PDB-4ibo: Crystal structure of a putative gluconate dehydrogenase from agro...

ID or keywords:

Entry

Database: PDB / ID: 4ibo

Title

Crystal structure of a putative gluconate dehydrogenase from agrobacterium tumefaciens (target EFI-506446)

Components

Gluconate dehydrogenase

Keywords

OXIDOREDUCTASE / putative gluconate dehydrogenase /

enzyme function initiative / EFI /

Structural Genomics

Function / homology

Function and homology information

oxidoreductase activity
Similarity search - Function

Biological species

Agrobacterium fabrum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Vetting, M.W. / Bouvier, J.T. / Groninger-Poe, F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)

Citation

Journal: To be Published
Title: Crystal structure of a putative gluconate dehydrogenase from agrobacterium tumefaciens (target EFI-506446)
Authors: Vetting, M.W. / Bouvier, J.T. / Groninger-Poe, F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)

History

Deposition	Dec 9, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 26, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 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_ref_seq_dif / 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_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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 / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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	4ibo.cif.gz	407.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4ibo.ent.gz	334.3 KB	Display	PDB format
PDBx/mmJSON format	4ibo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ib/4ibo ftp://data.pdbj.org/pub/pdb/validation_reports/ib/4ibo	HTTPS FTP

-
Related structure data

Related structure data	3enkS S: Starting model for refinement
Similar structure data	6f9q-d 3awd-d 3gaf-2 1zk4-1 4g81-d 1zjy-1 2qio-d 6tbb-2 6ci9-3 6y0s-1 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	TargetTrack: EFI-506441 TargetTrack: EFI-506446

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: Gluconate dehydrogenase

B: Gluconate dehydrogenase

C: Gluconate dehydrogenase

D: Gluconate dehydrogenase

hetero molecules

117 kDa, 4 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)	135.783, 135.783, 126.165
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-498- HOH
2	1	A-522- HOH

#1: Protein	Gluconate dehydrogenase Mass: 29237.209 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum (bacteria) / Strain: str. C58 / Gene: Atu1407 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CJ43
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 675 / 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: 2.87 Å³/Da / Density % sol: 57.16 %
Crystal grow	Temperature: 298 K / Method: sitting drop vapor diffusion / pH: 8.5 Details: Protein (10mM Tris pH 7.9; Reservoir (0.2 M Magnesium Chloride 0.1 M Tris:HCl pH 8.5 25% (w/v) PEG 3350); Cryoprotection (50 mM Magnesium Chloride 20 mM Tris:HCl pH 8.5 40% (w/v) PEG 3350), ...Details: Protein (10mM Tris pH 7.9; Reservoir (0.2 M Magnesium Chloride 0.1 M Tris:HCl pH 8.5 25% (w/v) PEG 3350); Cryoprotection (50 mM Magnesium Chloride 20 mM Tris:HCl pH 8.5 40% (w/v) PEG 3350), sitting drop vapor diffusion, temperature 298K

Crystal

Density Matthews: 2.87 Å³/Da / Density % sol: 57.16 %

Crystal grow

Temperature: 298 K / Method: sitting drop vapor diffusion / pH: 8.5
Details: Protein (10mM Tris pH 7.9; Reservoir (0.2 M Magnesium Chloride 0.1 M Tris:HCl pH 8.5 25% (w/v) PEG 3350); Cryoprotection (50 mM Magnesium Chloride 20 mM Tris:HCl pH 8.5 40% (w/v) PEG 3350), ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.9793 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 8, 2012 / Details: MIRRORS

Radiation

Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 2.1→117.592 Å / Num. all: 78427 / Num. obs: 78427 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / R_sym value: 0.088 / Net I/σ(I): 19.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.1-2.21	8.6	0.657	1.2	97907	11326	0.657	99.7
2.21-2.35	9.1	0.445	1.7	98272	10748	0.445	99.8
2.35-2.51	9.6	0.326	2.3	96547	10098	0.326	99.9
2.51-2.71	10	0.219	3.5	93958	9407	0.219	99.9
2.71-2.97	10.2	0.142	5.4	88807	8716	0.142	100
2.97-3.32	10.2	0.088	8.6	80707	7903	0.088	100
3.32-3.83	10.1	0.056	12.8	70889	6990	0.056	100
3.83-4.7	10	0.043	15.7	59930	5964	0.043	100
4.7-6.64	10	0.036	19.2	46417	4662	0.036	100
6.64-126.165	9.1	0.024	26.3	23901	2613	0.024	98.5

-
Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
MOSFLM		data reduction
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3ENK

3enk

Resolution: 2.1→53.293 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.8905 / SU ML: 0.17 / σ(F): 0 / σ(I): 0 / Phase error: 17.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1868	3945	5.03 %	RANDOM
R_work	0.1521	-	-	-
all	0.1539	78361	-	-
obs	0.1539	78361	99.74 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 145.2 Å² / B_iso mean: 32.229 Å² / B_iso min: 9.68 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→53.293 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7678	0	7	675	8360

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7894
X-RAY DIFFRACTION	f_angle_d	1.043	10713
X-RAY DIFFRACTION	f_chiral_restr	0.075	1218
X-RAY DIFFRACTION	f_plane_restr	0.004	1408
X-RAY DIFFRACTION	f_dihedral_angle_d	13.581	2880

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1-2.1256	0.2314	146	0.1895	2635	2781	100
2.1256-2.1525	0.2197	116	0.1889	2683	2799	99
2.1525-2.1808	0.2388	140	0.1803	2564	2704	100
2.1808-2.2107	0.2257	155	0.1812	2628	2783	100
2.2107-2.2423	0.2241	153	0.1717	2619	2772	100
2.2423-2.2758	0.2196	146	0.1701	2628	2774	100
2.2758-2.3113	0.2378	136	0.1677	2630	2766	100
2.3113-2.3492	0.2025	145	0.1586	2654	2799	100
2.3492-2.3897	0.1875	134	0.1647	2613	2747	100
2.3897-2.4332	0.1981	123	0.1516	2650	2773	100
2.4332-2.48	0.1983	131	0.1521	2657	2788	100
2.48-2.5306	0.2189	138	0.1557	2635	2773	100
2.5306-2.5856	0.2039	108	0.1501	2678	2786	100
2.5856-2.6458	0.1845	120	0.1496	2701	2821	100
2.6458-2.7119	0.1913	146	0.1544	2614	2760	100
2.7119-2.7853	0.2031	155	0.1635	2639	2794	100
2.7853-2.8672	0.199	157	0.1557	2652	2809	100
2.8672-2.9598	0.2109	148	0.1589	2629	2777	100
2.9598-3.0655	0.1976	134	0.1598	2677	2811	100
3.0655-3.1883	0.1892	137	0.1583	2651	2788	100
3.1883-3.3333	0.227	159	0.1569	2667	2826	100
3.3333-3.509	0.1871	158	0.1439	2651	2809	100
3.509-3.7288	0.1456	149	0.1399	2661	2810	100
3.7288-4.0167	0.1498	148	0.1352	2691	2839	100
4.0167-4.4207	0.1544	130	0.1293	2706	2836	100
4.4207-5.06	0.1566	144	0.1295	2698	2842	100
5.06-6.3733	0.1759	165	0.161	2726	2891	100
6.3733-53.31	0.1881	124	0.158	2779	2903	97

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	2.1647	0.3587	-0.4763	1.7628	-0.5556	1.4407	-0.0162	0.1428	0.0868	-0.2189	0.0415	-0.0331	-0.108	-0.0063	-0.035	0.1958	-0.0224	0.0104	0.1492	0.0079	0.1576	-57.3558	25.7554	38.7796
2	0.4898	-0.208	-0.0308	1.5212	0.037	1.5666	-0.0397	0.1009	-0.1796	-0.314	-0.0481	-0.0183	0.3274	-0.075	0.0659	0.261	-0.006	0.0556	0.161	-0.0125	0.213	-53.8447	8.4667	41.2614
3	1.83	0.3809	0.2034	2.1274	0.0995	0.829	-0.0878	0.3496	-0.1145	-0.5158	0.0627	0.2143	0.1062	-0.1374	0.0215	0.3249	-0.0155	-0.0036	0.2524	-0.0028	0.1995	-70.0507	8.2287	42.2546
4	0.9954	0.648	-0.7604	1.9784	-0.2631	1.3665	-0.0506	0.0139	-0.2162	-0.0821	-0.0326	0.0546	0.1536	-0.0521	0.0603	0.2123	-0.0103	0.0098	0.1408	0.009	0.1686	-70.5685	-34.272	61.788
5	2.4874	-0.8817	-0.1932	1.7506	0.2794	1.5734	-0.0143	-0.3983	-0.2778	0.1964	-0.0176	-0.0178	0.2226	0.018	0.0226	0.2398	-0.0394	-0.0197	0.1862	0.0489	0.1603	-69.1148	-29.4682	74.4046
6	1.7362	-0.5426	0.3285	1.5571	-0.27	0.3304	0.0305	0.1486	0.0455	-0.1389	0.0273	0.1425	0.0022	-0.0651	-0.072	0.2586	-0.0275	-0.003	0.2036	0.0136	0.2042	-72.7882	-14.6907	63.9876
7	1.0239	-0.2341	0.1212	2.1093	-0.8538	2.3102	0.0131	0.1219	0.0048	-0.4157	0.1015	0.3372	0.03	-0.3597	-0.107	0.2883	-0.0227	-0.0119	0.2249	0.0173	0.2726	-69.5946	-19.3391	48.6486
8	1.7402	-0.2757	-0.5259	2.5608	0.252	1.1711	-0.1033	-0.1383	0.0212	0.3035	0.1279	0.1764	0.0232	-0.1838	-0.0223	0.1599	0.0387	0.0338	0.1608	0.0224	0.1486	-82.9267	16.2221	68.143
9	0.4808	0.4636	-0.3984	1.2001	-0.3831	0.7367	-0.0114	-0.1152	-0.0991	0.0682	0.007	-0.0756	0.1361	0.0395	0.0033	0.2559	0.0043	0.0111	0.1903	-0.0023	0.1982	-70.3591	3.827	64.5156
10	2.5959	-1.0735	-0.4559	1.9207	0.5152	3.0846	0.0449	-0.1876	-0.0645	-0.4551	-0.0745	-0.6906	0.3177	0.544	0.0067	0.3655	0.0677	0.1202	0.2438	-0.001	0.3646	-41.8486	-26.0621	43.2504
11	0.3366	0.601	0.4016	2.2402	-0.0008	0.7497	-0.0476	-0.0298	0.0303	-0.444	0.0132	-0.335	0.1029	0.0863	0.0345	0.3801	0.0186	0.1301	0.1793	0.0082	0.2804	-47.3924	-10.2444	37.9036
12	0.9582	-0.5567	-0.2381	2.3581	0.7742	2.9862	-0.0265	-0.1423	0.2318	-0.0384	0.1604	-0.4873	-0.2241	0.4564	-0.1168	0.2534	-0.0381	0.0641	0.2118	-0.0236	0.3222	-48.8858	-13.4967	55.5815

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 85 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 86 through 181 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 182 through 256 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 4 through 71 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 72 through 94 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 95 through 181 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 182 through 256 )	B
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 4 through 94 )	C
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 95 through 256 )	C
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 1 through 58 )	D
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 59 through 181 )	D
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 182 through 256 )	D

-
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