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- PDB-2wjm: Lipidic sponge phase crystal structure of the photosynthetic reac... -

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Basic information

Entry
Database: PDB / ID: 2wjm
TitleLipidic sponge phase crystal structure of the photosynthetic reaction centre from Blastochloris viridis (low dose)
Components
  • (REACTION CENTER PROTEIN ...Photosynthetic reaction centre) x 3
  • PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT
KeywordsPHOTOSYNTHESIS / REACTION CENTRE / MEMBRANE PROTEIN / LIPIDS / MONOOLEIN / POSTTRANSLATIONAL MODIFICATION / THIOETHER BOND / UBIQUINONE / LIPIDIC SPONGE PHASE
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 ...Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / 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. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / Chem-MPG / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / PHOSPHATE ION / Reaction center protein H chain ...BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / Chem-MPG / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / PHOSPHATE ION / 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 speciesRHODOPSEUDOMONAS VIRIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWoehri, A.B. / Wahlgren, W.Y. / Malmerberg, E. / Johansson, L.C. / Neutze, R. / Katona, G.
CitationJournal: Biochemistry / Year: 2009
Title: Lipidic sponge phase crystal structure of a photosynthetic reaction center reveals lipids on the protein surface.
Authors: Wohri, A.B. / Wahlgren, W.Y. / Malmerberg, E. / Johansson, L.C. / Neutze, R. / Katona, G.
History
DepositionMay 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 21, 2011Group: Other
Revision 1.3Feb 1, 2012Group: Other
Revision 1.4Apr 25, 2012Group: Other
Revision 2.0Jun 14, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_sheet.id / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id
Revision 3.0Jan 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 3.1Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 3.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_chiral / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)143,68923
Polymers132,6724
Non-polymers11,01719
Water12,809711
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48650 Å2
ΔGint-357.41 kcal/mol
Surface area40270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.450, 138.498, 177.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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) RHODOPSEUDOMONAS 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 centre / 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) RHODOPSEUDOMONAS VIRIDIS (bacteria) / References: UniProt: P06008
#3: Protein REACTION CENTER PROTEIN L CHAIN / Photosynthetic reaction centre / 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) RHODOPSEUDOMONAS VIRIDIS (bacteria) / References: UniProt: P06009
#4: Protein REACTION CENTER PROTEIN M CHAIN / Photosynthetic reaction centre / PHOTOSYNTHETIC REACTION CENTER M SUBUNIT


Mass: 36063.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH (DSMZ)
Source: (natural) RHODOPSEUDOMONAS VIRIDIS (bacteria) / References: UniProt: P06010

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Non-polymers , 10 types, 730 molecules

#5: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Chemical ChemComp-DGA / DIACYL GLYCEROL / Diglyceride


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#7: Chemical
ChemComp-BCB / BACTERIOCHLOROPHYLL B / Bacteriochlorophyll


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


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6
#9: Chemical ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#10: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#11: Chemical ChemComp-MQ7 / MENAQUINONE-7 / Vitamin K2


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


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60
#13: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 711 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsDIACYL GLYCEROL (DGA): THIOETHER BOND THROUGH C1 CYS -H2O PROTOPORPHYRIN IX CONTAINING FE (HEM): ...DIACYL GLYCEROL (DGA): THIOETHER BOND THROUGH C1 CYS -H2O PROTOPORPHYRIN IX CONTAINING FE (HEM): COVALENTLY BONDED TO CYSTENES C87,C90,C132,135,C244,C247,C305,C308 N-FORMYLMETHIONINE (FME): N-TERMINAL POSTTRANSLATIONAL MODIFICATION OF THE H SUBUNIT
Sequence detailsN-TERMINUS IS PROCESSED BY A SIGNAL PEPTIDASE

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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: 2.67 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growMethod: lipidic cubic phase / pH: 8
Details: MONOOLEIN WAS MIXED WITH WATER IN RATIO OF 60:40 (W/W) UNTIL A VISCOUS NON-BIREFRINGENT LCP WAS FORMED. THEREAFTER, LIPIDIC-SPONGE PHASE INITIATING SOLUTION (20% JEFFAMINE M600, 1M HEPES ...Details: MONOOLEIN WAS MIXED WITH WATER IN RATIO OF 60:40 (W/W) UNTIL A VISCOUS NON-BIREFRINGENT LCP WAS FORMED. THEREAFTER, LIPIDIC-SPONGE PHASE INITIATING SOLUTION (20% JEFFAMINE M600, 1M HEPES PH=8.0, 0.7M (NH4)2SO4 AND 2.5% 1,2,3-HEPTANETRIOL) WAS ADDED IN A RATIO OF 1 TO 4 (V/V) AND EQUILIBRATED UNTIL PHASE SEPARATION HAS OCCURRED. THE UPPER LIPIDIC-SPONGE PHASE WAS HARVESTED AND 1UL WAS USED AS A PRECIPITANT SOLUTION TOGETHER WITH 1UL OF 25 MG/ML PROTEIN SOLUTION IN A HANGING-DROP, VAPOUR-DIFFUSION EXPERIMENT. TO IMPROVE CRYSTAL QUALITY 1UL OF ADDITIVE 1M TRI-NA-CITRATE HAS BEEN ADDED TO THE CRYSTALLIZATION DROP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 8, 2007 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.95→45.9 Å / Num. obs: 152112 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.1 / % possible all: 86.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PRC

2prc


Resolution: 1.95→176.78 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.567 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20122 7313 5 %RANDOM
Rwork0.17305 ---
obs0.17446 138487 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.466 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--2.93 Å20 Å2
3----2.91 Å2
Refinement stepCycle: LAST / Resolution: 1.95→176.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9187 0 764 711 10662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210349
X-RAY DIFFRACTIONr_bond_other_d0.0020.026943
X-RAY DIFFRACTIONr_angle_refined_deg2.092.05614182
X-RAY DIFFRACTIONr_angle_other_deg0.9723.00116712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59551170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38522.279408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.104151371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4051564
X-RAY DIFFRACTIONr_chiral_restr0.0880.21436
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211355
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022258
X-RAY DIFFRACTIONr_nbd_refined0.210.22196
X-RAY DIFFRACTIONr_nbd_other0.1990.27445
X-RAY DIFFRACTIONr_nbtor_refined0.1890.24959
X-RAY DIFFRACTIONr_nbtor_other0.0880.24725
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2657
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1510.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7071.55937
X-RAY DIFFRACTIONr_mcbond_other0.1911.52374
X-RAY DIFFRACTIONr_mcangle_it1.10129367
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.73235315
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4154.54797
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 432 -
Rwork0.256 8913 -
obs--83.92 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.72780.1410.5730.2718-0.05041.3283-0.0497-0.1412-0.00690.0371-0.0217-0.0928-0.0190.00940.0714-0.08680.0260.007-0.12860.0224-0.063142.774941.491776.9343
20.3582-0.12820.40210.1794-0.00271.6917-0.00150.0432-0.12750.05730.02350.04590.3134-0.1897-0.022-0.0288-0.02810.0424-0.141-0.0189-0.029627.863524.86136.4517
30.3902-0.04050.18040.19090.08220.9377-0.03550.08010.0391-0.00540.0023-0.0126-0.1106-0.06450.0332-0.0881-0.01320.0023-0.1637-0.0006-0.064828.380445.434935.4191
40.8574-0.2792-0.29270.61610.3471.296-0.06310.1911-0.19030.0041-0.01880.12760.2729-0.16970.0818-0.0479-0.038-0.00820.0043-0.0447-0.019624.387226.34149.2315
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 332
2X-RAY DIFFRACTION2L1 - 273
3X-RAY DIFFRACTION3M1 - 323
4X-RAY DIFFRACTION4H1 - 258

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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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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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