PDB-1uwa: L290F mutant rubisco from chlamydomonas

ID or keywords:

Entry

Database: PDB / ID: 1uwa

Title

L290F mutant rubisco from chlamydomonas

Components

(RIBULOSE BISPHOSPHATE CARBOXYLASE ...) x 2

Keywords

LYASE / 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

Biological species

CHLAMYDOMONAS REINHARDTII (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Karkehabadi, S. / Taylor, T.C. / Spreitzer, R.J. / Andersson, I.

Citation

Journal: 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

Deposition	Feb 3, 2004	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 12, 2005	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Jul 12, 2017	Group: 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 1.4	May 8, 2019	Group: Data collection / Experimental preparation Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow Item: _exptl_crystal_grow.temp
Revision 1.5	Dec 13, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1uwa.cif.gz	988 KB	Display	PDBx/mmCIF format
PDB format	pdb1uwa.ent.gz	817.9 KB	Display	PDB format
PDBx/mmJSON format	1uwa.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uw/1uwa ftp://data.pdbj.org/pub/pdb/validation_reports/uw/1uwa	HTTPS FTP

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Related structure data

Related structure data	1uw9C 1gk8S 1ir2 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1ir2-1 2vdi-d 1ir2-2 1uw9-d 2v69-d 2v68-d 1uzd-d 2v63-d 2vdh-d 1rco-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#11 - Nov 2000 Rubisco similarity (18)

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

559 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

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 number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	12 - 477
2	1	1	1	B	12 - 477
3	1	1	1	E	12 - 477
4	1	1	1	H	12 - 477
5	1	1	1	K	12 - 477
6	1	1	1	O	12 - 477
7	1	1	1	R	12 - 477
8	1	1	1	V	12 - 477
1	1	2	1	I	1 - 140
2	1	2	1	C	1 - 140
3	1	2	1	F	1 - 140
4	1	2	1	J	1 - 140
5	1	2	1	P	1 - 140
6	1	2	1	T	1 - 140
7	1	2	1	M	1 - 140
8	1	2	1	W	1 - 140

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.4912, 0.001218, -0.871), (0.000868, -1, -0.000908), (-0.871, -0.00031, -0.4912)	64.53, 168.89999, 110.6
2	given	(0.09365, -0.7774, -0.622), (0.2859, 0.6194, -0.7311), (0.9537, -0.1093, 0.28)	101.1, 100.3, 89.83
3	given	(-0.781, -0.2869, -0.5548), (-0.2889, -0.6215, 0.7282), (-0.5537, 0.729, 0.4024)	36.42, 68.55, -21.4
4	given	(0.09836, 0.285, 0.9535), (-0.7769, 0.6208, -0.1054), (-0.6219, -0.7303, 0.2825)	-123.8, 25.49, 110.8
5	given	(0.4914, 0.001234, -0.8709), (0.002343, -1, -9.4E-5), (-0.8709, -0.001995, -0.4914)	64.54, 168.89999, 110.8
6	given	(0.5861, 0.7786, 0.2241), (0.7784, -0.6179, 0.1113), (0.2251, 0.1093, -0.9682)	-93.05, 142.3, 164
7	given	(-0.685, 0.489, 0.5401), (0.4884, -0.2421, 0.8384), (0.5407, 0.838, -0.073)	-121.1, 42.44, 32.16
8	given	(-0.8058, -0.4904, 0.3319), (-0.4915, 0.2411, -0.8369), (0.3304, -0.8375, -0.4353)	-22.92, 125.9, 200.5
9	given	(0.09362, -0.7792, -0.6198), (0.2816, 0.6178, -0.7342), (0.955, -0.1058, 0.2773)	101, 100.8, 89.87
10	given	(-0.7811, -0.2796, -0.5583), (-0.2905, -0.6287, 0.7213), (-0.5527, 0.7256, 0.4098)	35.92, 69.74, -21.51
11	given	(0.1023, 0.2793, 0.9547), (-0.7722, 0.6274, -0.1008), (-0.6271, -0.7269, 0.2798)	-123.5, 24.66, 110.8
12	given	(0.5843, 0.7803, 0.223), (0.7789, -0.6163, 0.1158), (0.2278, 0.106, -0.9679)	-93.19, 141.89999, 164.39999
13	given	(-0.6814, 0.4942, 0.5399), (0.4915, -0.2377, 0.8378), (0.5423, 0.8363, -0.08092)	-121.5, 42.23, 33.21
14	given	(-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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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: saccharide / 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 Mass: 62.068 Da / Num. of mol.: 59 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2310 / Source method: isolated from a natural source / Formula: H₂O

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Details

Compound details	ENGINEERED 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.

Compound details

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

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.82 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.089
Detector	Date: May 3, 2003
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.089 Å / Relative weight: 1
Reflection	Resolution: 2.3→30 Å / Num. obs: 264805 / % possible obs: 96.6 % / Redundancy: 22.4 % / R_merge(I) obs: 0.14 / Net I/σ(I): 10
Reflection shell	Resolution: 2.26→2.31 Å / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 1.6 / % possible all: 93.4

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GK8

1gk8

Resolution: 2.3→30 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.205	10114	5.1 %	RANDOM
R_work	0.171	-	-	-
obs	0.172	189087	98.2 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 34.93 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.73 Å²	0 Å²	0.3 Å²
2-	-	-0.14 Å²	0 Å²
3-	-	-	-1.3 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	38232	0	412	2310	40954

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	39675
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.235	1.952	53695
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.004	5	4842
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	5675
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	30556
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	19282
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	2741
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.078	0.2	8
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.457	0.2	127
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.357	0.2	14
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.029	3	24130
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.981	5	38687
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.086	6	15545
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.364	8	15002
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	3612	tight positional	0.04	0.05
1	2	B	3612	tight positional	0.04	0.05
1	3	E	3612	tight positional	0.04	0.05
1	4	H	3612	tight positional	0.04	0.05
1	5	K	3612	tight positional	0.04	0.05
1	6	O	3612	tight positional	0.04	0.05
1	7	R	3612	tight positional	0.04	0.05
1	8	V	3612	tight positional	0.04	0.05
2	1	I	1120	tight positional	0.04	0.05
2	2	C	1120	tight positional	0.05	0.05
2	3	F	1120	tight positional	0.03	0.05
2	4	J	1120	tight positional	0.03	0.05
2	5	P	1120	tight positional	0.03	0.05
2	6	T	1120	tight positional	0.04	0.05
2	7	M	1120	tight positional	0.04	0.05
2	8	W	1120	tight positional	0.04	0.05
1	1	A	3612	tight thermal	0.12	0.5
1	2	B	3612	tight thermal	0.12	0.5
1	3	E	3612	tight thermal	0.12	0.5
1	4	H	3612	tight thermal	0.14	0.5
1	5	K	3612	tight thermal	0.12	0.5
1	6	O	3612	tight thermal	0.12	0.5
1	7	R	3612	tight thermal	0.12	0.5
1	8	V	3612	tight thermal	0.13	0.5
2	1	I	1120	tight thermal	0.09	0.5
2	2	C	1120	tight thermal	0.1	0.5
2	3	F	1120	tight thermal	0.09	0.5
2	4	J	1120	tight thermal	0.11	0.5
2	5	P	1120	tight thermal	0.09	0.5
2	6	T	1120	tight thermal	0.09	0.5
2	7	M	1120	tight thermal	0.1	0.5
2	8	W	1120	tight thermal	0.11	0.5

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.273	700
R_work	0.228	13282

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

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Sugars , 1 types, 8 molecules

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Non-polymers , 3 types, 2377 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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

-Sugars , 1 types, 8 molecules

-Non-polymers , 3 types, 2377 molecules

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-Experimental details

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Assembly

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

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Sugars , 1 types, 8 molecules

-
Non-polymers , 3 types, 2377 molecules

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Details

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Experimental details

-
Experiment

-
Sample preparation

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