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- PDB-1rsc: STRUCTURE OF AN EFFECTOR INDUCED INACTIVATED STATE OF RIBULOSE BI... -

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Basic information

Entry
Database: PDB / ID: 1rsc
TitleSTRUCTURE OF AN EFFECTOR INDUCED INACTIVATED STATE OF RIBULOSE BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE: THE BINARY COMPLEX BETWEEN ENZYME AND XYLULOSE BISPHOSPHATE
Components
  • RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)
  • RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)
KeywordsLYASE (CARBON-CARBON)
Function / homology
Function and homology information


photorespiration / carboxysome / 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 / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-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 / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-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
XYLULOSE-1,5-BISPHOSPHATE / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsNewman, J. / Gutteridge, S.
Citation
Journal: Structure / Year: 1994
Title: Structure of an effector-induced inactivated state of ribulose 1,5-bisphosphate carboxylase/oxygenase: the binary complex between enzyme and xylulose 1,5-bisphosphate.
Authors: Newman, J. / Gutteridge, S.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: The X-Ray Structure of Synechococcus Ribulose Bisphosphate Carboxylase(Slash)Oxygenase Activate Quaternary Complex at 2.2 Angstroms Resolution
Authors: Newman, J. / Gutteridge, S.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure Determination and Refinement of Ribulose-1,5-Bisphosphate Carboxylase(Slash)Oxygenase from Synechococcus Pcc6301
Authors: Newman, J. / Branden, C.-I. / Jones, T.A.
#3: Journal: J.Biol.Chem. / Year: 1990
Title: The Purification and Preliminary X-Ray Diffraction Studies of Recombinant Synechococcus Ribulose-1,5-Bisphosphate Carboxylase(Slash)Oxygenase from E. Coli
Authors: Newman, J. / Gutteridge, S.
History
DepositionMar 29, 1994Processing site: BNL
Revision 1.0May 8, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 5, 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 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type
Remark 700SHEET S1 IN *SHEET RECORDS BELOW IS THE L-SUBUNIT N-TERMINAL SHEET. S2 IN *SHEET* RECORDS BELOW IS ...SHEET S1 IN *SHEET RECORDS BELOW IS THE L-SUBUNIT N-TERMINAL SHEET. S2 IN *SHEET* RECORDS BELOW IS THE L-SUBUNIT C-TERM DOMAIN SHEET. S3 IN *SHEET* RECORDS BELOW IS THE S-SUBUNIT SHEET. THIS SHEET IS +1, -2X, -1.

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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)529,41524
Polymers526,93416
Non-polymers2,4818
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)224.400, 112.600, 200.300
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(0.054944, 0.991599, 0.117102), (0.991904, -0.067652, 0.107466), (0.114485, 0.110249, -0.987288)58.7175, -60.963, -12.2333
2given(-0.003182, 0.994466, 0.105014), (-0.993371, 0.008924, -0.114609), (-0.114912, -0.104682, 0.987845)63.5616, 104.7282, 11.9289
3given(0.998457, -0.055196, 0.006022), (-0.055177, -0.998471, -0.003268), (0.006193, 0.002931, -0.999977)1.2682, 46.8943, -0.8664
4given(-0.999944, 0.001258, -0.01049), (0.003491, -0.97647, -0.215626), (-0.009972, -0.215651, 0.97642)168.47231, 41.5537, 5.3874
5given(-0.056378, -0.992918, -0.104574), (-0.99322, 0.04511, 0.107144), (-0.101667, 0.109906, -0.988729)109.9048, 103.9911, 5.9656
6given(-0.001047, -0.993269, -0.115824), (0.99482, 0.012807, -0.100839), (0.101644, -0.115118, 0.988138)105.0512, -62.8662, -6.111
7given(-0.998542, 0.053826, 0.004015), (0.053403, 0.97441, 0.218344), (0.007841, 0.21824, -0.975864)167.20731, -3.7175, -5.5599
DetailsTHERE ARE 7 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. THESE 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 THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX CHAIN RESIDUES CHAIN RESIDUES 1 A 9 - 475 B 9 - 475 1 M 2 - 51 I 2 - 51 1 M 59 - 122 I 59 - 122 2 A 9 - 475 C 9 - 475 2 M 2 - 51 N 2 - 51 2 M 59 - 122 N 59 - 122 3 A 9 - 475 D 9 - 475 3 M 2 - 51 J 2 - 51 3 M 59 - 122 J 59 - 122 4 A 9 - 475 E 9 - 475 4 M 2 - 51 O 2 - 51 4 M 59 - 122 O 59 - 122 5 A 9 - 475 F 9 - 475 5 M 2 - 51 F 2 - 51 5 M 59 - 122 F 59 - 122 6 A 9 - 475 G 9 - 475 6 M 2 - 51 P 2 - 51 6 M 59 - 122 P 59 - 122 7 A 9 - 475 H 9 - 475 7 M 2 - 51 L 2 - 51 7 M 59 - 122 L 59 - 122

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Components

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


Mass: 52516.605 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 6301 / Cell line: S2
References: UniProt: P00880, ribulose-bisphosphate carboxylase
#2: Protein
RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)


Mass: 13350.182 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 6301 / Cell line: S2
References: UniProt: P04716, ribulose-bisphosphate carboxylase
#3: Sugar
ChemComp-XBP / XYLULOSE-1,5-BISPHOSPHATE


Type: saccharide / Mass: 310.090 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C5H12O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.75 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. obs: 145750 / % possible obs: 65 % / Num. measured all: 601269 / Rmerge(I) obs: 0.157

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.255 / Rfactor obs: 0.255 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36496 0 144 206 36846
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg0.91
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.62
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.788
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: 141681
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.62
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.788

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