PDB-8qj0: Room-temperature Serial Synchrotron Crystallography structure of ...

ID or keywords:

Entry

Database: PDB / ID: 8qj0

Title

Room-temperature Serial Synchrotron Crystallography structure of Spinacia oleracea RuBisCO

Components

Ribulose bisphosphate carboxylase large chain
Ribulose bisphosphate carboxylase small subunit, chloroplastic 2

Keywords

LYASE / Spinacia oleracea

Function / homology

Function and homology information

photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / chloroplast / magnesium ion binding
Similarity search - Function

Biological species

Spinacia oleracea (spinach)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Bjelcic, M. / Neutze, R. / Aurelius, O. / Nan, J. / Ursby, T.

Funding support

1items

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Room-temperature serial synchrotron crystallography structure of Spinacia oleracea RuBisCO.
Authors: Bjelcic, M. / Aurelius, O. / Nan, J. / Neutze, R. / Ursby, T.

History

Deposition	Sep 12, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 29, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jul 3, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8qj0.cif.gz	871 KB	Display	PDBx/mmCIF format
PDB format	pdb8qj0.ent.gz	706.4 KB	Display	PDB format
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Validation report

Summary document	8qj0_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	8qj0_full_validation.pdf.gz	1.8 MB	Display
Data in XML	8qj0_validation.xml.gz	84.6 KB	Display
Data in CIF	8qj0_validation.cif.gz	122.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qj/8qj0 ftp://data.pdbj.org/pub/pdb/validation_reports/qj/8qj0	HTTPS FTP

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Related structure data

Similar structure data	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 (19)

Deposited unit

S: Ribulose bisphosphate carboxylase small subunit, chloroplastic 2

T: Ribulose bisphosphate carboxylase small subunit, chloroplastic 2

U: Ribulose bisphosphate carboxylase small subunit, chloroplastic 2

V: Ribulose bisphosphate carboxylase small subunit, chloroplastic 2

L: Ribulose bisphosphate carboxylase large chain

M: Ribulose bisphosphate carboxylase large chain

N: Ribulose bisphosphate carboxylase large chain

O: Ribulose bisphosphate carboxylase large chain

hetero molecules

270 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	158.6, 157.12, 202.74
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	M-700- HOH
2	1	M-702- HOH
3	1	M-779- HOH
4	1	M-785- HOH
5	1	O-694- HOH
6	1	O-706- HOH
7	1	O-796- HOH
8	1	O-806- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TYR / End label comp-ID: TYR / Auth asym-ID: S / Label asym-ID: A / Auth seq-ID: 1 - 123 / Label seq-ID: 1 - 123

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24

#1: Protein	Ribulose bisphosphate carboxylase small subunit, chloroplastic 2 Mass: 14673.681 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q43832
#2: Protein	Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit Mass: 52849.742 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) References: UniProt: P00875, ribulose-bisphosphate carboxylase
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 995 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.51 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: SpRub solution at a concentration of 15 mg/mL (in a buffer of 20 mM HEPES, 5 mM MgCl2, pH 8.0), combined reservoir solution (0.2 M MgCl2x6H2O, 0.1 M Tris pH 7.0, 12% w/v PEG 8000

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Data collection

Diffraction	Mean temperature: 293 K / Serial crystal experiment: Y
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 4, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.3→97.78 Å / Num. obs: 112061 / % possible obs: 100 % / Redundancy: 770 % / CC_1/2: 0.9943 / R split: 0.0952 / Net I/σ(I): 7.96
Reflection shell	Resolution: 2.3→2.382 Å / Redundancy: 528 % / Mean I/σ(I) obs: 3.66 / Num. unique obs: 5554 / CC_1/2: 0.9523 / R split: 0.2388 / % possible all: 100
Serial crystallography sample delivery	Method: fixed target

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
CrystFEL	0.10.2	data reduction
CrystFEL	0.10.2	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→97.78 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.941 / WR_factor R_free: 0.194 / WR_factor R_work: 0.151 / SU B: 6.436 / SU ML: 0.156 / Average fsc free: 0.9704 / Average fsc work: 0.9814 / Cross valid method: FREE R-VALUE / ESU R: 0.331 / ESU R Free: 0.224
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2274	5444	4.865 %
R_work	0.1811	106454	-
all	0.183	-	-
obs	-	111898	99.893 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 25.303 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.206 Å²	0 Å²	-0 Å²
2-	-	0.652 Å²	0 Å²
3-	-	-	-0.858 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→97.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17873	0	16	995	18884

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	18389
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.016	16840
X-RAY DIFFRACTION	r_angle_refined_deg	2.149	1.833	24940
X-RAY DIFFRACTION	r_angle_other_deg	1.034	1.758	38702
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.886	5	2236
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.485	5	140
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.956	10	2910
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.912	10	888
X-RAY DIFFRACTION	r_chiral_restr	0.123	0.2	2647
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	22088
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	4488
X-RAY DIFFRACTION	r_nbd_refined	0.175	0.2	3246
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.138	0.2	14949
X-RAY DIFFRACTION	r_nbtor_refined	0.16	0.2	8793
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.068	0.2	10163
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	940
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.042	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.103	0.2	134
X-RAY DIFFRACTION	r_nbd_other	0.091	0.2	634
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.171	0.2	137
X-RAY DIFFRACTION	r_mcbond_it	3.146	2.251	8980
X-RAY DIFFRACTION	r_mcbond_other	3.146	2.251	8980
X-RAY DIFFRACTION	r_mcangle_it	4.745	4.042	11204
X-RAY DIFFRACTION	r_mcangle_other	4.745	4.043	11205
X-RAY DIFFRACTION	r_scbond_it	4.215	2.707	9409
X-RAY DIFFRACTION	r_scbond_other	4.216	2.708	9395
X-RAY DIFFRACTION	r_scangle_it	6.528	4.791	13736
X-RAY DIFFRACTION	r_scangle_other	6.528	4.792	13736
X-RAY DIFFRACTION	r_lrange_it	7.989	23.597	20320
X-RAY DIFFRACTION	r_lrange_other	7.977	23.525	20175
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.062	0.05	3840
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.068	0.05	3825
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.081	0.05	3774
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.064	0.05	3810
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.077	0.05	3801
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.068	0.05	3823
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.066	0.05	14298
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.061	0.05	14373
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.07	0.05	14247
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.057	0.05	14298
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.065	0.05	14290
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.07	0.05	14222

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	S	X-RAY DIFFRACTION	Local ncs	0.06168	0.0501
1	2	S	X-RAY DIFFRACTION	Local ncs	0.06168	0.0501
2	3	S	X-RAY DIFFRACTION	Local ncs	0.06811	0.0501
2	4	S	X-RAY DIFFRACTION	Local ncs	0.06811	0.0501
3	5	S	X-RAY DIFFRACTION	Local ncs	0.08096	0.0501
3	6	S	X-RAY DIFFRACTION	Local ncs	0.08096	0.0501
4	7	S	X-RAY DIFFRACTION	Local ncs	0.06405	0.0501
4	8	S	X-RAY DIFFRACTION	Local ncs	0.06405	0.0501
5	9	S	X-RAY DIFFRACTION	Local ncs	0.07686	0.0501
5	10	S	X-RAY DIFFRACTION	Local ncs	0.07686	0.0501
6	11	S	X-RAY DIFFRACTION	Local ncs	0.06816	0.0501
6	12	S	X-RAY DIFFRACTION	Local ncs	0.06816	0.0501
7	13	S	X-RAY DIFFRACTION	Local ncs	0.06641	0.05009
7	14	S	X-RAY DIFFRACTION	Local ncs	0.06641	0.05009
8	15	S	X-RAY DIFFRACTION	Local ncs	0.06118	0.05009
8	16	S	X-RAY DIFFRACTION	Local ncs	0.06118	0.05009
9	17	S	X-RAY DIFFRACTION	Local ncs	0.06969	0.05008
9	18	S	X-RAY DIFFRACTION	Local ncs	0.06969	0.05008
10	19	S	X-RAY DIFFRACTION	Local ncs	0.05719	0.05009
10	20	S	X-RAY DIFFRACTION	Local ncs	0.05719	0.05009
11	21	S	X-RAY DIFFRACTION	Local ncs	0.06505	0.05009
11	22	S	X-RAY DIFFRACTION	Local ncs	0.06505	0.05009
12	23	S	X-RAY DIFFRACTION	Local ncs	0.06979	0.05008
12	24	S	X-RAY DIFFRACTION	Local ncs	0.06979	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.3-2.36	0.253	432	0.207	7796	0.209	8228	0.967	0.977	100	0.168
2.36-2.424	0.254	371	0.204	7629	0.207	8000	0.964	0.977	100	0.167
2.424-2.495	0.259	404	0.207	7382	0.209	7786	0.965	0.977	100	0.169
2.495-2.571	0.248	368	0.198	7195	0.201	7563	0.966	0.979	100	0.159
2.571-2.656	0.241	349	0.202	7000	0.204	7349	0.969	0.978	100	0.162
2.656-2.749	0.3	311	0.214	6767	0.217	7090	0.961	0.978	99.8307	0.173
2.749-2.852	0.252	315	0.205	6571	0.207	6886	0.964	0.978	100	0.168
2.852-2.969	0.231	355	0.181	6221	0.184	6576	0.97	0.982	100	0.148
2.969-3.101	0.234	270	0.177	6094	0.18	6364	0.97	0.983	100	0.146
3.101-3.252	0.242	303	0.193	5704	0.196	6053	0.973	0.981	99.24	0.159
3.252-3.427	0.224	284	0.18	5515	0.182	5801	0.977	0.984	99.9655	0.154
3.427-3.635	0.215	260	0.161	5197	0.164	5457	0.974	0.988	100	0.138
3.635-3.886	0.205	270	0.155	4891	0.158	5161	0.979	0.989	100	0.134
3.886-4.196	0.197	237	0.156	4577	0.158	4814	0.98	0.988	100	0.138
4.196-4.596	0.2	196	0.155	4244	0.157	4440	0.978	0.987	100	0.141
4.596-5.137	0.187	214	0.147	3821	0.149	4035	0.983	0.989	100	0.133
5.137-5.929	0.224	175	0.181	3403	0.183	3578	0.974	0.984	100	0.159
5.929-7.255	0.216	145	0.172	2898	0.174	3043	0.974	0.984	100	0.146
7.255-10.232	0.175	111	0.162	2282	0.163	2393	0.984	0.986	100	0.137
10.232-97.78	0.262	74	0.252	1268	0.253	1400	0.945	0.961	95.8571	0.219

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