[English] 日本語
Yorodumi
- PDB-4fby: fs X-ray diffraction of Photosystem II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fby
Titlefs X-ray diffraction of Photosystem II
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 16
  • Cytochrome c-550
  • Photosystem Q(B) protein 1
KeywordsPHOTOSYNTHESIS / PHOTOSYSTEM / PS II / PS2 / MEMBRANE COMPLEX / TRANSMEMBRANE ALPHA-HELIX / X-RAY FREE ELECTRON LASER / PHOTOSYSTEM II / REACTION CENTER / IRON / MANGANESE / Light harvesting / electron transport / water oxidation / Thylakoid Membrane
Function / homology
Function and homology information


photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / extrinsic component of membrane / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / phosphate ion binding / photosynthesis, light reaction / : / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising ...Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Photosystem II PsbX, type 1 subfamily / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / OXYGEN EVOLVING SYSTEM / PHEOPHYTIN A ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / OXYGEN EVOLVING SYSTEM / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Photosystem II extrinsic protein V / Photosystem II extrinsic protein O / Photosystem II protein D1 1 / Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II reaction center protein M / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Photosystem II reaction center protein K / Photosystem II extrinsic protein U / Photosystem II reaction center protein X
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 6.56 Å
AuthorsKern, J. / Alonso-Mori, R. / Hellmich, J. / Tran, R. / Hattne, J. / Laksmono, H. / Gloeckner, C. / Echols, N. / Sierra, R.G. / Sellberg, J. ...Kern, J. / Alonso-Mori, R. / Hellmich, J. / Tran, R. / Hattne, J. / Laksmono, H. / Gloeckner, C. / Echols, N. / Sierra, R.G. / Sellberg, J. / Lassalle-Kaiser, B. / Gildea, R.J. / Glatzel, P. / Grosse-Kunstleve, R.W. / Latimer, M.J. / Mcqueen, T.A. / Difiore, D. / Fry, A.R. / Messerschmidt, M.M. / Miahnahri, A. / Schafer, D.W. / Seibert, M.M. / Sokaras, D. / Weng, T.-C. / Zwart, P.H. / White, W.E. / Adams, P.D. / Bogan, M.J. / Boutet, S. / Williams, G.J. / Messinger, J. / Sauter, N.K. / Zouni, A. / Bergmann, U. / Yano, J. / Yachandra, V.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Room temperature femtosecond X-ray diffraction of photosystem II microcrystals.
Authors: Kern, J. / Alonso-Mori, R. / Hellmich, J. / Tran, R. / Hattne, J. / Laksmono, H. / Glockner, C. / Echols, N. / Sierra, R.G. / Sellberg, J. / Lassalle-Kaiser, B. / Gildea, R.J. / Glatzel, P. ...Authors: Kern, J. / Alonso-Mori, R. / Hellmich, J. / Tran, R. / Hattne, J. / Laksmono, H. / Glockner, C. / Echols, N. / Sierra, R.G. / Sellberg, J. / Lassalle-Kaiser, B. / Gildea, R.J. / Glatzel, P. / Grosse-Kunstleve, R.W. / Latimer, M.J. / McQueen, T.A. / DiFiore, D. / Fry, A.R. / Messerschmidt, M. / Miahnahri, A. / Schafer, D.W. / Seibert, M.M. / Sokaras, D. / Weng, T.C. / Zwart, P.H. / White, W.E. / Adams, P.D. / Bogan, M.J. / Boutet, S. / Williams, G.J. / Messinger, J. / Sauter, N.K. / Zouni, A. / Bergmann, U. / Yano, J. / Yachandra, V.K.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Non-polymer description
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Dec 21, 2016Group: Data collection
Revision 1.4Nov 15, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.6Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Sep 13, 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_site
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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.pdbx_stereo_config / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Photosystem Q(B) protein 1
B: Photosystem II core light harvesting protein
C: Photosystem II CP43 protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Photosystem II manganese-stabilizing polypeptide
T: Photosystem II reaction center protein T
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
y: Photosystem II reaction center protein ycf12
X: Photosystem II reaction center protein X
Y: Photosystem II reaction center protein Y
Z: Photosystem II reaction center protein Z
G: Photosystem Q(B) protein 1
N: Photosystem II core light harvesting protein
P: Photosystem II CP43 protein
Q: Photosystem II D2 protein
R: Cytochrome b559 subunit alpha
S: Cytochrome b559 subunit beta
W: Photosystem II reaction center protein H
a: Photosystem II reaction center protein I
b: Photosystem II reaction center protein J
c: Photosystem II reaction center protein K
d: Photosystem II reaction center protein L
e: Photosystem II reaction center protein M
f: Photosystem II manganese-stabilizing polypeptide
g: Photosystem II reaction center protein T
h: Photosystem II 12 kDa extrinsic protein
i: Cytochrome c-550
m: Photosystem II reaction center protein ycf12
j: Photosystem II reaction center protein X
k: Photosystem II reaction center protein Y
l: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)741,330222
Polymers605,82340
Non-polymers135,507182
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.783, 227.764, 308.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asymmetric unit

-
Components

-
Protein , 2 types, 4 molecules AGVi

#1: Protein Photosystem Q(B) protein 1 / 32 kDa thylakoid membrane protein 1 / Photosystem II protein D1 1


Mass: 38265.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A444, photosystem II
#16: Protein Cytochrome c-550 / Cytochrome c-549 / Cytochrome c550 / Low-potential cytochrome c


Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A386

-
Photosystem II ... , 16 types, 32 molecules BNCPDQHWIaJbKcLdMeOfTgUhymXjYkZl

#2: Protein Photosystem II core light harvesting protein


Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ1
#3: Protein Photosystem II CP43 protein


Mass: 50287.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIF8
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8CM25, photosystem II
#7: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7227.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJ43
#8: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.4 kDa protein


Mass: 4410.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJZ6
#9: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 3974.712 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P59087
#10: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1K9
#11: Protein/peptide Photosystem II reaction center protein L / PSII-L / PSII 5 kDa protein


Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIN8
#12: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3981.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHA7
#13: Protein Photosystem II manganese-stabilizing polypeptide / MSP


Mass: 26851.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A431
#14: Protein/peptide Photosystem II reaction center protein T / PSII-T / PSII-Tc


Mass: 3878.728 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ0
#15: Protein Photosystem II 12 kDa extrinsic protein / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 11655.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1L5
#17: Protein/peptide Photosystem II reaction center protein ycf12


Mass: 5039.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJI1
#18: Protein/peptide Photosystem II reaction center protein X


Mass: 4191.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1R6
#19: Protein/peptide Photosystem II reaction center protein Y


Mass: 2400.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1
#20: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHJ2

-
Cytochrome b559 subunit ... , 2 types, 4 molecules ERFS

#5: Protein Cytochrome b559 subunit alpha / PSII reaction center subunit V


Mass: 9449.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIP0
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4936.704 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIN9

-
Sugars , 2 types, 28 molecules

#24: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C51H96O15
#31: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 13 types, 154 molecules

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


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#22: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#23: Chemical
ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C53H80O2
#25: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#26: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C41H78O12S
#27: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C45H86O10
#28: Chemical ChemComp-OEC / OXYGEN EVOLVING SYSTEM


Mass: 323.828 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O4
#29: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#30: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C40H56
#32: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#33: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#34: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#35: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

-
Details

Has protein modificationY
Sequence detailsCHAIN "Y" AND "k":THE DEPOSITORS KNOW THE SEQUENCE (UNIPROT ID Q8DKM3) BUT DUE TO POOR DENSITY ...CHAIN "Y" AND "k":THE DEPOSITORS KNOW THE SEQUENCE (UNIPROT ID Q8DKM3) BUT DUE TO POOR DENSITY CAN'T ASIGN IT WITH CERTAINTY TO THE DENSITY. INSTEAD CHAIN Y WAS MODELED AS POLY-ALA. MET ASP TRP ARG VAL LEU VAL VAL LEU LEU PRO VAL LEU LEU ALA ALA GLY TRP ALA VAL ARG ASN ILE LEU PRO TYR ALA VAL LYS GLN VAL GLN LYS LEU LEU GLN LYS ALA LYS ALA ALA THE SEQUENCE MATCHES TO UNIPROT REFERENCE Q8DKM3

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2984

-
Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.58 %
Crystal growTemperature: 298 K / pH: 7
Details: 4% PEG 2000, 5 mM CaCl2, 100 mM PIPES, pH 7.0, batch, temperature 298K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.323
DetectorType: CS-PAD / Detector: PIXEL / Date: Sep 19, 2011 / Details: KB MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.323 Å / Relative weight: 1
ReflectionResolution: 6.556→85.89 Å / Num. obs: 17962 / % possible obs: 98.1 % / Biso Wilson estimate: 10.83 Å2
Reflection shellResolution: 6.5→6.73 Å / Redundancy: 2.84 % / Mean I/σ(I) obs: 6.74 / % possible all: 89.6

-
Processing

Software
NameVersionClassificationNB
PHENIX1.7.3refinement
PDB_EXTRACT3.11data extraction
cctbx.xfeldata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BZ1

3bz1
PDB Unreleased entry


Resolution: 6.56→85.89 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 1.36 / σ(F): 1.48 / Phase error: 40.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.385 895 5 %
Rwork0.366 --
obs0.367 17914 97.8 %
all-18310 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.83 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 150.17 Å2
Baniso -1Baniso -2Baniso -3
1--3.9585 Å20 Å20 Å2
2--43.0052 Å2-0 Å2
3----39.0467 Å2
Refinement stepCycle: LAST / Resolution: 6.56→85.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41052 0 9180 0 50232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752048
X-RAY DIFFRACTIONf_angle_d1.48371500
X-RAY DIFFRACTIONf_dihedral_angle_d16.09519968
X-RAY DIFFRACTIONf_chiral_restr0.0957242
X-RAY DIFFRACTIONf_plane_restr0.0087548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.5556-6.96620.45681310.42722480X-RAY DIFFRACTION88
6.9662-7.50370.41931500.39132835X-RAY DIFFRACTION100
7.5037-8.25830.39961490.35262866X-RAY DIFFRACTION100
8.2583-9.4520.34711530.3272884X-RAY DIFFRACTION100
9.452-11.90350.34191520.31812923X-RAY DIFFRACTION100
11.9035-85.8920.38551600.39423031X-RAY DIFFRACTION100

+
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