PDB-2qnt: Crystal structure of protein of unknown function from Agrobacteri...

ID or keywords:

Entry

Database: PDB / ID: 2qnt

Title

Crystal structure of protein of unknown function from Agrobacterium tumefaciens str. C58

Components

Uncharacterized protein Atu1872

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Glyoxalase/bleomycin resistance protein/dioxygenase family related protein / PSI-2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / Uncharacterized protein

Function / homology

Function and homology information

Glyoxalase-like domain / Glyoxalase-like domain / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology

Biological species

Agrobacterium tumefaciens str. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.4 Å

Authors

Nocek, B. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of protein of unknown function from Agrobacterium tumefaciens str. C58.
Authors: Nocek, B. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Joachimiak, A.

History

Deposition	Jul 19, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 31, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2	Oct 16, 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 / pdbx_struct_special_symmetry / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 300

BIOMOLECULE: 1 SEE REMARK 350 FOR THE SOFTWARE GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2qnt.cif.gz	48.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2qnt.ent.gz	34.4 KB	Display	PDB format
PDBx/mmJSON format	2qnt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2qnt_validation.pdf.gz	434.9 KB	Display	wwPDB validaton report
Full document	2qnt_full_validation.pdf.gz	435.5 KB	Display
Data in XML	2qnt_validation.xml.gz	10.4 KB	Display
Data in CIF	2qnt_validation.cif.gz	13.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qn/2qnt ftp://data.pdbj.org/pub/pdb/validation_reports/qn/2qnt	HTTPS FTP

-
Related structure data

Similar structure data	2bdx-d 6ecf-3 1lmw-1 6rnw-d 6psg-4 2ae7-1 4bpt-4 1y1j-d 2ah9-3 7ker-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC5895

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein Atu1872

hetero molecules

16.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein Atu1872

hetero molecules

A: Uncharacterized protein Atu1872

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.329, 50.329, 105.076
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-253- HOH

#1: Protein	Uncharacterized protein Atu1872 / AGR_C_3434p Mass: 16467.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Species: Agrobacterium tumefaciens / Strain: C58 / Gene: AGR_C_3434, Atu1872 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UE88, UniProt: A9CII6*PLUS
#2: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.02 Å³/Da / Density % sol: 39.12 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Li2SO4, 0.1 M Hepes, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2006 / Details: mirrors
Radiation	Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.4→40 Å / Num. all: 27485 / Num. obs: 27485 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / B_iso Wilson estimate: 26.5 Å² / R_merge(I) obs: 0.077 / Net I/σ(I): 17.7
Reflection shell	Resolution: 1.4→1.42 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.27 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1335 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-3000		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.4→40 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.952 / SU B: 1.752 / SU ML: 0.035 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19907	1375	5 %	RANDOM
R_work	0.16873	-	-	-
all	0.1714	27393	-	-
obs	0.17025	26018	99.93 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 11.267 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.28 Å²	0 Å²	0 Å²
2-	-	0.28 Å²	0 Å²
3-	-	-	-0.56 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1051	0	15	154	1220

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.021	1189
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	859
X-RAY DIFFRACTION	r_angle_refined_deg	1.639	1.942	1619
X-RAY DIFFRACTION	r_angle_other_deg	1.042	3	2053
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.994	5	147
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.246	22.113	71
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.249	15	197
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.853	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	159
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1366
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	300
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	197
X-RAY DIFFRACTION	r_nbd_other	0.201	0.2	881
X-RAY DIFFRACTION	r_nbtor_refined	0.191	0.2	574
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.2	669
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	101
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	0.138	0.2	9
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.242	0.2	65
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.167	0.2	26
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	1.182	1.5	827
X-RAY DIFFRACTION	r_mcbond_other	0.262	1.5	272
X-RAY DIFFRACTION	r_mcangle_it	1.382	2	1097
X-RAY DIFFRACTION	r_scbond_it	1.937	3	580
X-RAY DIFFRACTION	r_scangle_it	2.426	4.5	515
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.4→1.436 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.278	93	-
R_work	0.225	1886	-
obs	-	-	99.9 %

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	47.2791	15.8433	-2.4212	13.6575	6.1619	5.9486	-0.5145	-0.0484	-0.4057	-0.2338	0.0668	0.3727	-0.04	0.1102	0.4477	0.0743	-0.0989	-0.0151	0.129	0.0382	0.0433	11.0324	14.5038	65.5694
2	3.6759	-1.8293	-0.615	8.4938	0.7933	1.6718	0.005	-0.0031	0.4586	-0.2122	0.0932	-0.3006	-0.2543	0.3058	-0.0982	0.0605	-0.0464	-0.0062	0.0912	-0.0079	0.0864	3.619	7.4452	60.8011
3	0.6211	-0.7689	-0.1138	7.5071	2.3148	3.4368	-0.0895	-0.0992	-0.047	-0.0794	0.0905	-0.1648	0.1804	0.0796	-0.0009	0.0762	0.0106	0.0135	0.0787	0.0218	0.0607	2.2537	-8.0311	54.713
4	15.2182	-2.917	-2.3357	9.5198	0.9093	2.9038	0.1111	0.1016	-0.3819	0.0495	-0.1218	-0.2778	0.5789	0.2717	0.0108	0.1253	0.078	0.0547	0.0093	0.0264	0.0648	7.7417	-15.392	49.4414
5	15.7707	-9.9628	5.4715	9.7285	-0.5864	4.4256	-0.13	0.544	0.8032	0.0211	-0.2907	-0.7056	0.3186	0.6948	0.4207	0.0166	0.0359	0.0411	0.1075	0.1182	0.1573	11.2521	-10.0833	45.1799
6	4.6597	1.606	4.5118	0.8406	3.1515	18.7787	-0.2775	0.0885	-0.5405	-0.5303	0.0265	-0.3758	-0.1647	0.775	0.251	-0.0852	0.0112	0.0592	0.1132	0.082	0.117	13.2527	-5.5029	44.6536
7	4.3267	0.1623	0.8295	5.0847	-1.5034	7.1765	0.0177	-0.1457	0.0969	0.129	-0.135	-0.1935	0.2605	0.6781	0.1173	-0.0036	0.0451	-0.0105	0.1288	0.0468	0.0818	12.431	-6.9366	55.8701
8	1.6245	2.1231	-1.6807	5.1812	-3.9264	6.4656	-0.1701	-0.0411	0.0268	-0.0388	-0.0317	-0.1357	0.3878	0.223	0.2018	0.0553	0.0259	0.0057	0.0572	0.0334	0.078	4.9451	-9.0534	55.5418
9	12.0103	-1.3021	-3.1177	4.833	0.1938	2.2831	0.0228	-0.4102	-0.1616	0.3215	-0.0831	0.0264	0.3916	-0.0156	0.0603	0.1308	-0.0112	0.0333	0.0657	0.0251	0.0359	-2.0382	-12.2998	65.7926
10	2.0186	3.2645	12.6507	5.7533	15.6273	128.571	-0.3637	-0.6676	-0.5571	0.1326	0.7917	-0.6288	3.1147	-1.9363	-0.428	0.3713	-0.0779	0.149	0.3796	0.0303	0.2914	-6.1335	-19.0875	58.8615
11	1.3387	0.2857	1.0025	5.3307	-2.2278	2.7586	-0.0279	0.1478	-0.1446	0.002	-0.2314	0.1685	0.2385	-0.1366	0.2593	0.0838	-0.0249	0.0359	0.089	-0.0207	0.0671	-6.8704	-9.2111	49.724
12	2.3864	0.7434	-1.5954	1.3384	1.1983	5.8766	-0.0444	0.1054	-0.134	-0.1404	0.1437	-0.1286	-0.2189	0.4211	-0.0993	0.0746	-0.0115	0.0069	0.0971	-0.0127	0.0637	5.9939	-0.0609	36.3166
13	6.2608	-1.3756	-0.7695	5.2413	1.9273	2.5464	-0.0919	0.1766	-0.3511	0.0351	0.1393	-0.1328	0.2813	0.0355	-0.0474	0.113	0.0061	0.0074	0.0623	-0.0397	0.0311	0.6664	-8.5951	34.1353
14	5.7631	-3.2935	-0.8888	7.3531	1.4315	6.0413	0.3169	0.6523	0.2533	-0.7851	-0.3875	-0.0076	-0.5778	-0.4555	0.0706	0.1879	0.0727	-0.0003	0.1195	0.0324	0.0023	-3.6453	6.1423	31.7023
15	1.1914	0.1102	-0.4683	3.3073	-1.1646	2.6746	-0.0183	0.1033	-0.034	-0.0764	-0.0651	-0.0356	-0.0564	0.0294	0.0834	0.089	-0.0058	0.0071	0.0595	-0.0014	0.0428	0.0174	-3.1801	40.3589

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-5 - -1
2	X-RAY DIFFRACTION	2	A	0 - 4
3	X-RAY DIFFRACTION	3	A	5 - 11
4	X-RAY DIFFRACTION	4	A	12 - 16
5	X-RAY DIFFRACTION	5	A	17 - 21
6	X-RAY DIFFRACTION	6	A	22 - 29
7	X-RAY DIFFRACTION	7	A	30 - 39
8	X-RAY DIFFRACTION	8	A	40 - 49
9	X-RAY DIFFRACTION	9	A	50 - 56
10	X-RAY DIFFRACTION	10	A	57 - 63
11	X-RAY DIFFRACTION	11	A	64 - 70
12	X-RAY DIFFRACTION	12	A	71 - 85
13	X-RAY DIFFRACTION	13	A	86 - 95
14	X-RAY DIFFRACTION	14	A	96 - 104
15	X-RAY DIFFRACTION	15	A	105 - 122

-
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

-
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