PDB-3tev: The crystal structure of glycosyl hydrolase from Deinococcus radi...

ID or keywords:

Entry

Database: PDB / ID: 3tev

Title

The crystal structure of glycosyl hydrolase from Deinococcus radiodurans R1

Components

Glycosyl hyrolase, family 3

Keywords

HYDROLASE / PSI-BIOLOGY / midwest center for structural genomics / structural genomic / MCSG

Function / homology

Function and homology information

hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function

Biological species

Deinococcus radiodurans (radioresistant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Chang, C. / Hatzos-Skintges, C. / Kohler, M. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The crystal structure of glycosyl hydrolase from Deinococcus radiodurans R1
Authors: Chang, C. / Hatzos-Skintges, C. / Kohler, M. / Clancy, S. / Joachimiak, A.

History

Deposition	Aug 15, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 31, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 27, 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

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Download

PDBx/mmCIF format	3tev.cif.gz	258.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3tev.ent.gz	213.2 KB	Display	PDB format
PDBx/mmJSON format	3tev.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tev_validation.pdf.gz	423.9 KB	Display	wwPDB validaton report
Full document	3tev_full_validation.pdf.gz	426.8 KB	Display
Data in XML	3tev_validation.xml.gz	27.1 KB	Display
Data in CIF	3tev_validation.cif.gz	37.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/te/3tev ftp://data.pdbj.org/pub/pdb/validation_reports/te/3tev	HTTPS FTP

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Related structure data

Similar structure data	3c0s-d 4g2o-d 4u9q-2 4tuf-2 5oxt-1 6e29-2 3gka-2 5v01-d 5oy1-d 6pb9-d Search similar-shape structures by Omokage search (details) 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: APC100088

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glycosyl hyrolase, family 3

B: Glycosyl hyrolase, family 3

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

1

A: Glycosyl hyrolase, family 3

defined by author&software
38.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glycosyl hyrolase, family 3

defined by author&software
38.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	146.841, 146.841, 108.733
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	79
Space group name H-M	I4

#1: Protein	Glycosyl hyrolase, family 3 Mass: 38068.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Strain: R1 / Gene: DR_1333 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9RUP9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.85 Å³/Da / Density % sol: 68.04 %
Crystal grow	Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 24% PEG1500, 20% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2011
Radiation	Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. all: 51153 / Num. obs: 51087 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7 % / R_merge(I) obs: 0.109 / Net I/σ(I): 33.8
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 7.1 % / R_merge(I) obs: 0.826 / Mean I/σ(I) obs: 2.76 / Num. unique all: 2561 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
PDB_EXTRACT	3.1	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MLPHARE		phasing
DM		phasing
SHELXDE		phasing
RESOLVE		phasing
ARP/wARP		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.3→50 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.381 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.164
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2178	2585	5.1 %	RANDOM
R_work	0.1812	-	-	-
all	0.183	50884	-	-
obs	0.183	50884	99.46 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 129.48 Å² / B_iso mean: 49.4493 Å² / B_iso min: 26.95 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.07 Å²	0 Å²	0 Å²
2-	-	-0.07 Å²	0 Å²
3-	-	-	0.14 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4728	0	0	186	4914

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.021	4891
X-RAY DIFFRACTION	r_angle_refined_deg	1.362	1.964	6654
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.153	5	636
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.092	22.684	231
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.886	15	776
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.365	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	746
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	3824
X-RAY DIFFRACTION	r_mcbond_it	1.593	1.5	3157
X-RAY DIFFRACTION	r_mcangle_it	2.958	2	5029
X-RAY DIFFRACTION	r_scbond_it	3.337	3	1734
X-RAY DIFFRACTION	r_scangle_it	5.76	4.5	1625
X-RAY DIFFRACTION	r_rigid_bond_restr	1.675	3	4891

LS refinement shell

Resolution: 2.302→2.361 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.271	189	-
R_work	0.216	3557	-
all	-	3746	-
obs	-	3746	99.02 %

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	0.2992	0.0478	-0.2141	0.2243	0.0303	0.2846	0.0031	0.0279	-0.0037	-0.0117	-0.003	0.0139	-0.0027	-0.0349	-0.0001	0.1193	-0.0004	0.0046	0.1259	0.0031	0.13	62.8673	43.066	25.1937
2	2.476	-4.0817	-0.651	18.2131	6.5486	7.9254	0.1306	0.5914	0.4568	-0.3303	-0.5644	0.3355	-0.1976	-0.1884	0.4337	0.0627	-0.0486	0.0487	0.2914	0.0539	0.3518	49.0645	33.2979	51.6575
3	0.1012	0.0675	0.104	0.0596	-0.0281	0.7856	0.0078	-0.0024	-0.0131	-0.0031	-0.0018	-0.0127	0.0515	-0.0629	-0.006	0.1201	-0.0063	0.0035	0.1313	0.003	0.1416	56.1647	33.1176	41.6572
4	0.0072	0.0077	0.0024	0.3047	-0.0327	0.0073	-0.0359	-0.0162	0.009	0.0586	0.0641	0.0603	-0.0303	-0.0059	-0.0282	0.1682	-0.0034	0.0306	0.1581	0.0138	0.1735	52.0146	44.6699	56.9041
5	0.0194	-0.0131	0.0415	0.1916	-0.0366	0.1218	0.0056	-0.0128	-0.0195	0.0301	0.0235	-0.0228	0.016	0.032	-0.0291	0.1278	-0.0073	0.0069	0.1268	0.0062	0.1391	59.7946	36.7865	49.2319
6	2.9135	-2.282	1.8757	5.3629	-3.3328	2.179	-0.0205	-0.1836	0.0817	0.1756	0.0305	0.0448	-0.0975	-0.0638	-0.01	0.1393	0.0139	0.0156	0.1346	-0.006	0.1339	58.0309	61.8278	52.3884
7	0.0754	0.0241	0.006	0.0344	-0.1028	0.4224	0.0143	-0.021	-0.0038	0.0125	-0.0046	-0.0062	-0.0112	0.0007	-0.0097	0.1242	-0.0016	0.0081	0.1255	0.0025	0.1413	69.2757	47.2309	52.2681
8	4.468	-1.8133	-2.7407	0.7369	1.1121	1.6835	0.1045	0.4348	0.075	-0.021	-0.1181	-0.0404	-0.0242	-0.2829	0.0136	0.1265	-0.0277	0.0241	0.1572	0.0189	0.1081	62.4626	61.5248	40.9754
9	0.1627	-0.0848	0.0217	0.0766	-0.0434	0.1034	0.0055	-0.0036	-0.0112	0.0003	0.0055	-0.0009	-0.0328	0.0169	-0.011	0.1221	-0.0062	0.0071	0.1248	0.0029	0.1364	73.2628	52.4497	34.0364
10	0.847	0.0023	-0.0316	1.0684	0.0205	0.0016	0.0323	-0.0369	-0.1033	-0.047	-0.0235	-0.0563	-0.003	0.001	-0.0088	0.0092	0.0109	0.0191	0.1415	-0.0057	0.1405	69.1632	32.287	32.8285
11	0.2524	-0.0183	-0.1168	0.2409	0.0349	0.2897	0.0009	-0.0239	0.0003	0.0002	0.003	-0.0204	0.0184	0.0341	-0.0039	0.1177	0.0033	0.0054	0.1243	-0.0037	0.1314	83.7277	43.1453	11.4667
12	5.4946	-3.0466	-1.0926	15.4662	-6.5848	3.9706	-0.0882	-0.5093	0.5219	0.5055	-0.0619	-0.8488	-0.2382	0.261	0.15	0.0668	0.0435	-0.0074	0.1875	0.0092	0.204	97.7276	33.4188	-14.7119
13	0.0944	0.072	-0.0628	0.0759	-0.0342	0.0557	0.0006	-0.0173	-0.0053	0.0054	0.015	-0.0139	0.0239	0.0364	-0.0156	0.1278	0.0156	0.0038	0.1337	-0.007	0.143	90.6953	33.0403	-4.8311
14	0.0889	-0.244	-0.0042	1.9705	0.4231	0.1383	-0.0016	0.0223	0.0617	-0.2336	0.0465	-0.256	-0.1027	0.0272	-0.0449	0.1313	0.0014	0.0317	0.1369	-0.0075	0.1917	94.7689	44.5691	-20.0859
15	0.0772	0.1609	-0.0388	0.3446	-0.0841	0.0207	-0.0064	0.0129	-0.0054	-0.0362	0.013	0.0124	0.0098	-0.0014	-0.0067	0.1338	0.0154	0.0045	0.1305	-0.0045	0.1344	87.0124	36.7251	-12.3842
16	1.0759	1.7685	1.4318	3.018	2.4549	1.9981	0.0124	0.0906	-0.1357	-0.0129	0.0734	-0.1378	-0.0146	0.0395	-0.0858	0.1304	0.0001	0.0088	0.1472	-0.0168	0.1502	89.1255	61.9086	-15.4025
17	0.1917	-0.0405	-0.0467	0.0345	0.0878	0.2537	0.0123	0.0199	0.0081	-0.0112	-0.0045	0.0063	-0.0124	-0.005	-0.0078	0.1278	0.002	0.0052	0.1272	-0.0032	0.1391	77.6121	47.2466	-15.3513
18	7.2103	4.8083	-8.6013	3.6238	-6.2728	10.9522	0.4801	-0.8363	-0.1825	0.1634	-0.5817	0.0839	-0.3232	1.215	0.1016	0.1459	-0.0082	0.0079	0.1661	-0.0544	0.1521	84.5893	61.4395	-4.1935
19	0.1224	-0.0841	-0.0498	0.0599	0.0372	0.1412	-0.0013	0.0046	0.0029	-0.01	0.0077	0.0024	-0.0319	-0.0165	-0.0063	0.1253	0.0033	0.0057	0.1245	-0.0031	0.1369	73.528	52.4855	2.8486
20	1.9416	-1.1587	0.3047	1.9537	-0.575	0.1703	-0.038	-0.0774	-0.101	0.0754	0.0641	0.0826	-0.0223	-0.0173	-0.0261	0.0258	0.0316	0.0385	0.1372	-0.0082	0.1361	77.6969	32.3642	4.0892

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 77
2	X-RAY DIFFRACTION	2	A	78 - 104
3	X-RAY DIFFRACTION	3	A	105 - 133
4	X-RAY DIFFRACTION	4	A	134 - 152
5	X-RAY DIFFRACTION	5	A	153 - 183
6	X-RAY DIFFRACTION	6	A	184 - 193
7	X-RAY DIFFRACTION	7	A	194 - 261
8	X-RAY DIFFRACTION	8	A	262 - 272
9	X-RAY DIFFRACTION	9	A	273 - 321
10	X-RAY DIFFRACTION	10	A	322 - 332
11	X-RAY DIFFRACTION	11	B	7 - 77
12	X-RAY DIFFRACTION	12	B	78 - 104
13	X-RAY DIFFRACTION	13	B	105 - 133
14	X-RAY DIFFRACTION	14	B	134 - 152
15	X-RAY DIFFRACTION	15	B	153 - 183
16	X-RAY DIFFRACTION	16	B	184 - 193
17	X-RAY DIFFRACTION	17	B	194 - 261
18	X-RAY DIFFRACTION	18	B	262 - 272
19	X-RAY DIFFRACTION	19	B	273 - 321
20	X-RAY DIFFRACTION	20	B	322 - 332

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