PDB-1ydh: X-ray structure of a lysine decarboxylase-like protein from arabi...

ID or keywords:

Entry

Database: PDB / ID: 1ydh

Title

X-ray structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene at5g11950

Components

At5g11950

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE INITIATIVE / PSI / Center for Eukaryotic Structural Genomics / CESG / AT5G11950 / LYSINE DECARBOXYLASE-LIKE PROTEIN

Function / homology

Function and homology information

cytokinin riboside 5'-monophosphate phosphoribohydrolase activity / : / cytokinin biosynthetic process / protein homodimerization activity / nucleus / plasma membrane / cytosol
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.152 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: Proteins / Year: 2006
Title: X-ray crystal structures of the conserved hypothetical proteins from Arabidopsis thaliana gene loci At5g11950 and AT2g37210.
Authors: Jeon, W.B. / Allard, S.T.M. / Bingman, C.A. / Bitto, E. / Han, B.W. / Wesenberg, G.E. / Phillips Jr., G.N.

History

Deposition	Dec 23, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 11, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 11, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	1ydh.cif.gz	89.3 KB	Display	PDBx/mmCIF format
PDB format	pdb1ydh.ent.gz	71 KB	Display	PDB format
PDBx/mmJSON format	1ydh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	1ydh_validation.pdf.gz	465.5 KB	Display	wwPDB validaton report
Full document	1ydh_full_validation.pdf.gz	470.4 KB	Display
Data in XML	1ydh_validation.xml.gz	19.5 KB	Display
Data in CIF	1ydh_validation.cif.gz	28.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yd/1ydh ftp://data.pdbj.org/pub/pdb/validation_reports/yd/1ydh	HTTPS FTP

-
Related structure data

Related structure data	2a33C C: citing same article (ref.)
Similar structure data	6hgj-d 4rsq-12 1p2o-4 6er2-d 1p2o-5 6tdg-1 2riw-d 3pzf-d 4rsq-4 1vis-d 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.19912

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: At5g11950

B: At5g11950

hetero molecules

48.8 kDa, 2 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)	121.589, 80.427, 50.709
Angle α, β, γ (deg.)	90.00, 102.97, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-850- HOH

#1: Protein	At5g11950 Mass: 24239.244 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT5G11950 / Plasmid: PVP-13 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) P(LACI+RARE) / References: UniProt: Q84MC2
#2: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.63 % Description: UNMODELED DENSITY BETWEEN ASP 94A AND ILE 133B IS POSSIBLY DUE TO AN L-LYSINE MOLECULE
Crystal grow	Temperature: 293 K / pH: 7 Details: 10 MG/ML PROTEIN, 13% MPEG 2K, 0.28 M POTASSIUM NITRATE, 0.1 M MOPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.9794

Detector

Type: APS-1 / Detector: CCD / Date: Dec 15, 2004
Details: SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR

Radiation

Monochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR: WATER COOLED
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 2.152→35.451 Å / Num. obs: 25771 / % possible obs: 99.9 % / Redundancy: 6.9 % / R_merge(I) obs: 0.384 / Χ²: 0.951 / Net I/σ(I): 6.266

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Χ²	% possible all
2.15-2.23	6.2	0.384	2.401	2460	0.657	100
2.28-2.37		0.33		2474	0.65	100
2.37-2.48		0.31		2465	0.691	100
2.48-2.61		0.258		2482	0.802	100
2.61-2.77		0.229		2468	0.939	100
2.77-2.99		0.197		2481	1.092	100
2.99-3.29		0.166		2473	1.157	100
3.29-3.76		0.142		2489	1.209	100
3.76-4.74		0.127		2500	1.163	100
4.74-50		0.119		2537	1.105	99.6

-
Phasing

Phasing

Method:

SAD

Phasing MAD

D res high: 2.3 Å / D res low: 30 Å / FOM : 0.27 / Reflection: 19977

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	20.086	0.054	5.01	SE	27.8	0.62
2	90.255	21.268	12.549	SE	24.8	0.59
3	15.68	1.684	20.177	SE	34.1	0.71
4	61.38	39.957	13.454	SE	53.3	0.67
5	24.608	3.559	19.156	SE	36.8	0.65
6	83.776	26.253	19.511	SE	23	0.5
7	92.108	28.058	16.003	SE	32.8	0.53
8	64.36	36.189	12.147	SE	32.2	0.62
9	15.635	8.523	16.537	SE	43.3	0.66
10	81.094	29.784	4.881	SE	19.2	0.45
11	99.196	33.716	3.067	SE	55.4	0.88
12	92.511	36.154	14.191	SE	32.5	0.48
13	75.88	33.897	18.398	SE	28.2	0.48
14	102.073	30.487	2.86	SE	46.5	0.66
15	90.225	17.148	24.296	SE	30.3	0.38
16	89.742	12.521	22.627	SE	50.7	0.55

Phasing MAD shell

Resolution (Å)	FOM	Reflection
8.19-30	0.39	1020
5.2-8.19	0.36	1738
4.07-5.2	0.32	2232
3.46-4.07	0.31	2614
3.06-3.46	0.3	2866
2.77-3.06	0.25	3003
2.55-2.77	0.2	3205
2.37-2.55	0.16	3299

Phasing dm

FOM : 0.66 / FOM acentric: 0.66 / FOM centric: 0.67 / Reflection: 19977 / Reflection acentric: 19237 / Reflection centric: 740

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
6.6-29.694	0.92	0.92	0.84	939	835	104
4.1-6.6	0.9	0.9	0.75	2829	2671	158
3.3-4.1	0.85	0.86	0.77	3563	3412	151
2.9-3.3	0.72	0.72	0.64	3438	3329	109
2.5-2.9	0.53	0.53	0.55	5783	5639	144
2.3-2.5	0.34	0.34	0.29	3425	3351	74

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.06	phasing
RESOLVE	2.06	phasing
REFMAC	refmac_5.2.0005	refinement

Refinement

Method to determine structure:

SAD / Resolution: 2.152→35.45 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.938 / WR_factor R_free: 0.212 / WR_factor R_work: 0.159 / SU B: 4.455 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, 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	0.213	1300	5.063 %	RANDOM
R_work	0.159	-	-	-
all	0.16164	-	-	-
obs	0.16164	25679	99.1 %	-

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: 31.14 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.915 Å²	0 Å²	0.386 Å²
2-	-	-0.158 Å²	0 Å²
3-	-	-	-0.584 Å²

Refinement step

Cycle: LAST / Resolution: 2.152→35.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2798	0	20	319	3137

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	2859
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.939	1.98	3839
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.547	5	363
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.733	23.729	118
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.836	15	516
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.845	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	429
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2111
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	1397
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	1968
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.199	0.2	271
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	0.271	0.2	36
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.17	0.2	21
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	1.579	2	1872
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.656	4	2860
X-RAY DIFFRACTION	r_scbond_it	5.121	6	1136
X-RAY DIFFRACTION	r_scangle_it	6.985	8	979
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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 (%)
2.152-2.208	0.304	73	0.188	1698	1911	92.674
2.208-2.268	0.223	105	0.184	1740	1852	99.622
2.268-2.334	0.255	75	0.176	1717	1797	99.722
2.334-2.405	0.254	98	0.182	1667	1770	99.718
2.405-2.484	0.26	89	0.182	1576	1668	99.82
2.484-2.571	0.292	80	0.172	1575	1659	99.759
2.571-2.668	0.268	81	0.176	1516	1607	99.378
2.668-2.777	0.199	84	0.174	1434	1523	99.672
2.777-2.9	0.218	68	0.173	1386	1468	99.046
2.9-3.041	0.219	75	0.159	1323	1403	99.644
3.041-3.206	0.211	67	0.161	1271	1347	99.332
3.206-3.4	0.199	71	0.15	1186	1265	99.368
3.4-3.634	0.212	60	0.144	1142	1206	99.668
3.634-3.924	0.199	54	0.137	1042	1101	99.546
3.924-4.297	0.167	61	0.136	964	1025	100
4.297-4.801	0.175	40	0.13	885	925	100
4.801-5.539	0.188	37	0.144	782	819	100
5.539-6.773	0.19	34	0.18	675	709	100
6.773-9.529	0.214	30	0.165	512	542	100
9.529-66.519	0.179	18	0.177	288	320	95.625

-
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://pdbjlvh1.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