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- PDB-1rbl: STRUCTURE DETERMINATION AND REFINEMENT OF RIBULOSE 1,5 BISPHOSPHA... -

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Entry
Database: PDB / ID: 1rbl
TitleSTRUCTURE DETERMINATION AND REFINEMENT OF RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM SYNECHOCOCCUS PCC6301
Components(RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE ...) x 2
KeywordsLYASE / LYASE(CARBON-CARBON)
Function / homology
Function and homology information


carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / 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, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / 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 / FORMIC ACID / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsNewman, J. / Gutteridge, S. / Branden, C.-I. / Jones, T.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure determination and refinement of ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301.
Authors: Newman, J. / Branden, C.I. / Jones, T.A.
#1: Journal: To be Published
Title: The X-Ray Structure of Synechococcus Ribulose Bisphosphate Carboxylase(Slash)Oxygenase Activated Quaternary Complex at 2.2 Angstroms Resolution
Authors: Newman, J. / Gutteridge, S.
History
DepositionMay 12, 1993Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.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.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX HELICES A, B, BB, C, AND D PRESENTED ON THE HELIX RECORD BELOW ARE THE HELICES OF THE N-TERMINAL DOMAIN.
Remark 700SHEET SHEET LN1 IS -2X, +1, +2X. THE DSSP RUN DID NOT INDICATE THAT STRAND 2 WAS INDEED A STRAND. ...SHEET SHEET LN1 IS -2X, +1, +2X. THE DSSP RUN DID NOT INDICATE THAT STRAND 2 WAS INDEED A STRAND. HOWEVER, THE A/B BARREL IS CLEARLY THAT, SO STRAND 2 IS INCLUDED AS A "REAL" STRAND. SHEET SS1 IS +1,-2X,-1. THE SHEET PRESENTED AS *LC1* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)
M: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)
B: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)
I: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)
C: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)
N: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)
D: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)
J: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)
E: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)
O: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)
F: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)
K: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)
G: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)
P: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)
H: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)
L: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)521,79940
Polymers518,38816
Non-polymers3,41224
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)223.900, 111.900, 199.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 176
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.055254, 0.991591, 0.117024), (0.991747, -0.068084, 0.108639), (0.115693, 0.110056, -0.987169)58.517, -60.7791, -12.3183
2given(-0.001556, 0.994481, 0.10491), (-0.993326, 0.010562, -0.114852), (-0.115326, -0.104388, 0.987827)63.2441, 104.7247, 11.962
3given(0.99839, -0.056422, 0.005795), (-0.056413, -0.998406, -0.001652), (0.005879, 0.001323, -0.999982)1.3587, 47.2797, -0.7736
4given(-0.999944, 0.000591, -0.010574), (0.001717, -0.976187, -0.216926), (-0.010451, -0.216932, 0.976131)168.35741, 41.8985, 5.4785
5given(-0.055113, -0.992904, -0.105381), (-0.993265, 0.043745, 0.107292), (-0.10192, 0.110584, -0.988627)109.876, 104.0256, 5.968
6given(-0.000233, -0.99328, -0.115738), (0.99467, 0.011703, -0.10244), (0.103106, -0.115145, 0.987983)105.2909, -62.7286, -6.2316
7given(-0.998513, 0.054364, 0.004006), (0.053928, 0.974438, 0.218086), (0.007953, 0.217978, -0.975921)167.1207, -3.8899, -5.5733
DetailsTHESE ARE THE ROTATION/TRANSLATION COMPONENTS TO MAP AN LS MONOMER (AM) ONTO THE REST OF THE MOLECULE. THESE MATRICES WERE OBTAINED FROM X-PLOR AFTER REFINEMENT OF THE WHOLE L8S8 920710. MTRIX 1 TAKES AM TO BI. MTRIX 2 TAKES AM TO CN. MTRIX 3 TAKES AM TO DJ. MTRIX 4 TAKES AM TO EO. MTRIX 5 TAKES AM TO FK. MTRIX 6 TAKES AM TO GP. MTRIX 7 TAKES AM TO HL.

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Components

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RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE ... , 2 types, 16 molecules ABCDEFGHMINJOKPL

#1: Protein
RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)


Mass: 51872.836 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 6301
References: UniProt: P00880, ribulose-bisphosphate carboxylase
#2: Protein
RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)


Mass: 12925.646 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 6301
References: UniProt: P04716, ribulose-bisphosphate carboxylase

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Sugars , 1 types, 8 molecules

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


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O13P2

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Non-polymers , 3 types, 308 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: RBL_ ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: RBL_SYNP6 SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE PRO 38 ARG A 41 VAL 39 PHE A 42 GLN 88 ALA A 91 ARG 353 ALA A 356 ASP 64 ALA M 76 LYS 66 ALA M 78 SER 67 ALA M 79 GLN 97 GLU M 109 VAL 101 SER M 113

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Newman, J., (1990) J. Biol. Chem., 265, 15154. / PH range low: 7 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130-40 mg/mlenzyme solution1drop
212-16 %PEG40001drop
325 mMphosphate1drop
41 mM1dropNaN3
512-16 %PEG40001reservoir
625 mMphosphate1reservoir
71 mM1reservoirNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 100 Å / Num. obs: 218276 / % possible obs: 86.2 % / Num. measured all: 852051 / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.26 Å / % possible obs: 51.7 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.2 / Rfactor obs: 0.2 / Highest resolution: 2.2 Å
Details: THERE ARE SEVEN NON-CRYSTALLOGRAPHIC SYMMETRY OPERATORS, AND THESE MUST BE USED TO GENERATE THE ENTIRE L8S8 MOLECULE. THE FORMAT OF THE FOLLOWING TRANSFORMATIONS IS FROM X-PLOR, THUS THE ...Details: THERE ARE SEVEN NON-CRYSTALLOGRAPHIC SYMMETRY OPERATORS, AND THESE MUST BE USED TO GENERATE THE ENTIRE L8S8 MOLECULE. THE FORMAT OF THE FOLLOWING TRANSFORMATIONS IS FROM X-PLOR, THUS THE SYMMETRY RELATED CHAINS ARE GENERATED BY R'=R*R + T, R=ROTATION MATRIX, T=TRANSLATION.
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36496 0 200 292 36988
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.26
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.26
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 7 Å / Num. reflection all: 218276 / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg26.12
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.26

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