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- PDB-1uwa: L290F mutant rubisco from chlamydomonas -

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Basic information

Entry
Database: PDB / ID: 1uwa
TitleL290F mutant rubisco from chlamydomonas
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: 2.3 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 1.3Jul 12, 2017Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_conn_angle / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._diffrn_source.pdbx_synchrotron_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.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
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.temp
Revision 1.5Dec 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 / 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 / _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
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)558,91191
Polymers552,20516
Non-polymers6,70575
Water41,6152310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area131860 Å2
ΔGint-432 kcal/mol
Surface area117680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.983, 177.709, 122.663
Angle α, β, γ (deg.)90.00, 117.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31E
41H
51K
61O
71R
81V
12I
22C
32F
42J
52P
62T
72M
82W

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A12 - 477
2111B12 - 477
3111E12 - 477
4111H12 - 477
5111K12 - 477
6111O12 - 477
7111R12 - 477
8111V12 - 477
1121I1 - 140
2121C1 - 140
3121F1 - 140
4121J1 - 140
5121P1 - 140
6121T1 - 140
7121M1 - 140
8121W1 - 140

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.4912, 0.001218, -0.871), (0.000868, -1, -0.000908), (-0.871, -0.00031, -0.4912)64.53, 168.89999, 110.6
2given(0.09365, -0.7774, -0.622), (0.2859, 0.6194, -0.7311), (0.9537, -0.1093, 0.28)101.1, 100.3, 89.83
3given(-0.781, -0.2869, -0.5548), (-0.2889, -0.6215, 0.7282), (-0.5537, 0.729, 0.4024)36.42, 68.55, -21.4
4given(0.09836, 0.285, 0.9535), (-0.7769, 0.6208, -0.1054), (-0.6219, -0.7303, 0.2825)-123.8, 25.49, 110.8
5given(0.4914, 0.001234, -0.8709), (0.002343, -1, -9.4E-5), (-0.8709, -0.001995, -0.4914)64.54, 168.89999, 110.8
6given(0.5861, 0.7786, 0.2241), (0.7784, -0.6179, 0.1113), (0.2251, 0.1093, -0.9682)-93.05, 142.3, 164
7given(-0.685, 0.489, 0.5401), (0.4884, -0.2421, 0.8384), (0.5407, 0.838, -0.073)-121.1, 42.44, 32.16
8given(-0.8058, -0.4904, 0.3319), (-0.4915, 0.2411, -0.8369), (0.3304, -0.8375, -0.4353)-22.92, 125.9, 200.5
9given(0.09362, -0.7792, -0.6198), (0.2816, 0.6178, -0.7342), (0.955, -0.1058, 0.2773)101, 100.8, 89.87
10given(-0.7811, -0.2796, -0.5583), (-0.2905, -0.6287, 0.7213), (-0.5527, 0.7256, 0.4098)35.92, 69.74, -21.51
11given(0.1023, 0.2793, 0.9547), (-0.7722, 0.6274, -0.1008), (-0.6271, -0.7269, 0.2798)-123.5, 24.66, 110.8
12given(0.5843, 0.7803, 0.223), (0.7789, -0.6163, 0.1158), (0.2278, 0.106, -0.9679)-93.19, 141.89999, 164.39999
13given(-0.6814, 0.4942, 0.5399), (0.4915, -0.2377, 0.8378), (0.5423, 0.8363, -0.08092)-121.5, 42.23, 33.21
14given(-0.8039, -0.4937, 0.3318), (-0.4922, 0.2389, -0.8371), (0.334, -0.8362, -0.435)-22.65, 126.1, 200.60001

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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: 52730.855 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, 2377 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.: 59 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2310 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED MUTATION LEU 290 PHE IN CHAINS A, B, E, H, K, O, R AND V. RUBISCO CATALYZES TWO ...ENGINEERED MUTATION 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.

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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: 41.82 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 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: MAX II / Beamline: I711 / Wavelength: 1.089
DetectorDate: May 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.089 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 264805 / % possible obs: 96.6 % / Redundancy: 22.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10
Reflection shellResolution: 2.26→2.31 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.6 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GK8

1gk8


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.259 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.517 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.205 10114 5.1 %RANDOM
Rwork0.171 ---
obs0.172 189087 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å20.3 Å2
2---0.14 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38232 0 412 2310 40954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02139675
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.95253695
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00454842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.25675
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0230556
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.219282
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.22741
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4570.2127
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3570.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.029324130
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.981538687
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.086615545
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.364815002
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3612tight positional0.040.05
12B3612tight positional0.040.05
13E3612tight positional0.040.05
14H3612tight positional0.040.05
15K3612tight positional0.040.05
16O3612tight positional0.040.05
17R3612tight positional0.040.05
18V3612tight positional0.040.05
21I1120tight positional0.040.05
22C1120tight positional0.050.05
23F1120tight positional0.030.05
24J1120tight positional0.030.05
25P1120tight positional0.030.05
26T1120tight positional0.040.05
27M1120tight positional0.040.05
28W1120tight positional0.040.05
11A3612tight thermal0.120.5
12B3612tight thermal0.120.5
13E3612tight thermal0.120.5
14H3612tight thermal0.140.5
15K3612tight thermal0.120.5
16O3612tight thermal0.120.5
17R3612tight thermal0.120.5
18V3612tight thermal0.130.5
21I1120tight thermal0.090.5
22C1120tight thermal0.10.5
23F1120tight thermal0.090.5
24J1120tight thermal0.110.5
25P1120tight thermal0.090.5
26T1120tight thermal0.090.5
27M1120tight thermal0.10.5
28W1120tight thermal0.110.5
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.273 700
Rwork0.228 13282

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