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- PDB-6ftl: Rubisco from Skeletonema marinoi -

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Basic information

Entry
Database: PDB / ID: 6ftl
TitleRubisco from Skeletonema marinoi
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
KeywordsLYASE / PHOTOSYNTHESIS / CARBON DIOXIDE FIXATION / DIATOM
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / plastid / photosynthesis / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site ...Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase large chain / Ribulose-bisphosphate carboxylase
Similarity search - Component
Biological speciesSkeletonema marinoi (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAndersson, I. / Valegard, K.
Funding support Sweden, 2items
OrganizationGrant numberCountry
European UnionQLK3-CT-2002-01945 Sweden
Formas Sweden
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications.
Authors: Valegard, K. / Andralojc, P.J. / Haslam, R.P. / Pearce, F.G. / Eriksen, G.K. / Madgwick, P.J. / Kristoffersen, A.K. / van Lun, M. / Klein, U. / Eilertsen, H.C. / Parry, M.A.J. / Andersson, I.
History
DepositionFeb 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Apr 17, 2019Group: Data collection / Structure summary / Category: chem_comp / pdbx_seq_map_depositor_info
Item: _chem_comp.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.0Apr 24, 2019Group: Data collection / Polymer sequence
Category: chem_comp / entity_poly / pdbx_seq_map_depositor_info
Item: _chem_comp.mon_nstd_flag / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.mon_nstd_flag / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.1Jan 17, 2024Group: 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain
I: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
C: Ribulose bisphosphate carboxylase large chain
J: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
E: Ribulose bisphosphate carboxylase large chain
K: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
G: Ribulose bisphosphate carboxylase large chain
L: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,43034
Polymers278,7918
Non-polymers2,63926
Water6,359353
1
A: Ribulose bisphosphate carboxylase large chain
I: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
C: Ribulose bisphosphate carboxylase large chain
J: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
E: Ribulose bisphosphate carboxylase large chain
K: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
G: Ribulose bisphosphate carboxylase large chain
L: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
hetero molecules

A: Ribulose bisphosphate carboxylase large chain
I: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
C: Ribulose bisphosphate carboxylase large chain
J: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
E: Ribulose bisphosphate carboxylase large chain
K: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
G: Ribulose bisphosphate carboxylase large chain
L: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)562,86168
Polymers557,58316
Non-polymers5,27852
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area120960 Å2
ΔGint-361 kcal/mol
Surface area119480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.022, 111.022, 396.361
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-604-

HOH

21G-632-

HOH

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Components

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Protein , 2 types, 8 molecules ACEGIJKL

#1: Protein
Ribulose bisphosphate carboxylase large chain


Mass: 53847.074 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Skeletonema marinoi (Diatom)
References: UniProt: A0A3B6UEX0*PLUS, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit


Mass: 15850.783 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Skeletonema marinoi (Diatom) / References: UniProt: A0A3B6UEX1*PLUS

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Sugars , 1 types, 4 molecules

#4: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O13P2

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Non-polymers , 3 types, 375 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.05 M HEPES pH 7.5, 0.05 M NaCl, 7-13% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.087 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.087 Å / Relative weight: 1
ReflectionResolution: 2.6→19.96 Å / Num. obs: 75003 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 4.2
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.956 / % possible all: 75.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MZ2

5mz2


Resolution: 2.6→19.96 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.888 / SU B: 27.771 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3822 5.1 %RANDOM
Rwork0.171 ---
obs0.175 70943 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19532 0 160 353 20045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01920126
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218750
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.95927292
X-RAY DIFFRACTIONr_angle_other_deg1.015343022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4825.0042477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65523.519932
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.304153171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.06315144
X-RAY DIFFRACTIONr_chiral_restr0.0980.22960
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222876
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024788
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_it0.651.9859928
X-RAY DIFFRACTIONr_mcbond_other0.651.9859927
X-RAY DIFFRACTIONr_mcangle_it1.162.97412396
X-RAY DIFFRACTIONr_mcangle_other1.162.97412397
X-RAY DIFFRACTIONr_scbond_it0.5072.01310198
X-RAY DIFFRACTIONr_scbond_other0.5072.01310198
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9233.00614897
X-RAY DIFFRACTIONr_long_range_B_refined2.22815.40522949
X-RAY DIFFRACTIONr_long_range_B_other2.2215.42422889
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 198 -
Rwork0.296 3936 -
obs--74.69 %
Refinement TLS params.Method: refined / Origin x: 64.0231 Å / Origin y: 60.4473 Å / Origin z: 16.4588 Å
111213212223313233
T0.0881 Å2-0.0378 Å2-0.0173 Å2-0.1341 Å20.019 Å2--0.0245 Å2
L0.0607 °2-0.0053 °20.0394 °2-0.0556 °2-0.0376 °2--0.1389 °2
S0.01 Å °-0.0793 Å °0.0024 Å °-0.0344 Å °0.0012 Å °-0.0187 Å °0.0447 Å °-0.0597 Å °-0.0112 Å °

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