PDB-3zxw: STRUCTURE OF ACTIVATED RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS...

ID or keywords:

Entry

Database: PDB / ID: 3zxw

Title

STRUCTURE OF ACTIVATED RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

Components

(RIBULOSE BISPHOSPHATE CARBOXYLASE ...

RuBisCO) x 2

Keywords

LYASE / CO2/O2 SPECIFICITY / CARBON DIOXIDE FIXATION /

PHOTOSYNTHESIS /

THERMOSTABILITY /

PHOTORESPIRATION /

MONOOXYGENASE /

HYDROXYLATION /

CHLOROPLAST /

CALVIN CYCLE / THERMOPHILIC CYANOBACTERIA

Function / homology

Function and homology information

photorespiration /

carboxysome /

ribulose-bisphosphate carboxylase /

ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle /

monooxygenase activity / magnesium ion binding /

cytoplasm
Similarity search - Function

Biological species

THERMOSYNECHOCOCCUS ELONGATUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Terlecka, B. / Wilhelmi, V. / Bialek, W. / Gubernator, B. / Szczepaniak, A. / Hofmann, E.

Citation

Journal: To be Published
Title: Structure of Ribulose-1,5-Bisphosphate Carboxylase Oxygenase from Thermosynechococcus Elongatus
Authors: Terlecka, B. / Wilhelmi, V. / Bialek, W. / Gubernator, B. / Szczepaniak, A. / Hofmann, E.

History

Deposition	Aug 16, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 27, 2018	Group: Data collection / Derived calculations / Category: pdbx_struct_conn_angle / struct_conn Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3zxw.cif.gz	457.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3zxw.ent.gz	387 KB	Display	PDB format
PDBx/mmJSON format	3zxw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zx/3zxw ftp://data.pdbj.org/pub/pdb/validation_reports/zx/3zxw	HTTPS FTP

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Related structure data

Related structure data	2ybvC C: citing same article (ref.)
Similar structure data	1rbl-d 1ir1-1 1rsc-d 4mkv-1 1rco-d 1rcx-d 1upp-1 8ruc-1 4rub-1 1rbo-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#11 - Nov 2000 Rubisco similarity (17)

Deposited unit

A: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

B: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

C: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

D: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

E: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

F: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

G: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

H: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

hetero molecules

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

1

A: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

B: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

C: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

D: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

E: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

F: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

G: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

H: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

hetero molecules

A: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

B: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

C: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

D: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

E: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

F: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

G: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

H: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

hetero molecules

defined by author&software
542 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	111.500, 111.500, 397.000
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	C-2152- HOH
2	1	C-2162- HOH
3	1	C-2167- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	G
3	1	C
4	1	E
1	2	B
2	2	F
3	2	D
4	2	H
1	3	A
2	3	G
1	4	E
2	4	C
1	5	B
2	5	F
3	5	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	12 - 89
2	1	1	2	G	12 - 89
3	1	1	2	C	12 - 89
4	1	1	2	E	12 - 89
1	2	1	2	A	93 - 475
2	2	1	2	G	93 - 475
3	2	1	2	C	93 - 475
4	2	1	2	E	93 - 475
1	1	2	2	B	14 - 25
2	1	2	2	F	14 - 25
3	1	2	2	D	14 - 25
4	1	2	2	H	14 - 25
1	2	2	2	B	27 - 106
2	2	2	2	F	27 - 106
3	2	2	2	D	27 - 106
4	2	2	2	H	27 - 106
1	1	3	2	A	90 - 92
2	1	3	2	G	90 - 92
1	1	4	2	E	90 - 92
2	1	4	2	C	90 - 92
1	1	5	2	B	26
2	1	5	2	F	26
3	1	5	2	D	26

NCS ensembles :

ID
1
2
3
4
5

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.004639, -1, -0.002172), (0.9949, 0.004835, -0.1011), (0.1011, -0.001692, 0.9949)	-6.729, 0.00591, 0.3305
2	given	(-0.9948, -0.006256, 0.1013), (-0.003863, -0.995, -0.09939), (0.1014, -0.09927, 0.9899)	-6.699, -6.66, -0.0589
3	given	(0.001265, 0.9957, 0.09293), (-1, -0.000943, -0.003507), (-0.003404, -0.09294, 0.9957)	-0.07644, -6.795, -0.3089
4	given	(-0.000793, -1, -0.004161), (0.9945, -0.000353, -0.1047), (0.1047, -0.004222, 0.9945)	-6.713, 0.06493, 0.2659
5	given	(-0.9951, -0.00402, 0.09914), (-0.006712, -0.9942, -0.1077), (0.09899, -0.1078, 0.9892)	-6.649, -6.905, -0.372
6	given	(-0.003737, 0.9962, 0.08669), (-0.9999, -0.002806, -0.01085), (-0.01057, -0.08673, 0.9962)	-0.4589, -6.819, -0.5371

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RIBULOSE BISPHOSPHATE CARBOXYLASE ... , 2 types, 8 molecules ACEGBDFH

#1: Protein	RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN / RUBISCO LARGE SUBUNIT Mass: 53134.324 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) Strain: BP-1 / Plasmid: PUC18RBCLXSTH.EL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] References: UniProt: Q8DIS5, ribulose-bisphosphate carboxylase
#2: Protein	RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN Mass: 13999.818 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) Strain: BP-1 / Plasmid: PUC18RBCLXSTH.EL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] References: UniProt: Q8DIS7, ribulose-bisphosphate carboxylase

#1: Protein

RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN / RUBISCO LARGE SUBUNIT

Mass: 53134.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

THERMOSYNECHOCOCCUS ELONGATUS (bacteria)
Strain: BP-1 / Plasmid: PUC18RBCLXSTH.EL / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA]
References: UniProt: Q8DIS5,

ribulose-bisphosphate carboxylase

#2: Protein

RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

Mass: 13999.818 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

THERMOSYNECHOCOCCUS ELONGATUS (bacteria)
Strain: BP-1 / Plasmid: PUC18RBCLXSTH.EL / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA]
References: UniProt: Q8DIS7,

ribulose-bisphosphate carboxylase

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Sugars , 1 types, 4 molecules

#4: Sugar	ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE Type: saccharideCarbohydrate / Mass: 356.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₁₃P₂

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Non-polymers , 3 types, 920 molecules

#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 905 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 49 % / Description: NONE
Crystal grow	pH: 8 Details: 80 MM HEPES, 20 MM MGCL2, 8% (W/V) PEG4000, 30% (V/V) GLYCEROL, PH=8

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978946
Detector	Type: MARRESEARCH / Detector: CCD / Date: Dec 11, 2009 / Details: MIRRORS
Radiation	Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978946 Å / Relative weight: 1
Reflection	Resolution: 2.1→20 Å / Num. obs: 144795 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / R_merge(I) obs: 0.11 / Net I/σ(I): 14.9
Reflection shell	Resolution: 2.1→2.15 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 3.2 / % possible all: 92

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0088	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: RUBISCO FROM TH.ELONGATUS WITHOUT LIGANDS

Resolution: 2.1→19.92 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.94 / SU B: 4.571 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2135	7450	5.1 %	RANDOM
R_work	0.18102	-	-	-
obs	0.18276	137341	100 %	-

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: 35.997 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.3 Å²	0 Å²	0 Å²
2-	-	0.3 Å²	0 Å²
3-	-	-	-0.61 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→19.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17668	0	154	905	18727

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	18323
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.013	1.953	24871
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.339	5	2236
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.802	23.829	888
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.182	15	2972
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.721	15	124
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	2652
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	14128
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
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
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.559	1.5	1183
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.163	2	1914
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.762	3	750
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.867	4.5	722
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	1849	tight positional	0.08	0.05
1	2	G	1849	tight positional	0.1	0.05
1	3	C	1849	tight positional	0.07	0.05
1	4	E	1849	tight positional	0.09	0.05
2	1	B	368	tight positional	0.01	0.05
2	2	F	368	tight positional	0.01	0.05
2	3	D	368	tight positional	0.01	0.05
2	4	H	368	tight positional	0.01	0.05
3	1	A	12	tight positional	0.01	0.05
4	1	E	12	tight positional	0.02	0.05
5	1	B	4	tight positional	0	0.05
5	2	F	4	tight positional	0.01	0.05
5	3	D	4	tight positional	0	0.05
1	1	A	1796	medium positional	0.2	0.5
1	2	G	1796	medium positional	0.17	0.5
1	3	C	1796	medium positional	0.17	0.5
1	4	E	1796	medium positional	0.21	0.5
2	1	B	389	medium positional	0.01	0.5
2	2	F	389	medium positional	0.01	0.5
2	3	D	389	medium positional	0.01	0.5
2	4	H	389	medium positional	0.01	0.5
3	2	G	7	medium positional	0.02	0.5
4	2	C	7	medium positional	0.01	0.5
5	1	B	7	medium positional	0.01	0.5
5	2	F	7	medium positional	0.01	0.5
5	3	D	7	medium positional	0.01	0.5
1	1	A	1849	tight thermal	1.1	0.5
1	2	G	1849	tight thermal	0.71	0.5
1	3	C	1849	tight thermal	0.81	0.5
1	4	E	1849	tight thermal	0.7	0.5
2	1	B	368	tight thermal	0.02	0.5
2	2	F	368	tight thermal	0.02	0.5
2	3	D	368	tight thermal	0.02	0.5
2	4	H	368	tight thermal	0.03	0.5
3	1	A	12	tight thermal	0.05	0.5
4	1	E	12	tight thermal	0.03	0.5
5	1	B	4	tight thermal	0.01	0.5
5	2	F	4	tight thermal	0.02	0.5
5	3	D	4	tight thermal	0.02	0.5
1	1	A	1796	medium thermal	1.11	2
1	2	G	1796	medium thermal	0.65	2
1	3	C	1796	medium thermal	0.69	2
1	4	E	1796	medium thermal	0.64	2
2	1	B	389	medium thermal	0.02	2
2	2	F	389	medium thermal	0.02	2
2	3	D	389	medium thermal	0.02	2
2	4	H	389	medium thermal	0.02	2
3	2	G	7	medium thermal	0.03	2
4	2	C	7	medium thermal	0.03	2
5	1	B	7	medium thermal	0.01	2
5	2	F	7	medium thermal	0.01	2
5	3	D	7	medium thermal	0.01	2

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_work	0.238	9706	-
R_free	-	0	-
obs	-	-	100 %

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RIBULOSE BISPHOSPHATE CARBOXYLASE ... , 2 types, 8 molecules ACEGBDFH

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Sugars , 1 types, 4 molecules

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Non-polymers , 3 types, 920 molecules

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-Sugars , 1 types, 4 molecules

-Non-polymers , 3 types, 920 molecules

-Experimental details

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Components

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RIBULOSE BISPHOSPHATE CARBOXYLASE ... , 2 types, 8 molecules ACEGBDFH

-
Sugars , 1 types, 4 molecules

-
Non-polymers , 3 types, 920 molecules

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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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Processing

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About Yorodumi

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News

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+
Jul 12, 2017. Major update of PDB

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Yorodumi