PDB-1z8k: X-ray structure of allene oxide cyclase from Arabidopsis thaliana...

ID or keywords:

Entry

Database: PDB / ID: 1z8k

Title

X-ray structure of allene oxide cyclase from Arabidopsis thaliana at3g25770

Components

At3g25770 protein

Keywords

ISOMERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / AT3G25770 / Center for Eukaryotic Structural Genomics / jasmonic acid biosynthesis / plant protein

Function / homology

Function and homology information

allene-oxide cyclase / allene-oxide cyclase activity / stromule / jasmonic acid biosynthetic process / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / response to cold / chloroplast / cytosol
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.712 Å

Authors

Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: To be published
Title: X-ray structure of allene oxide cyclase from Arabidopsis thaliana at3g25770
Authors: Center for Eukaryotic Structural Genomics (CESG)

History

Deposition	Mar 30, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 12, 2005	Provider: repository / Type: Initial release
Revision 1.1	Feb 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.3	Oct 11, 2017	Group: Refinement description / Category: software
Revision 1.4	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	1z8k.cif.gz	131.2 KB	Display	PDBx/mmCIF format
PDB format	pdb1z8k.ent.gz	100.8 KB	Display	PDB format
PDBx/mmJSON format	1z8k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	1z8k_validation.pdf.gz	433.5 KB	Display	wwPDB validaton report
Full document	1z8k_full_validation.pdf.gz	435 KB	Display
Data in XML	1z8k_validation.xml.gz	32.4 KB	Display
Data in CIF	1z8k_validation.cif.gz	47.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z8/1z8k ftp://data.pdbj.org/pub/pdb/validation_reports/z8/1z8k	HTTPS FTP

-
Related structure data

Similar structure data	4cq6-d 2gin-2 2q4i-d 2dio-d 4cq7-d 4h6c-3 2brj-d 3tbg-4 5ch5-d 5lrr-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: GO.15839

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: At3g25770 protein

B: At3g25770 protein

C: At3g25770 protein

63.9 kDa, 3 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)	64.412, 100.013, 105.386
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	At3g25770 protein Mass: 21299.947 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT3G25770 / Plasmid: PVP-27 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q9LS02, allene-oxide cyclase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 57.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 10 mg/ml protein, 11% PEG 8K, 0.100 M SODIUM ACETATE, pH 4.5, vapor diffusion, hanging drop, temperature 293K

-
Data collection

Diffraction

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

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 0.97924, 0.97156, 0.97947

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR

Radiation

Monochromator: CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97924	1
2	0.97156	1
3	0.97947	1

Reflection

D res low: 50 Å

Redundancy (%)	ID	Number	R_merge(I) obs	Χ²	D res high (Å)	% possible obs
14.1	1	73976	0.075	1.013	1.71	100
10.6	2	75368	0.074	0.942	1.69	98.1
14	3	74216	0.075	0.941	1.71	100

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
3.68	50	100	1	0.045	1.178	14
2.92	3.68	100	1	0.058	1.093	14.5
2.55	2.92	100	1	0.065	1.149	14.5
2.32	2.55	100	1	0.083	1.162	14.5
2.15	2.32	100	1	0.096	1.18	14.5
2.03	2.15	100	1	0.104	0.959	14.5
1.93	2.03	100	1	0.13	0.889	14.3
1.84	1.93	100	1	0.172	0.832	14.3
1.77	1.84	100	1	0.214	0.811	13.9
1.71	1.77	100	1	0.252	0.818	12.4
3.64	50	93.3	2	0.042	0.922	11.1
2.89	3.64	96.1	2	0.057	0.995	11.1
2.52	2.89	97.6	2	0.064	1.037	11
2.29	2.52	98.4	2	0.086	1.1	11
2.13	2.29	98.9	2	0.099	1.112	10.8
2	2.13	99.3	2	0.112	0.918	10.8
1.9	2	99.6	2	0.147	0.849	10.8
1.82	1.9	99.8	2	0.191	0.82	10.5
1.75	1.82	99.8	2	0.24	0.817	9.9
1.69	1.75	98.6	2	0.286	0.804	8.9
3.68	50	100	3	0.041	0.916	14
2.92	3.68	100	3	0.057	1.005	14.5
2.55	2.92	100	3	0.066	1.055	14.5
2.32	2.55	100	3	0.088	1.085	14.5
2.15	2.32	100	3	0.102	1.104	14.5
2.03	2.15	100	3	0.116	0.92	14.5
1.93	2.03	100	3	0.149	0.855	14.3
1.84	1.93	100	3	0.201	0.812	14.2
1.77	1.84	100	3	0.259	0.804	13.6
1.71	1.77	99.9	3	0.305	0.803	11.6

Reflection

Resolution: 1.71→48.166 Å / Num. obs: 73976 / % possible obs: 100 % / Redundancy: 14.1 % / R_merge(I) obs: 0.075 / Χ²: 1.013 / Net I/σ(I): 19.995

Reflection shell

Diffraction-ID: 1 / % possible obs: 100 %

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Χ²	% possible all
1.71-1.77	12.4	0.252	5.811	7298	0.818	99.9
1.77-1.84	13.9	0.214		7326	0.811
1.84-1.93	14.3	0.172		7287	0.832
1.93-2.03	14.3	0.13		7327	0.889
2.03-2.15	14.5	0.104		7354	0.959
2.15-2.32	14.5	0.096		7335	1.18
2.32-2.55	14.5	0.083		7379	1.162
2.55-2.92	14.5	0.065		7420	1.149
2.92-3.68	14.5	0.058		7468	1.093
3.68-50	14	0.045		7782	1.178

-
Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD

D res high: 1.8 Å / D res low: 20 Å / FOM : 0.44 / Reflection: 63255

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.9792	5.02	-4.24
1	3 wavelength	2	0.9795	2.47	-12.87
1	3 wavelength	3	0.9716	2.92	-7.92

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	21.365	0.57	0.092	0.002	0.504
2	Se	39.007	0.624	0.455	0.017	0.54
3	Se	23.177	0.135	0.315	0.997	0.463

Phasing MAD shell

Resolution (Å)	FOM	Reflection
6.35-20	0.77	3230
4.05-6.35	0.68	5323
3.18-4.05	0.63	6737
2.7-3.18	0.6	7865
2.39-2.7	0.49	8837
2.17-2.39	0.38	9716
1.99-2.17	0.27	10442
1.86-1.99	0.18	11105

Phasing dm

FOM : 0.69 / FOM acentric: 0.69 / FOM centric: 0.7 / Reflection: 63255 / Reflection acentric: 57863 / Reflection centric: 5392

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
5.1-19.991	0.94	0.94	0.91	2891	2252	639
3.2-5.1	0.93	0.93	0.9	8629	7559	1070
2.6-3.2	0.84	0.84	0.77	10682	9705	977
2.3-2.6	0.73	0.74	0.67	10701	9871	830
1.9-2.3	0.61	0.61	0.56	18818	17586	1232
1.8-1.9	0.39	0.39	0.34	11534	10890	644

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.08	phasing
RESOLVE	2.08	phasing
REFMAC	refmac_5.2.0005	refinement

Refinement

Method to determine structure:

MAD / Resolution: 1.712→50 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.952 / SU B: 1.419 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: INITIAL MODEL GENERATED BY ARP/WARP, SELENIUM C COEFFICIENT FOR STRUCTURE FACTOR CALCULATION SET TO -9.0000, MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18	3725	5 %	RANDOM
R_work	0.149	-	-	-
all	0.15031	-	-	-
obs	0.15031	70173	99.86 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 14.97 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.51 Å²	0 Å²	0 Å²
2-	-	-0.1 Å²	0 Å²
3-	-	-	0.61 Å²

Refinement step

Cycle: LAST / Resolution: 1.712→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4092	0	0	741	4833

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	4233
X-RAY DIFFRACTION	r_angle_refined_deg	1.394	1.995	5747
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.463	5	519
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.567	24.611	180
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.324	15	707
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.11	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	632
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3215
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	2004
X-RAY DIFFRACTION	r_nbtor_refined	0.314	0.2	2956
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	630
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.154	0.2	57
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.215	0.2	56
X-RAY DIFFRACTION	r_mcbond_it	1.22	2	2653
X-RAY DIFFRACTION	r_mcangle_it	2.059	4	4204
X-RAY DIFFRACTION	r_scbond_it	3.42	6	1778
X-RAY DIFFRACTION	r_scangle_it	4.931	8	1543

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	Num. reflection all	% reflection obs (%)
1.712-1.756	0.201	261	0.17	5062	5423	98.156
1.756-1.805	0.22	250	0.154	5000	5250	100
1.805-1.857	0.179	252	0.153	4865	5117	100
1.857-1.914	0.194	250	0.152	4742	4992	100
1.914-1.977	0.184	234	0.151	4580	4814	100
1.977-2.046	0.185	218	0.144	4476	4694	100
2.046-2.123	0.205	241	0.144	4288	4529	100
2.123-2.21	0.174	238	0.148	4124	4362	100
2.21-2.308	0.184	211	0.149	3982	4193	100
2.308-2.42	0.196	211	0.154	3796	4007	100
2.42-2.551	0.201	184	0.16	3621	3805	100
2.551-2.706	0.18	186	0.157	3442	3628	100
2.706-2.892	0.169	161	0.152	3235	3396	100
2.892-3.124	0.171	152	0.149	3032	3184	100
3.124-3.421	0.177	153	0.143	2800	2953	100
3.421-3.824	0.154	144	0.134	2536	2680	100
3.824-4.413	0.126	108	0.122	2284	2392	100
4.413-5.4	0.173	120	0.135	1908	2028	100
5.4-7.616	0.209	84	0.183	1518	1602	100
7.616-72.548	0.209	67	0.186	882	955	99.372

-
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://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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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