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- PDB-5zf0: X-ray Structure of the Electron Transfer Complex between Ferredox... -

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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 PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / 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 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Electron transport accessory-like domain superfamily / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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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

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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)

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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

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Details

Has protein modificationY

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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: 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

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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

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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 %

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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

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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

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