3: PsaX
A4: Photosystem I P700 chlorophyll a apoprotein A1
B4: Photosystem I P700 chlorophyll a apoprotein A2
C4: Photosystem I iron-sulfur center
D4: Photosystem I reaction center subunit II
E4: Photosystem I reaction center subunit IV
F4: Photosystem I reaction center subunit III
I4: Photosystem I reaction center subunit VIII
J4: Photosystem I reaction center subunit IX
K4: Photosystem I reaction center subunit PsaK
L4: Photosystem I reaction center subunit XI
M4: Photosystem I reaction center subunit XII
X4: PsaX
A6: Photosystem I P700 chlorophyll a apoprotein A1
B6: Photosystem I P700 chlorophyll a apoprotein A2
C6: Photosystem I iron-sulfur center
D6: Photosystem I reaction center subunit II
E6: Photosystem I reaction center subunit IV
F6: Photosystem I reaction center subunit III
I6: Photosystem I reaction center subunit VIII
J6: Photosystem I reaction center subunit IX
K6: Photosystem I reaction center subunit PsaK
L6: Photosystem I reaction center subunit XI
M6: Photosystem I reaction center subunit XII
X6: PsaX
A5: Photosystem I P700 chlorophyll a apoprotein A1
B5: Photosystem I P700 chlorophyll a apoprotein A2
C5: Photosystem I iron-sulfur center
D5: Photosystem I reaction center subunit II
E5: Photosystem I reaction center subunit IV
F5: Photosystem I reaction center subunit III
I5: Photosystem I reaction center subunit VIII
J5: Photosystem I reaction center subunit IX
K5: Photosystem I reaction center subunit PsaK
L5: Photosystem I reaction center subunit XI
M5: Photosystem I reaction center subunit XII
X5: PsaX
P1: Ferredoxin-1
P2: Ferredoxin-1
P3: Ferredoxin-1
P4: Ferredoxin-1
P6: Ferredoxin-1
P5: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,223,592852
Polymers1,607,30678
Non-polymers616,287774
Water00
1
A1: Photosystem I P700 chlorophyll a apoprotein A1
B1: Photosystem I P700 chlorophyll a apoprotein A2
C1: Photosystem I iron-sulfur center
D1: Photosystem I reaction center subunit II
E1: Photosystem I reaction center subunit IV
F1: Photosystem I reaction center subunit III
I1: Photosystem I reaction center subunit VIII
J1: Photosystem I reaction center subunit IX
K1: Photosystem I reaction center subunit PsaK
L1: Photosystem I reaction center subunit XI
M1: Photosystem I reaction center subunit XII
X1: PsaX
A2: Photosystem I P700 chlorophyll a apoprotein A1
B2: Photosystem I P700 chlorophyll a apoprotein A2
C2: Photosystem I iron-sulfur center
D2: Photosystem I reaction center subunit II
E2: Photosystem I reaction center subunit IV
F2: Photosystem I reaction center subunit III
I2: Photosystem I reaction center subunit VIII
J2: Photosystem I reaction center subunit IX
K2: Photosystem I reaction center subunit PsaK
L2: Photosystem I reaction center subunit XI
M2: Photosystem I reaction center subunit XII
X2: PsaX
A3: Photosystem I P700 chlorophyll a apoprotein A1
B3: Photosystem I P700 chlorophyll a apoprotein A2
C3: Photosystem I iron-sulfur center
D3: Photosystem I reaction center subunit II
E3: Photosystem I reaction center subunit IV
F3: Photosystem I reaction center subunit III
I3: Photosystem I reaction center subunit VIII
J3: Photosystem I reaction center subunit IX
K3: Photosystem I reaction center subunit PsaK
L3: Photosystem I reaction center subunit XI
M3: Photosystem I reaction center subunit XII
X3: PsaX
P1: Ferredoxin-1
P2: Ferredoxin-1
P3: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,111,796426
Polymers803,65339
Non-polymers308,143387
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A4: Photosystem I P700 chlorophyll a apoprotein A1
B4: Photosystem I P700 chlorophyll a apoprotein A2
C4: Photosystem I iron-sulfur center
D4: Photosystem I reaction center subunit II
E4: Photosystem I reaction center subunit IV
F4: Photosystem I reaction center subunit III
I4: Photosystem I reaction center subunit VIII
J4: Photosystem I reaction center subunit IX
K4: Photosystem I reaction center subunit PsaK
L4: Photosystem I reaction center subunit XI
M4: Photosystem I reaction center subunit XII
X4: PsaX
A6: Photosystem I P700 chlorophyll a apoprotein A1
B6: Photosystem I P700 chlorophyll a apoprotein A2
C6: Photosystem I iron-sulfur center
D6: Photosystem I reaction center subunit II
E6: Photosystem I reaction center subunit IV
F6: Photosystem I reaction center subunit III
I6: Photosystem I reaction center subunit VIII
J6: Photosystem I reaction center subunit IX
K6: Photosystem I reaction center subunit PsaK
L6: Photosystem I reaction center subunit XI
M6: Photosystem I reaction center subunit XII
X6: PsaX
A5: Photosystem I P700 chlorophyll a apoprotein A1
B5: Photosystem I P700 chlorophyll a apoprotein A2
C5: Photosystem I iron-sulfur center
D5: Photosystem I reaction center subunit II
E5: Photosystem I reaction center subunit IV
F5: Photosystem I reaction center subunit III
I5: Photosystem I reaction center subunit VIII
J5: Photosystem I reaction center subunit IX
K5: Photosystem I reaction center subunit PsaK
L5: Photosystem I reaction center subunit XI
M5: Photosystem I reaction center subunit XII
X5: PsaX
P4: Ferredoxin-1
P6: Ferredoxin-1
P5: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,111,796426
Polymers803,65339
Non-polymers308,143387
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)214.101, 239.668, 265.605
Angle α, β, γ (deg.)90.00, 101.08, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 12 molecules A1A2A3A4A6A5B1B2B3B4B6B5

#1: Protein
Photosystem I P700 chlorophyll a apoprotein A1 / PsaA


Mass: 83267.773 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A405, photosystem I
#2: Protein
Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 82992.453 Da / Num. of mol.: 6 / Fragment: UNP residues 2-741 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A407, photosystem I

-
Protein , 2 types, 12 molecules C1C2C3C4C6C5P1P2P3P4P6P5

#3: Protein
Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8678.011 Da / Num. of mol.: 6 / Fragment: UNP residues 2-81 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A415, photosystem I
#13: Protein
Ferredoxin-1 / Ferredoxin I


Mass: 10722.764 Da / Num. of mol.: 6 / Fragment: UNP residues 2-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / Gene: petF1, petF, tsl1009 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3C9

-
Photosystem I reaction center subunit ... , 8 types, 48 molecules D1D2D3D4D6D5E1E2E3E4E6E5F1F2F3F4F6F5I1I2I3I4I6I5J1J2J3J4J6J5...

#4: Protein
Photosystem I reaction center subunit II / Photosystem I 16 kDa polypeptide / PSI-D


Mass: 15258.297 Da / Num. of mol.: 6 / Fragment: UNP residues 2-139 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A420
#5: Protein
Photosystem I reaction center subunit IV / Photosystem I 8.1 kDa protein / p30 protein


Mass: 8268.290 Da / Num. of mol.: 6 / Fragment: UNP residues 2-76 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A423
#6: Protein
Photosystem I reaction center subunit III / PSI-F


Mass: 17716.586 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A401
#7: Protein/peptide
Photosystem I reaction center subunit VIII


Mass: 4297.234 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A427
#8: Protein/peptide
Photosystem I reaction center subunit IX


Mass: 4770.698 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A429
#9: Protein
Photosystem I reaction center subunit PsaK / Light-harvesting 8.0 kDa polypeptide / Photosystem I subunit X


Mass: 8483.983 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A425
#10: Protein
Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 16156.569 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: Q8DGB4
#11: Protein/peptide
Photosystem I reaction center subunit XII / PSI-M


Mass: 3426.115 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A403

-
Protein/peptide , 1 types, 6 molecules X1X2X3X4X6X5

#12: Protein/peptide
PsaX


Mass: 3845.508 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria)

-
Non-polymers , 8 types, 774 molecules

#14: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 576 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#15: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C31H46O2
#16: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 132 / Source method: obtained synthetically / Formula: C40H56
#17: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#18: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Fe4S4
#19: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C45H86O10
#20: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#21: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.32 Å3/Da / Density % sol: 71.5 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 4.6 / Details: 41% PEG200, 100 mM acetate buffer, 100 mM NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 4.2→158.04 Å / Num. obs: 191480 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 8.7
Reflection shellResolution: 4.2→4.43 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 2.3 / Num. unique all: 27882 / Num. unique obs: 212827 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLM1.0.7data reduction
SCALA3.3.20data scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JB0

1jb0


Resolution: 4.2→158.04 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.37705 9092 5 %RANDOM
Rwork0.35302 ---
obs0.35423 181835 99.88 %-
Displacement parametersBiso mean: 158.055 Å2
Refinement stepCycle: LAST / Resolution: 4.2→158.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms108852 0 39642 0 148494
LS refinement shellResolution: 4.199→4.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 674 -
Rwork0.446 13218 -
obs--98.57 %

+
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