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- PDB-1uw9: L290F-A222T chlamydomonas Rubisco mutant -

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Basic information

Entry
Database: PDB / ID: 1uw9
TitleL290F-A222T chlamydomonas Rubisco mutant
Components(RIBULOSE BISPHOSPHATE CARBOXYLASE ...RuBisCO) x 2
KeywordsLYASE / RUBISCO / PHOTOSYNTHESIS / PHOTORESPIRATION / OXIDOREDUCTASE / MONOOXYGENASE / CARBON DIOXIDE FIXATION
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / 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 / Ribulose bisphosphate carboxylase small subunit, chloroplastic 1 / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKarkehabadi, S. / Taylor, T.C. / Spreitzer, R.J. / Andersson, I.
CitationJournal: Biochemistry / Year: 2005
Title: Altered Intersubunit Interactions in Crystal Structures of Catalytically Compromised Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase
Authors: Karkehabadi, S. / Taylor, T.C. / Spreitzer, R.J. / Andersson, I.
History
DepositionFeb 3, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 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 / struct_conn
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
B: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
C: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
E: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
F: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
H: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
I: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
J: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
K: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
M: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
O: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
P: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
R: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
T: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
V: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
W: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)558,90287
Polymers552,44516
Non-polymers6,45771
Water50,7842819
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.073, 178.196, 120.463
Angle α, β, γ (deg.)90.00, 120.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.3791, 0.4875, 0.7865), (0.4878, -0.6171, 0.6175), (0.7864, 0.6178, -0.003834)8.926, 131.60001, -74.52
2given(0.2511, 0.968, -0.001311), (0.968, -0.2511, -0.000909), (-0.001209, -0.001041, -1)-67.39, 87.2, 17.05
3given(0.3768, -0.4903, -0.7859), (-0.4745, 0.6265, -0.6184), (0.7955, 0.6059, 0.003402)72.51, 55.41, -73.73
4given(0.3721, -0.4773, 0.7961), (-0.4941, 0.6242, 0.6052), (-0.7857, -0.6186, -0.003552)58.03, 45.86, 91.36
5given(-0.3803, 0.4873, 0.7861), (0.491, -0.6139, 0.6181), (0.7838, 0.621, -0.005782)-8.873, 131.2, -74.62
6given(-0.37, 0.4814, -0.7946), (0.4806, -0.6328, -0.6072), (-0.7951, -0.6065, 0.002824)4.762, 143.60001, 90.51
7given(-0.2503, -0.9681, 0.007761), (-0.9681, 0.2502, -0.01231), (0.009977, -0.0106, -0.9999)130.39999, 101.2, 17.61
8given(-1, -0.00074, -0.008347), (0.000636, -0.9999, 0.01238), (-0.008356, 0.01238, 0.9999)63.23, 188, -0.9257
9given(0.2451, 0.9695, 0.0015), (0.9695, -0.2451, -0.002284), (0.000147, 0.000151, -1)-67.35, 86.71, 16.84
10given(-0.3694, 0.4854, -0.7924), (0.4766, -0.6331, -0.61), (-0.7978, -0.603, 0.002554)4.326, 143.89999, 90.4
11given(0.3741, -0.4909, -0.7868), (-0.4716, 0.6298, -0.6172), (0.7985, 0.6019, 0.004126)72.63, 54.96, -73.31
12given(0.3728, -0.4765, 0.7962), (-0.4963, 0.6226, 0.605), (-0.784, -0.6207, -0.00439)57.94, 46.05, 91.61
13given(-0.2415, -0.9703, 0.01158), (-0.9704, 0.2414, -0.007339), (0.004325, -0.01301, -0.9999)130.39999, 102.3, 18.07
14given(-1, -0.001236, -0.007342), (0.001153, -0.9999, 0.01129), (-0.007356, 0.01128, 0.9999)63.28, 188, -0.9052
DetailsFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350

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Components

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RIBULOSE BISPHOSPHATE CARBOXYLASE ... , 2 types, 16 molecules ABEHKORVCFIJMPTW

#1: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN / RUBISCO LARGE SUBUNIT / RIBULOSE-1 / 5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN


Mass: 52760.883 Da / Num. of mol.: 8 / Mutation: YES / Source method: isolated from a natural source / Source: (natural) CHLAMYDOMONAS REINHARDTII (plant)
References: UniProt: P00877, ribulose-bisphosphate carboxylase
#2: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1 / RUBISCO SMALL SUBUNIT 1


Mass: 16294.788 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) CHLAMYDOMONAS REINHARDTII (plant)
References: UniProt: P00873, ribulose-bisphosphate carboxylase

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Sugars , 1 types, 8 molecules

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


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

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Non-polymers , 3 types, 2882 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2819 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED MUTATION ALA 222 THR AND LEU 290 PHE IN CHAINS A, B, E, H, K, O, R AND V. RUBISCO ...ENGINEERED MUTATION ALA 222 THR AND LEU 290 PHE IN CHAINS A, B, E, H, K, O, R AND V. RUBISCO CATALYZES TWO REACTIONS: THE CARBOXYLATION OF D- RIBULOSE 1,5-BISPHOSPHATE, THE PRIMARY EVENT IN PHOTOSYNTHETIC CARBON DIOXIDE FIXATION, AS WELL AS THE OXIDATIVE FRAGMENTATION OF THE PENTOSE SUBSTRATE IN THE PHOTORESPIRATION PROCESS. BOTH REACTIONS OCCUR SIMULTANEOUSLY AND IN COMPETITION AT THE SAME ACTIVE SITE.
Sequence detailsRESIDUE 46 IN THE LARGE SUBUNITS (CHAIN A B E H K O R V) HAS BEEN IDENTIFIED AS A PROLINE.

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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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 0 MM HEPES PH 7.5, 8-12% PEG 4 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG PROTEIN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorDate: Feb 23, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. obs: 295370 / % possible obs: 88.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.9
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.8 / % possible all: 83.5

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GK8

1gk8


Resolution: 2.05→20 Å / SU B: 4.513 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.184
RfactorNum. reflection% reflectionSelection details
Rfree0.19421 11867 5 %RANDOM
Rwork0.1569 ---
obs0.1569 226650 89 %-
Displacement parametersBiso mean: 18.147 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20.12 Å2
2---0.17 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38304 0 396 2819 41519

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