PDB-3km2: As-isolated TOMATO CHLOROPLAST SUPEROXIDE DISMUTASE

ID or keywords:

Entry

Database: PDB / ID: 3km2

Title

As-isolated TOMATO CHLOROPLAST SUPEROXIDE DISMUTASE

Components

Superoxide dismutase [Cu-Zn], chloroplastic

Keywords

OXIDOREDUCTASE / TOMATO CU / ZN SUPEROXIDE DISMUTASE / ANTIOXIDANT / METAL-BINDING / CHLOROPLAST / DISULFIDE BOND / TRANSIT PEPTIDE

Function / homology

Function and homology information

superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / chloroplast / copper ion binding
Similarity search - Function

Biological species

Solanum lycopersicum (tomato)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Galaleldeen, A. / Taylor, A.B. / Hart, P.J.

Citation

Journal: To be Published
Title: Biophysical properties of tomato chloroplast sod
Authors: Galaleldeen, A. / Taylor, A.B. / Hart, P.J.

History

Deposition	Nov 9, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 1, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.pdbx_dist_value / _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_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3km2.cif.gz	630.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3km2.ent.gz	525 KB	Display	PDB format
PDBx/mmJSON format	3km2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/km/3km2 ftp://data.pdbj.org/pub/pdb/validation_reports/km/3km2	HTTPS FTP

-
Related structure data

Related structure data	3km1C 3mkgC 1hl5S 3hog C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6foi-1 3t5w-4 2zkx-1 2gbv-5 3kh3-6 6a9o-2 2zky-1 1sos-2 3gzo-2 1pu0-4 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) 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) 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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#94 - Oct 2007 Superoxide Dismutase similarity (8)

Deposited unit

A: Superoxide dismutase [Cu-Zn], chloroplastic

B: Superoxide dismutase [Cu-Zn], chloroplastic

C: Superoxide dismutase [Cu-Zn], chloroplastic

D: Superoxide dismutase [Cu-Zn], chloroplastic

E: Superoxide dismutase [Cu-Zn], chloroplastic

F: Superoxide dismutase [Cu-Zn], chloroplastic

G: Superoxide dismutase [Cu-Zn], chloroplastic

H: Superoxide dismutase [Cu-Zn], chloroplastic

I: Superoxide dismutase [Cu-Zn], chloroplastic

J: Superoxide dismutase [Cu-Zn], chloroplastic

K: Superoxide dismutase [Cu-Zn], chloroplastic

L: Superoxide dismutase [Cu-Zn], chloroplastic

M: Superoxide dismutase [Cu-Zn], chloroplastic

N: Superoxide dismutase [Cu-Zn], chloroplastic

O: Superoxide dismutase [Cu-Zn], chloroplastic

P: Superoxide dismutase [Cu-Zn], chloroplastic

Q: Superoxide dismutase [Cu-Zn], chloroplastic

R: Superoxide dismutase [Cu-Zn], chloroplastic

S: Superoxide dismutase [Cu-Zn], chloroplastic

T: Superoxide dismutase [Cu-Zn], chloroplastic

U: Superoxide dismutase [Cu-Zn], chloroplastic

V: Superoxide dismutase [Cu-Zn], chloroplastic

W: Superoxide dismutase [Cu-Zn], chloroplastic

X: Superoxide dismutase [Cu-Zn], chloroplastic

hetero molecules

377 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Superoxide dismutase [Cu-Zn], chloroplastic

B: Superoxide dismutase [Cu-Zn], chloroplastic

hetero molecules

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

2

C: Superoxide dismutase [Cu-Zn], chloroplastic

D: Superoxide dismutase [Cu-Zn], chloroplastic

hetero molecules

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

3

E: Superoxide dismutase [Cu-Zn], chloroplastic

F: Superoxide dismutase [Cu-Zn], chloroplastic

hetero molecules

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

4

G: Superoxide dismutase [Cu-Zn], chloroplastic

H: Superoxide dismutase [Cu-Zn], chloroplastic

hetero molecules

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

5

I: Superoxide dismutase [Cu-Zn], chloroplastic

J: Superoxide dismutase [Cu-Zn], chloroplastic

hetero molecules

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

6

K: Superoxide dismutase [Cu-Zn], chloroplastic

L: Superoxide dismutase [Cu-Zn], chloroplastic

hetero molecules

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

7

M: Superoxide dismutase [Cu-Zn], chloroplastic

N: Superoxide dismutase [Cu-Zn], chloroplastic

hetero molecules

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

8

O: Superoxide dismutase [Cu-Zn], chloroplastic

P: Superoxide dismutase [Cu-Zn], chloroplastic

hetero molecules

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

9

Q: Superoxide dismutase [Cu-Zn], chloroplastic

R: Superoxide dismutase [Cu-Zn], chloroplastic

hetero molecules

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

10

S: Superoxide dismutase [Cu-Zn], chloroplastic

T: Superoxide dismutase [Cu-Zn], chloroplastic

hetero molecules

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

11

U: Superoxide dismutase [Cu-Zn], chloroplastic

V: Superoxide dismutase [Cu-Zn], chloroplastic

hetero molecules

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

12

W: Superoxide dismutase [Cu-Zn], chloroplastic

X: Superoxide dismutase [Cu-Zn], chloroplastic

hetero molecules

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

Unit cell

Length a, b, c (Å)	142.033, 144.523, 192.178
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 1 - 153 / Label seq-ID: 1 - 153

#1: Protein	... Superoxide dismutase [Cu-Zn], chloroplastic Mass: 15644.372 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: SODCP.2 / Plasmid: PAG8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14831, superoxide dismutase
#2: Chemical	... ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn

#1: Protein

...
Superoxide dismutase [Cu-Zn], chloroplastic

Mass: 15644.372 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Solanum lycopersicum (tomato) / Gene: SODCP.2 / Plasmid: PAG8H / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14831, superoxide dismutase

#2: Chemical

...
ChemComp-ZN / ZINC ION

Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53.17 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 65% MPD, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2823 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2823 Å / Relative weight: 1
Reflection	Resolution: 3.1→50 Å / Num. obs: 73425 / % possible obs: 99.5 % / Redundancy: 4.8 % / B_iso Wilson estimate: 58.6 Å² / R_sym value: 0.112 / Net I/σ(I): 13.5
Reflection shell	Resolution: 3.1→3.21 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 7196 / R_sym value: 0.444 / % possible all: 99.6

-
Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.4_4)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HL5

1hl5

Resolution: 3.1→48.978 Å / SU ML: 1.06 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.252	3653	5.06 %	random
R_work	0.2201	-	-	-
obs	0.2217	72254	97.61 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 22.119 Å² / k_sol: 0.303 e/Å³

Displacement parameters

B_iso mean: 60.5 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.1212 Å²	0 Å²	0 Å²
2-	-	3.4717 Å²	0 Å²
3-	-	-	-12.1542 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→48.978 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26136	0	24	0	26160

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	26568
X-RAY DIFFRACTION	f_angle_d	1.318	36192
X-RAY DIFFRACTION	f_dihedral_angle_d	17.524	9240
X-RAY DIFFRACTION	f_chiral_restr	0.074	4320
X-RAY DIFFRACTION	f_plane_restr	0.005	4896

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1089	X-RAY DIFFRACTION	POSITIONAL	0.225
1	2	B	1089	X-RAY DIFFRACTION	POSITIONAL	0.225
1	3	C	1089	X-RAY DIFFRACTION	POSITIONAL	0.197
1	4	D	1089	X-RAY DIFFRACTION	POSITIONAL	0.333
1	5	E	1089	X-RAY DIFFRACTION	POSITIONAL	0.164
1	6	F	1089	X-RAY DIFFRACTION	POSITIONAL	0.165
1	7	G	1089	X-RAY DIFFRACTION	POSITIONAL	0.183
1	8	H	1089	X-RAY DIFFRACTION	POSITIONAL	0.201
1	9	I	1089	X-RAY DIFFRACTION	POSITIONAL	0.192
1	10	J	1089	X-RAY DIFFRACTION	POSITIONAL	0.32
1	11	K	1089	X-RAY DIFFRACTION	POSITIONAL	0.166
1	12	L	1089	X-RAY DIFFRACTION	POSITIONAL	0.277
1	13	M	1089	X-RAY DIFFRACTION	POSITIONAL	0.216
1	14	N	1089	X-RAY DIFFRACTION	POSITIONAL	0.187
1	15	O	1089	X-RAY DIFFRACTION	POSITIONAL	0.232
1	16	P	1089	X-RAY DIFFRACTION	POSITIONAL	0.257
1	17	Q	1089	X-RAY DIFFRACTION	POSITIONAL	0.202
1	18	R	1089	X-RAY DIFFRACTION	POSITIONAL	0.471
1	19	S	1089	X-RAY DIFFRACTION	POSITIONAL	0.189
1	20	T	1089	X-RAY DIFFRACTION	POSITIONAL	0.211
1	21	U	1089	X-RAY DIFFRACTION	POSITIONAL	0.36
1	22	V	1089	X-RAY DIFFRACTION	POSITIONAL	0.161
1	23	W	1089	X-RAY DIFFRACTION	POSITIONAL	0.215
1	24	X	1089	X-RAY DIFFRACTION	POSITIONAL	0.385

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.1-3.1166	0.3467	123	0.3117	2260	X-RAY DIFFRACTION	85
3.1166-3.1593	0.3503	153	0.301	2634	X-RAY DIFFRACTION	98
3.1593-3.2044	0.3299	136	0.2883	2624	X-RAY DIFFRACTION	98
3.2044-3.2522	0.3296	133	0.2884	2608	X-RAY DIFFRACTION	98
3.2522-3.303	0.2736	119	0.2697	2647	X-RAY DIFFRACTION	98
3.303-3.3571	0.3098	133	0.2565	2644	X-RAY DIFFRACTION	98
3.3571-3.415	0.3189	132	0.2504	2647	X-RAY DIFFRACTION	98
3.415-3.4771	0.2458	126	0.2519	2632	X-RAY DIFFRACTION	99
3.4771-3.544	0.2799	160	0.2534	2648	X-RAY DIFFRACTION	99
3.544-3.6163	0.2538	133	0.2338	2638	X-RAY DIFFRACTION	99
3.6163-3.6949	0.2658	150	0.2269	2626	X-RAY DIFFRACTION	99
3.6949-3.7808	0.2615	156	0.2161	2617	X-RAY DIFFRACTION	99
3.7808-3.8753	0.2497	152	0.2103	2653	X-RAY DIFFRACTION	99
3.8753-3.9801	0.2549	132	0.2088	2683	X-RAY DIFFRACTION	99
3.9801-4.0971	0.2063	157	0.1955	2621	X-RAY DIFFRACTION	99
4.0971-4.2293	0.246	155	0.1906	2665	X-RAY DIFFRACTION	99
4.2293-4.3804	0.2244	140	0.1822	2647	X-RAY DIFFRACTION	98
4.3804-4.5556	0.1797	151	0.1787	2638	X-RAY DIFFRACTION	98
4.5556-4.7628	0.1913	148	0.1779	2661	X-RAY DIFFRACTION	98
4.7628-5.0137	0.2218	131	0.1889	2653	X-RAY DIFFRACTION	98
5.0137-5.3274	0.224	130	0.1992	2706	X-RAY DIFFRACTION	98
5.3274-5.7382	0.26	146	0.2216	2636	X-RAY DIFFRACTION	98
5.7382-6.3146	0.2133	124	0.1983	2714	X-RAY DIFFRACTION	98
6.3146-7.2258	0.206	154	0.1942	2656	X-RAY DIFFRACTION	97
7.2258-9.0942	0.249	147	0.1886	2676	X-RAY DIFFRACTION	96
9.0942-48.9843	0.226	132	0.2041	2767	X-RAY DIFFRACTION	95

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi