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- PDB-4ac5: Lipidic sponge phase crystal structure of the Bl. viridis reactio... -

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Basic information

Entry
Database: PDB / ID: 4ac5
TitleLipidic sponge phase crystal structure of the Bl. viridis reaction centre solved using serial femtosecond crystallography
Components
  • (REACTION CENTER PROTEIN ...) x 3
  • PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT
KeywordsPHOTOSYNTHESIS / LIPIDIC-SPONGE PHASE / REACTION CENTER / ELECTRON TRANSPORT / CELL MEMBRANE / METAL- BINDING / TRANSMEMBRANE / FORMYLATION / CHROMOPHORE / LIPOPROTEIN
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / photosynthetic electron transport in photosystem II / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Multiheme cytochrome c family profile. / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Multiheme cytochrome c family profile. / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit
Similarity search - Component
Biological speciesBLASTOCHLORIS VIRIDIS (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 8.2 Å
AuthorsJohansson, L.C. / Arnlund, D. / White, T.A. / Katona, G. / DePonte, D.P. / Weierstall, U. / Doak, R.B. / Shoeman, R.L. / Lomb, L. / Malmerberg, E. ...Johansson, L.C. / Arnlund, D. / White, T.A. / Katona, G. / DePonte, D.P. / Weierstall, U. / Doak, R.B. / Shoeman, R.L. / Lomb, L. / Malmerberg, E. / Davidsson, J. / Nass, K. / Liang, M. / Andreasson, J. / Aquila, A. / Bajt, S. / Barthelmess, M. / Barty, A. / Bogan, M.J. / Bostedt, C. / Bozek, J.D. / Caleman, C. / Coffee, R. / Coppola, N. / Ekeberg, T. / Epp, S.W. / Erk, B. / Fleckenstein, H. / Foucar, L. / Graafsma, H. / Gumprecht, L. / Hajdu, J. / Hampton, C.Y. / Hartmann, R. / Hartmann, A. / Hauser, G. / Hirsemann, H. / Holl, P. / Hunter, M.S. / Kassemeyer, S. / Kimmel, N. / Kirian, R.A. / Maia, F.R.N.C. / Marchesini, S. / Martin, A.V. / Reich, C. / Rolles, D. / Rudek, B. / Rudenko, A. / Schlichting, I. / Schulz, J. / Seibert, M.M. / Sierra, R. / Soltau, H. / Starodub, D. / Stellato, F. / Stern, S. / Struder, L. / Timneanu, N. / Ullrich, J. / Wahlgren, W.Y. / Wang, X. / Weidenspointner, G. / Wunderer, C. / Fromme, P. / Chapman, H.N. / Spence, J.C.H. / Neutze, R.
CitationJournal: Nat.Methods / Year: 2012
Title: Lipidic Phase Membrane Protein Serial Femtosecond Crystallography.
Authors: Johansson, L.C. / Arnlund, D. / White, T.A. / Katona, G. / Deponte, D.P. / Weierstall, U. / Doak, R.B. / Shoeman, R.L. / Lomb, L. / Malmerberg, E. / Davidsson, J. / Nass, K. / Liang, M. / ...Authors: Johansson, L.C. / Arnlund, D. / White, T.A. / Katona, G. / Deponte, D.P. / Weierstall, U. / Doak, R.B. / Shoeman, R.L. / Lomb, L. / Malmerberg, E. / Davidsson, J. / Nass, K. / Liang, M. / Andreasson, J. / Aquila, A. / Bajt, S. / Barthelmess, M. / Barty, A. / Bogan, M.J. / Bostedt, C. / Bozek, J.D. / Caleman, C. / Coffee, R. / Coppola, N. / Ekeberg, T. / Epp, S.W. / Erk, B. / Fleckenstein, H. / Foucar, L. / Graafsma, H. / Gumprecht, L. / Hajdu, J. / Hampton, C.Y. / Hartmann, R. / Hartmann, A. / Hauser, G. / Hirsemann, H. / Holl, P. / Hunter, M.S. / Kassemeyer, S. / Kimmel, N. / Kirian, R.A. / Maia, F.R.N.C. / Marchesini, S. / Martin, A.V. / Reich, C. / Rolles, D. / Rudek, B. / Rudenko, A. / Schlichting, I. / Schulz, J. / Seibert, M.M. / Sierra, R. / Soltau, H. / Starodub, D. / Stellato, F. / Stern, S. / Struder, L. / Timneanu, N. / Ullrich, J. / Wahlgren, W.Y. / Wang, X. / Weidenspointner, G. / Wunderer, C. / Fromme, P. / Chapman, H.N. / Spence, J.C.H. / Neutze, R.
History
DepositionDec 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Other
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.source
Revision 1.3Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.4Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT
H: REACTION CENTER PROTEIN H CHAIN
L: REACTION CENTER PROTEIN L CHAIN
M: REACTION CENTER PROTEIN M CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,82417
Polymers132,7004
Non-polymers9,12413
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46140 Å2
ΔGint-361.8 kcal/mol
Surface area41410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.500, 84.600, 375.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules C

#1: Protein PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT / CYTOCHROME C558/C559


Mass: 37450.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH (DSMZ)
Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P07173

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REACTION CENTER PROTEIN ... , 3 types, 3 molecules HLM

#2: Protein REACTION CENTER PROTEIN H CHAIN / PHOTOSYNTHETIC REACTION CENTER H SUBUNIT


Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH (DSMZ)
Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P06008
#3: Protein REACTION CENTER PROTEIN L CHAIN / PHOTOSYNTHETIC REACTION CENTER L SUBUNIT


Mass: 30600.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH (DSMZ)
Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P06009
#4: Protein REACTION CENTER PROTEIN M CHAIN / PHOTOSYNTHETIC REACTION CENTER M SUBUNIT


Mass: 36091.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH (DSMZ)
Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P06010

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Non-polymers , 6 types, 13 molecules

#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical
ChemComp-BCB / BACTERIOCHLOROPHYLL B


Mass: 909.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O6
#7: Chemical ChemComp-BPB / BACTERIOPHEOPHYTIN B


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6
#8: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#9: Chemical ChemComp-MQ7 / MENAQUINONE-7


Mass: 648.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H64O2
#10: Chemical ChemComp-NS5 / 15-cis-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 265

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 64 %
Description: THE DATA WERE COLLECTED AT THE LINAC COHERENT LIGHT SOURCE USING SERIAL FEMTOSECOND CRYSTALLOGRAPHY TO PROVE THAT THE SPONGE PHASE CRYSTALLISATION METHOD IS COMPATABLE WITH SERIAL ...Description: THE DATA WERE COLLECTED AT THE LINAC COHERENT LIGHT SOURCE USING SERIAL FEMTOSECOND CRYSTALLOGRAPHY TO PROVE THAT THE SPONGE PHASE CRYSTALLISATION METHOD IS COMPATABLE WITH SERIAL FEMTOSECOND CRYSTALLOGRAPHY. THE DATA WAS MERGED FROM 265 MICROCRYSTALS USING THE IN-HOUSE PROGRAM CRYSTFEL 0.1.0 AND INDEXAMAJIG.
Crystal growpH: 7.9
Details: BATCH CRYSTALLIZATIONS WERE SET UP IN SEPTUM-SEALED GLASS VIALS CONTAINING 100 UL PROTEIN (20-30 MG/ML) , 100 UL LIPIDIC SPONGE PHASE (12 % MONOOLEIN, 17.5 % JEFFAMINE M- 600, 1.0 M HEPES PH ...Details: BATCH CRYSTALLIZATIONS WERE SET UP IN SEPTUM-SEALED GLASS VIALS CONTAINING 100 UL PROTEIN (20-30 MG/ML) , 100 UL LIPIDIC SPONGE PHASE (12 % MONOOLEIN, 17.5 % JEFFAMINE M- 600, 1.0 M HEPES PH 8.0, 0.7 M (NH4)2SO4, 2.5 % 1,2,3- HEPTANETRIOL) AND 50 UL 1.0-1.2 M TRI-SODIUM CITRATE

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Data collection

DiffractionMean temperature: 288 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: AMO / Wavelength: 6.2 / Wavelength: 6.2 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2010
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 6.2 Å / Relative weight: 1
ReflectionResolution: 7.4→46.1 Å / Num. obs: 2431 / % possible obs: 85 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.5 / Net I/σ(I): 1.9
Reflection shellResolution: 7.37→7.62 Å / Redundancy: 1.1 % / % possible all: 21.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
CrystFEL0.1.0 INDEXAMAJIGdata reduction
MONTECARLO INTEGRATIONdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WJN

2wjn


Resolution: 8.2→46.1 Å / Cor.coef. Fo:Fc: 0.665 / SU ML: 9.332 / Cross valid method: THROUGHOUT / ESU R Free: 7.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.384 95 4.8 %RANDOM
Rwork0.35071 ---
obs0.35239 1899 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.401 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 8.2→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9185 0 650 0 9835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02210205
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.652.04814048
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7751166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.85922.26407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54151365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.741564
X-RAY DIFFRACTIONr_chiral_restr0.0540.21432
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218003
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0491.55822
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.08829354
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.04834383
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.0894.54694
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 8.202→8.414 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.611 1 -
Rwork0.414 140 -
obs--91.56 %

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