PDB-2py8: RbcX - Yorodumi

ID or keywords:

Entry

Database: PDB / ID: 2py8

Title

RbcX

Components

Hypothetical protein rbcX

Keywords

CHAPERONE / All helical fold

Function / homology

Function and homology information

ribulose bisphosphate carboxylase complex assembly / carboxysome / carbon fixation / photosynthesis / protein folding chaperone / cytoplasm
Similarity search - Function

Biological species

Synechocystis sp. PCC 6803 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.45 Å

Authors

Tanaka, S. / Sawaya, M.R. / Kerfeld, C.A. / Yeates, T.O.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of the RuBisCO chaperone RbcX from Synechocystis sp. PCC6803.
Authors: Tanaka, S. / Sawaya, M.R. / Kerfeld, C.A. / Yeates, T.O.

History

Deposition	May 15, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2py8.cif.gz	108.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2py8_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	2py8_full_validation.pdf.gz	1.3 MB	Display
Data in XML	2py8_validation.xml.gz	19.6 KB	Display
Data in CIF	2py8_validation.cif.gz	26.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/py/2py8 ftp://data.pdbj.org/pub/pdb/validation_reports/py/2py8	HTTPS FTP

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Related structure data

Similar structure data	5v7w-d 6g0w-d 3smj-d 5iwd-d 1slc-1 7los-2 3m5r-1 1bm9-1 2wci-d 2gnx-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Hypothetical protein rbcX

B: Hypothetical protein rbcX

C: Hypothetical protein rbcX

D: Hypothetical protein rbcX

hetero molecules

67.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Hypothetical protein rbcX

C: Hypothetical protein rbcX

hetero molecules

defined by author&software
33.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Hypothetical protein rbcX

hetero molecules

A: Hypothetical protein rbcX

hetero molecules

defined by author&software
33.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: Hypothetical protein rbcX

hetero molecules

D: Hypothetical protein rbcX

hetero molecules

defined by author&software
33.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	129.832, 129.832, 92.742
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	C-601- PE4
2	1	B-618- HOH

Details

The chain B and chain C form a dimer, and the chain A and chain D form another dimer.

#1: Protein	Hypothetical protein rbcX Mass: 16613.441 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC6803 / Gene: rbcX / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q55670
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 Mass: 354.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₈ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.94 Å³/Da / Density % sol: 58.16 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 30% PEG 400, 0.1M potassium/sodium phosphate, 0.2M lithium sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.2 / Wavelength: 0.97947,0.97969,0.97182

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2005

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97947	1
2	0.97969	1
3	0.97182	1

Reflection

D res high: 3.3 Å / D res low: 90 Å / % possible obs: 100

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs
7.4	1	11.3	168367	0.094	1.09	22720
6.8	2	9.5	84452	0.106	1.04	12475
7.4	3	10.4	170353	0.1	1.09	22996

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
7.11	90	99.8	1	0.048	1.051	7.7
5.64	7.11	100	1	0.077	1.047	7.6
4.93	5.64	100	1	0.081	1.066	7.1
4.48	4.93	100	1	0.081	1.008	7.3
4.16	4.48	100	1	0.109	1.067	7.4
3.91	4.16	100	1	0.15	1.089	7.4
3.72	3.91	100	1	0.202	1.122	7.4
3.55	3.72	100	1	0.254	1.155	7.4
3.42	3.55	100	1	0.318	1.171	7.4
3.3	3.42	100	1	0.49	1.162	7.4
7.11	90	99.9	2	0.057	1.067	6.4
5.64	7.11	100	2	0.085	1.078	6.8
4.93	5.64	100	2	0.09	1.035	6.5
4.48	4.93	99.9	2	0.09	1.026	6.7
4.16	4.48	100	2	0.123	1.088	6.9
3.91	4.16	100	2	0.168	1.005	6.9
3.72	3.91	100	2	0.231	1.054	6.9
3.55	3.72	100	2	0.285	1.032	6.9
3.42	3.55	100	2	0.372	1.052	6.9
3.3	3.42	100	2	0.572	0.945	6.9
7.11	90	99.9	3	0.049	1.113	7.7
5.64	7.11	100	3	0.08	1.023	7.6
4.93	5.64	100	3	0.085	1.052	7.1
4.48	4.93	100	3	0.084	0.977	7.3
4.16	4.48	100	3	0.117	1.098	7.4
3.91	4.16	100	3	0.167	1.08	7.4
3.72	3.91	100	3	0.232	1.144	7.4
3.55	3.72	100	3	0.295	1.146	7.4
3.42	3.55	100	3	0.392	1.197	7.4
3.3	3.42	100	3	0.611	1.082	7.4

Reflection

Resolution: 2.45→90 Å / Num. all: 29666 / Num. obs: 29666 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / B_iso Wilson estimate: 62.6 Å² / R_merge(I) obs: 0.059 / R_sym value: 0.059 / Χ²: 1.038 / Net I/σ(I): 16.7

Reflection shell

Resolution: 2.45→2.54 Å / Redundancy: 7.9 % / R_merge(I) obs: 0.541 / Num. unique all: 2896 / Χ²: 1.032 / % possible all: 100

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 3.3 Å / D res low: 20 Å / FOM : 0.327 / FOM acentric: 0.34 / FOM centric: 0.257 / Reflection: 12359 / Reflection acentric: 10357 / Reflection centric: 2002

Phasing MAD set

Highest resolution: 3.3 Å / Lowest resolution: 20 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	0.97	0.92	11.2	15.7	0.48	0.37	10355	2002
2	0.98	0.96	11.6	17.2	0.43	0.31	10290	1997
3	2.14	1	0	0	0	0	10357	2002

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	12.25-20	0.85	0.74	14	16.6	0.96	0.72	128	91
1	8.83-12.25	0.88	0.75	12.4	15.5	0.96	0.76	308	136
1	6.9-8.83	0.87	0.81	9.9	12.3	1.04	0.75	561	180
1	5.67-6.9	0.91	0.86	8.7	11.7	1.01	0.65	899	233
1	4.8-5.67	0.96	0.92	8.7	13.7	0.78	0.46	1314	273
1	4.17-4.8	0.99	1.01	9.8	13.9	0.55	0.33	1802	314
1	3.68-4.17	0.99	1	11.6	16.7	0.33	0.2	2372	366
1	3.3-3.68	0.99	0.99	13.6	21.2	0.21	0.12	2971	409
2	12.25-20	0.9	0.85	14.1	18.3	0.79	0.54	128	91
2	8.83-12.25	0.96	0.89	12.3	19.6	0.81	0.51	308	136
2	6.9-8.83	0.93	0.95	10.6	14.8	0.84	0.54	561	180
2	5.67-6.9	0.95	0.92	9.7	14.6	0.79	0.46	899	233
2	4.8-5.67	0.97	0.96	10	14.5	0.62	0.4	1314	273
2	4.17-4.8	0.98	0.97	10.5	16	0.48	0.28	1802	314
2	3.68-4.17	0.99	0.99	11.6	18	0.33	0.18	2373	366
2	3.3-3.68	0.99	0.99	13.6	20.5	0.23	0.13	2905	404
3	12.25-20	1.09	1	0	0	0	0	128	91
3	8.83-12.25	1.13	1	0	0	0	0	308	136
3	6.9-8.83	1.53	1	0	0	0	0	561	180
3	5.67-6.9	4.24	1	0	0	0	0	899	233
3	4.8-5.67	2.32	1	0	0	0	0	1314	273
3	4.17-4.8	1.76	1	0	0	0	0	1802	314
3	3.68-4.17	2.18	1	0	0	0	0	2373	366
3	3.3-3.68	2.65	1	0	0	0	0	2972	409

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	62.684	0.705	0.19	0.054	0.094
2	Se	71.008	0.724	0.332	0.032	0.092
3	Se	91.503	0.691	0.748	0.078	0.085
4	Se	86.998	0.617	0.348	0.088	0.057
5	Se	118.137	0.816	0.178	0.086	0.056
6	Se	53.526	0.705	0.19	0.053	0.082
7	Se	55.213	0.724	0.332	0.032	0.073
8	Se	69.711	0.691	0.748	0.078	0.066
9	Se	87.072	0.618	0.347	0.089	0.045
10	Se	100.173	0.816	0.178	0.087	0.044
11	Se	52.76	0.705	0.19	0.054	0
12	Se	56.421	0.724	0.332	0.031	0
13	Se	73.756	0.691	0.748	0.077	0
14	Se	66.228	0.619	0.347	0.09	0
15	Se	89.426	0.816	0.18	0.087	0

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
12.25-20	0.572	0.657	0.453	219	128	91
8.83-12.25	0.563	0.599	0.482	444	308	136
6.9-8.83	0.612	0.663	0.455	741	561	180
5.67-6.9	0.567	0.613	0.393	1132	899	233
4.8-5.67	0.461	0.493	0.308	1587	1314	273
4.17-4.8	0.345	0.37	0.205	2116	1802	314
3.68-4.17	0.222	0.237	0.123	2739	2373	366
3.3-3.68	0.147	0.154	0.1	3381	2972	409

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 29549

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
9.53-100	24.7	0.891	510
7.63-9.53	26.5	0.905	512
6.62-7.63	28.7	0.891	558
5.92-6.62	33	0.87	616
5.41-5.92	32.4	0.883	685
5.01-5.41	30	0.9	731
4.69-5.01	30.1	0.913	787
4.42-4.69	28.3	0.896	826
4.19-4.42	31.6	0.89	867
4-4.19	34	0.858	920
3.83-4	40.6	0.818	956
3.68-3.83	40.1	0.839	999
3.55-3.68	42.2	0.835	1004
3.43-3.55	42.2	0.803	1076
3.32-3.43	46.1	0.797	1100
3.22-3.32	82.7	0.695	1137
3.13-3.22	90.7	0.691	1161
3.04-3.13	86.8	0.693	1205
2.97-3.04	90.6	0.708	1213
2.9-2.97	89.5	0.686	1238
2.83-2.9	90.2	0.692	1292
2.77-2.83	91.3	0.703	1309
2.71-2.77	89	0.71	1321
2.65-2.71	91.4	0.686	1368
2.6-2.65	91.7	0.682	1386
2.55-2.6	89.4	0.657	1425
2.51-2.55	90.1	0.648	1432
2.45-2.51	90.5	0.511	1915

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction

Refinement

Method to determine structure:

MAD / Resolution: 2.45→19.5 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.935 / SU B: 13.571 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.249	1495	5.1 %	RANDOM
R_work	0.209	-	-	-
obs	0.211	29544	99.92 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 58.617 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.01 Å²	0 Å²	0 Å²
2-	-	-0.01 Å²	0 Å²
3-	-	-	0.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→19.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3686	0	54	87	3827

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.021	3792
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2542
X-RAY DIFFRACTION	r_angle_refined_deg	1.137	1.97	5131
X-RAY DIFFRACTION	r_angle_other_deg	0.878	3	6225
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.132	5	456
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.812	24.545	187
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.087	15	671
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.588	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	609
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4118
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	712
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	967
X-RAY DIFFRACTION	r_nbd_other	0.172	0.2	2419
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	1832
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	2013
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	112
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.184	0.2	41
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.226	0.2	97
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.14	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	3.677	2	2498
X-RAY DIFFRACTION	r_mcbond_other	1.047	2	914
X-RAY DIFFRACTION	r_mcangle_it	4.739	3	3727
X-RAY DIFFRACTION	r_scbond_it	3.821	2	1582
X-RAY DIFFRACTION	r_scangle_it	5.366	3	1404

LS refinement shell

Resolution: 2.451→2.514 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.384	95	-
R_work	0.301	1995	-
obs	-	2090	99.05 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.6217	-2.3533	-3.7291	2.5295	3.2501	5.3267	-0.3804	0.0851	-0.1723	0.5329	0.1989	0.042	0.6128	0.3655	0.1815	-0.1963	-0.0251	0.0286	-0.2172	-0.0891	-0.405	47.586	41.229	48.235
2	6.4833	0.7559	1.2735	1.2008	-0.1003	1.7335	-0.0003	0.3221	-0.4609	0.068	0.0906	-0.0349	0.1963	0.1317	-0.0903	-0.3124	0.0777	0.0553	-0.1179	0.0609	-0.3982	39.962	91.223	61.016
3	3.5076	0.3762	0.534	0.9132	-0.0642	1.2279	-0.1424	0.4522	0.4116	0.0642	0.0911	0.1434	-0.0833	-0.0065	0.0513	-0.3133	0.0823	0.0127	-0.1984	0.0742	-0.3503	34.639	99.334	61.852
4	6.7978	-1.5683	2.054	5.9986	-1.2386	10.5164	0.1954	0.1844	1.1206	-0.579	0.2939	-0.5265	-1.3151	0.1367	-0.4893	0.2138	-0.163	0.3281	-0.2289	-0.0521	-0.243	51.188	62.255	42.361

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 120	2 - 120
2	X-RAY DIFFRACTION	2	B	B	2 - 115	2 - 115
3	X-RAY DIFFRACTION	3	C	C	2 - 123	2 - 123
4	X-RAY DIFFRACTION	4	D	D	2 - 104	2 - 104

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