PDB-3e8x: Putative NAD-dependent epimerase/dehydratase from Bacillus halodurans.

ID or keywords:

Entry

Database: PDB / ID: 3e8x

Title

Putative NAD-dependent epimerase/dehydratase from Bacillus halodurans.

Components

Putative NAD-dependent epimerase/dehydratase

Keywords

structural genomics / unknown function / APC7755 / NADP / epimerase/dehydratase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

nucleotide binding
Similarity search - Function

Biological species

Bacillus halodurans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Osipiuk, J. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: X-ray crystal structure of putative NAD-dependent epimerase/dehydratase from Bacillus halodurans.
Authors: Osipiuk, J. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.

History

Deposition	Aug 20, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 2, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	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_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_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	3e8x.cif.gz	64.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3e8x.ent.gz	47.5 KB	Display	PDB format
PDBx/mmJSON format	3e8x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3e8x_validation.pdf.gz	799.9 KB	Display	wwPDB validaton report
Full document	3e8x_full_validation.pdf.gz	802.8 KB	Display
Data in XML	3e8x_validation.xml.gz	14.2 KB	Display
Data in CIF	3e8x_validation.cif.gz	19.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e8/3e8x ftp://data.pdbj.org/pub/pdb/validation_reports/e8/3e8x	HTTPS FTP

-
Related structure data

Similar structure data	7jmb-d 4xt7-1 5un7-d 6xhp-d 1ozj-d 3tmk-4 1tmh-2 4nvt-1 3sd9-d 5d2m-2 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
Other databases	TargetDB: APC7755

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative NAD-dependent epimerase/dehydratase

hetero molecules

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

1

A: Putative NAD-dependent epimerase/dehydratase

hetero molecules

A: Putative NAD-dependent epimerase/dehydratase

hetero molecules

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

Unit cell

Length a, b, c (Å)	113.687, 113.687, 63.645
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Putative NAD-dependent epimerase/dehydratase Mass: 26211.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH1520 / Plasmid: pET15b modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KCP9
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: 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: 3.92 Å³/Da / Density % sol: 68.64 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 40% PEG-300, 0.1 M phosphate-citrate buffer, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2008
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. all: 24007 / Num. obs: 24007 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 % / B_iso Wilson estimate: 50.6 Å² / R_merge(I) obs: 0.089 / Χ²: 2.208 / Net I/σ(I): 51.6
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 11.3 % / R_merge(I) obs: 0.848 / Mean I/σ(I) obs: 2.42 / Num. unique all: 914 / Χ²: 0.896 / % possible all: 73.7

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.006	data extraction
SBC-Collect		data collection
SHELXD		phasing
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.1→50 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.965 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 7.13 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.134 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.193	1225	5.1 %	RANDOM
R_work	0.172	-	-	-
all	0.173	23940	-	-
obs	0.173	23940	95.39 %	-

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 max: 69.42 Å² / B_iso mean: 49.399 Å² / B_iso min: 23.37 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.87 Å²	0 Å²	0 Å²
2-	-	-1.87 Å²	0 Å²
3-	-	-	3.75 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1643	0	49	154	1846

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	1826
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1244
X-RAY DIFFRACTION	r_angle_refined_deg	1.705	1.997	2502
X-RAY DIFFRACTION	r_angle_other_deg	1.058	3	3063
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.278	5	242
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.226	24.405	84
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.907	15	330
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.189	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	287
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2036
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	349
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	321
X-RAY DIFFRACTION	r_nbd_other	0.209	0.2	1301
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	831
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	952
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.191	0.2	113
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.127	0.2	7
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.272	0.2	24
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.217	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	0.767	1.5	1382
X-RAY DIFFRACTION	r_mcbond_other	0.22	1.5	451
X-RAY DIFFRACTION	r_mcangle_it	0.995	2	1813
X-RAY DIFFRACTION	r_scbond_it	2.027	3	786
X-RAY DIFFRACTION	r_scangle_it	2.643	4.5	673

LS refinement shell

Resolution: 2.095→2.149 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.339	67	-
R_work	0.268	1282	-
all	-	1349	-
obs	-	1349	73.92 %

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	12.882	0.8622	6.3758	27.6135	10.0455	9.7356	0.2173	0.7586	-1.1854	-0.5668	-0.2329	0.6417	0.159	-0.2159	0.0157	-0.2014	0.056	0.0318	0.0115	-0.0034	-0.0449	38.2748	14.1714	12.422
2	19.0837	-10.4936	2.8085	8.8843	-7.8559	14.1683	-0.058	0.4534	0.4294	0.1698	-0.0367	-0.3453	-1.1662	0.877	0.0946	-0.0236	-0.0747	0.0208	-0.1178	0.0432	-0.0172	48.8794	22.801	18.8619
3	0.7953	-1.5282	-0.3277	4.6651	-3.6534	10.7469	-0.1245	0.2093	-0.0404	0.2736	0.1404	-0.3746	-0.3384	0.6265	-0.0158	-0.2014	-0.0025	0.0184	-0.1713	-0.0237	-0.053	49.006	14.0512	17.2449
4	6.928	-7.4182	1.2204	16.245	0.1243	2.3882	0.0472	0.5259	-0.4921	-0.2963	-0.15	-0.2715	0.41	-0.1382	0.1028	-0.1363	-0.0021	0.0416	-0.1366	-0.0456	-0.0184	44.9097	10.1712	11.9529
5	34.3578	-8.9044	-2.4918	8.0876	4.2425	17.8405	0.6881	0.839	2.68	-0.2258	0.2927	-0.3626	-1.2431	0.3729	-0.9809	-0.0201	0.0571	0.1218	-0.0496	0.0878	0.1717	42.7854	29.3596	11.207
6	13.9898	-6.5158	-5.6327	4.6489	1.2239	3.4815	0.3606	0.2023	0.6301	-0.3131	-0.0791	-0.3975	-0.4881	-0.1418	-0.2815	-0.12	0.0102	0.0077	-0.0854	0.0558	-0.1106	46.149	23.7353	9.4616
7	5.1207	-2.4704	1.3359	40.9289	19.8403	11.4424	0.0049	0.3787	0.1976	-0.7127	0.2509	1.3919	-0.5725	-0.3667	-0.2558	-0.0712	0.0747	0.0133	0.0653	0.1268	-0.003	31.9063	26.0961	11.403
8	6.8884	-3.0142	-1.3981	4.3831	3.0709	6.7239	0.0251	0.1114	0.1445	-0.017	0.1807	-0.0719	-0.3051	-0.022	-0.2058	-0.2403	0.0289	0.0133	-0.1524	0.0842	-0.0711	37.5174	19.8768	18.2802
9	52.5211	1.6429	1.5162	39.3915	9.0196	2.09	0.4541	1.7705	1.2766	-0.2089	1.5245	-4.0739	0.3298	1.7722	-1.9785	0.1249	0.006	0.0055	0.2782	-0.1852	0.5558	44.2673	35.6764	27.6672
10	4.0221	-2.2802	0.4564	8.5217	-0.3368	4.9746	-0.0763	-0.0667	0.421	0.0566	0.1685	-0.4894	-0.3276	0.2513	-0.0922	-0.1816	0.0741	0.0402	-0.1394	0.0435	0.0247	34.304	30.8774	25.4271
11	3.0458	0.1903	-0.6595	8.3259	-0.064	5.3184	0.115	0.5663	0.0515	-0.4386	-0.157	0.8235	-0.2621	-0.7749	0.042	-0.1852	0.0577	-0.0142	-0.0115	0.0234	0.0291	28.2017	18.23	17.7643
12	1.758	-0.612	-1.1622	3.3058	5.8129	10.226	-0.2488	0.0641	0.1578	-0.0802	0.1384	0.0991	-0.8053	-0.2964	0.1104	-0.1512	0.0299	0.0148	-0.188	-0.0016	0.0409	38.9396	18.6713	31.735
13	5.3832	0.9198	5.0245	17.7268	-6.9833	14.147	-0.2677	-0.6029	0.4211	0.5948	-0.0585	-1.2454	-0.115	1.1278	0.3262	-0.0943	0.1007	-0.0658	0.0004	-0.0825	0.1868	40.2123	28.8265	41.7571
14	13.0307	0.6579	6.6491	2.4541	1.9383	4.4537	-0.0225	-0.4633	-0.0612	0.175	0.0781	-0.0772	0.095	-0.0269	-0.0556	-0.1732	0.0622	-0.0023	-0.1783	0.0075	-0.0359	35.1045	24.441	33.7703
15	5.5133	-0.5634	0.5304	2.5566	0.3128	2.34	-0.1623	-0.1504	0.0413	0.117	0.1338	0.098	-0.1351	-0.1524	0.0284	-0.1892	0.0367	0.0145	-0.2266	0.036	-0.0983	35.8394	16.68	29.3595
16	8.8033	-1.7242	-5.3269	5.0064	0.2502	7.9334	-0.1345	-0.9216	-0.0505	0.5355	0.211	-0.2728	-0.055	0.7029	-0.0764	-0.1345	0.0608	-0.0991	-0.1105	0.0277	-0.0316	49.1479	11.4468	36.2938
17	9.0305	3.0373	3.49	4.1757	1.3987	4.2284	-0.0984	0.123	-0.1581	0.1927	0.0902	-0.2062	0.024	0.1497	0.0081	-0.206	0.03	-0.0032	-0.2235	0.0244	-0.0703	46.9871	11.0053	26.1073
18	2.3532	-1.5715	0.7321	2.5173	1.1084	1.9658	-0.06	-0.3439	-0.0403	0.3813	-0.0217	0.1439	0.1791	-0.1507	0.0818	-0.1587	0.0072	-0.0005	-0.1866	0.061	-0.0906	40.0574	8.8184	31.6632
19	17.8011	2.8185	4.001	9.4664	-4.0356	3.3161	0.0222	-0.8154	-0.2361	0.3034	0.0603	-0.2581	0.3073	0.0771	-0.0825	-0.1158	0.056	0.008	-0.1731	0.0092	-0.054	46.6296	1.4774	30.6689

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	0 - 6	21 - 27
2	X-RAY DIFFRACTION	2	A	A	7 - 14	28 - 35
3	X-RAY DIFFRACTION	3	A	A	15 - 20	36 - 41
4	X-RAY DIFFRACTION	4	A	A	21 - 29	42 - 50
5	X-RAY DIFFRACTION	5	A	A	30 - 34	51 - 55
6	X-RAY DIFFRACTION	6	A	A	35 - 54	56 - 75
7	X-RAY DIFFRACTION	7	A	A	55 - 62	76 - 83
8	X-RAY DIFFRACTION	8	A	A	63 - 74	84 - 95
9	X-RAY DIFFRACTION	9	A	A	75 - 80	96 - 101
10	X-RAY DIFFRACTION	10	A	A	81 - 91	102 - 112
11	X-RAY DIFFRACTION	11	A	A	92 - 105	113 - 126
12	X-RAY DIFFRACTION	12	A	A	106 - 114	127 - 135
13	X-RAY DIFFRACTION	13	A	A	115 - 125	136 - 146
14	X-RAY DIFFRACTION	14	A	A	126 - 135	147 - 156
15	X-RAY DIFFRACTION	15	A	A	136 - 154	157 - 175
16	X-RAY DIFFRACTION	16	A	A	155 - 171	176 - 192
17	X-RAY DIFFRACTION	17	A	A	172 - 190	193 - 211
18	X-RAY DIFFRACTION	18	A	A	191 - 202	212 - 223
19	X-RAY DIFFRACTION	19	A	A	203 - 213	224 - 234

-
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