PDB-5dxd: Crystal structure of Putative beta-glucanase (Rv0315 ortholog) fr...

ID or keywords:

Entry

Database: PDB / ID: 5dxd

Title

Crystal structure of Putative beta-glucanase (Rv0315 ortholog) from Mycobacterium abscessus

Components

Putative beta-glucanase

Keywords

HYDROLASE / SSGCID / Mycobacterium / Mycobacterium abscessus / Putative beta-glucanase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

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

Biological species

Mycobacterium abscessus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.7 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of Putative beta-glucanase (Rv0315 ortholog) from Mycobacterium abcesus
Authors: Abendroth, J. / Davies, D.R. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Sep 23, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 4, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 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_prerelease_seq / pdbx_struct_oper_list / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5dxd.cif.gz	206.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5dxd.ent.gz	162.9 KB	Display	PDB format
PDBx/mmJSON format	5dxd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dx/5dxd ftp://data.pdbj.org/pub/pdb/validation_reports/dx/5dxd	HTTPS FTP

-
Related structure data

Related structure data	4pq9S S: Starting model for refinement
Similar structure data	1iqq-d 6ub2-3 3toi-2 4pq9-2 4xdq-d 1qds-d 4tvt-d 2x1u-1 4ek0-d 4qgo-1 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	TargetTrack: SSGCID-MyabA.18623.a

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (3)

Deposited unit

A: Putative beta-glucanase

B: Putative beta-glucanase

hetero molecules

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

1

A: Putative beta-glucanase

hetero molecules

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

2

B: Putative beta-glucanase

hetero molecules

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

Unit cell

Length a, b, c (Å)	52.390, 52.390, 223.350
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	78
Space group name H-M	P4₃

#1: Protein	Putative beta-glucanase Mass: 29084.109 Da / Num. of mol.: 2 / Fragment: MyabA.18623.a.B2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: MAB_1840c / Plasmid: MyabA.18623.a.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1MNM2
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.64 Å³/Da / Density % sol: 53 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: Rigaku Reagents screen JCSG+ A2: 20% PEG 3350, 100mM Na3citrate/citric acid pH 5.5; MyabA.18623.a.B2.PS02117 at 17.1 mg/mg; cryo: 20% EG; tray 257193 a3; puck rdn7-6

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 6, 2014

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection twin

Operator: h,-k,-l / Fraction: 0.47

Reflection

Resolution: 1.7→50 Å / Num. all: 65807 / Num. obs: 65575 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.25 % / R_merge F obs: 0.998 / R_merge(I) obs: 0.066 / R_rim(I) all: 0.091 / Χ²: 0.952 / Net I/σ(I): 15.88 / Num. measured all: 278726

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.7-1.74	2.59	0.663	0.524	2.04	12381	2575	2574	0.65	97.8
1.74-1.79		0.69	0.492	3.38	12592	2486	2485	0.548	100
1.79-1.84		0.795	0.405	4.28	12879	2436	2435	0.449	100
1.84-1.9		0.846	0.332	5.33	13207	2370	2370	0.366	100
1.9-1.96		0.93	0.253	7.05	13474	2302	2302	0.278	100
1.96-2.03		0.945	0.198	9.15	13879	2247	2247	0.216	100
2.03-2.11		0.961	0.169	11.07	13954	2158	2158	0.183	100
2.11-2.19		0.978	0.144	13.03	14043	2087	2087	0.156	100
2.19-2.29		0.982	0.13	14.85	14295	2001	2001	0.14	100
2.29-2.4		0.985	0.117	17.91	15780	1920	1920	0.125	100
2.4-2.53		0.989	0.111	19.31	15849	1825	1825	0.118	100
2.53-2.69		0.991	0.099	21.87	15820	1748	1748	0.105	100
2.69-2.87		0.994	0.088	24.75	15968	1663	1663	0.093	100
2.87-3.1		0.996	0.073	30.69	15918	1548	1548	0.077	100
3.1-3.4		0.997	0.063	37.76	16876	1416	1416	0.065	100
3.4-3.8		0.998	0.059	43.14	17564	1315	1315	0.062	100
3.8-4.39		0.998	0.056	44.06	15672	1184	1183	0.059	99.9
4.39-5.38		0.998	0.06	43.14	13010	1011	1010	0.062	99.9
5.38-7.6		0.998	0.065	37.13	10183	817	817	0.068	100
7.6-50		0.998	0.055	36.81	5382	520	513	0.058	98.7

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2 Å	47.43 Å
Translation	2 Å	47.43 Å

-
Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
ARP		model building
PHENIX	dev_2165	refinement
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4pq9

4pq9

Resolution: 1.7→47.43 Å / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.62 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1894	1952	2.98 %	Random selection
R_work	0.1486	63325	-	-
obs	0.1527	65477	99.66 %	-

Solvent computation

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

Displacement parameters

B_iso max: 43.8 Å² / B_iso mean: 14.4555 Å² / B_iso min: 4.86 Å²

Refinement step

Cycle: final / Resolution: 1.7→47.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3718	0	2	402	4122
B_iso mean	-	-	9.21	19.51	-
Num. residues	-	-	-	-	466

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3861
X-RAY DIFFRACTION	f_angle_d	0.94	5272
X-RAY DIFFRACTION	f_chiral_restr	0.056	507
X-RAY DIFFRACTION	f_plane_restr	0.007	698
X-RAY DIFFRACTION	f_dihedral_angle_d	12.759	2170

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7002-1.7426	0.3047	132	0.2192	4448	4580	95
1.7426-1.7895	0.2725	121	0.2011	4450	4571	96
1.7895-1.842	0.3061	111	0.1881	4548	4659	97
1.842-1.9012	0.2061	152	0.1751	4521	4673	97
1.9012-1.9689	0.2401	135	0.1616	4502	4637	97
1.9689-2.0474	0.2348	136	0.1537	4551	4687	97
2.0474-2.14	0.1909	130	0.1535	4540	4670	97
2.14-2.2521	0.1642	123	0.1472	4574	4697	97
2.2521-2.3922	0.1546	155	0.1483	4526	4681	97
2.3922-2.5752	0.2021	158	0.1453	4484	4642	97
2.5752-2.8312	0.1768	152	0.145	4533	4685	97
2.8312-3.2337	0.1833	149	0.1512	4545	4694	97
3.2337-4.0475	0.1797	146	0.1405	4555	4701	97
4.0475-11.9261	0.1476	146	0.1239	4548	4694	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	1.5603	0.2634	-0.2673	0.794	-0.7136	0.6879	-0.028	-0.1369	-0.0226	0.0324	0.0181	-0.0026	0.1025	0.1221	0.0021	0.0823	-0.0018	-0.0166	0.0608	0.0009	0.0943	-3.0272	31.5299	98.9353
2	0.9719	0.2214	-0.0403	0.7926	-0.0619	0.4632	-0.0348	0.1558	0.0029	-0.0833	0.0319	-0.0261	-0.0227	0.012	0.0065	0.0786	-0.0098	-0.0037	0.0853	-0.004	0.0581	-7.6696	30.0743	89.4187
3	0.8412	-0.7835	0.2532	4.2925	-0.1563	0.296	0.0222	-0.0465	-0.0343	0.0051	0.0192	0.3956	0.0238	-0.1549	-0.0105	0.0536	-0.0117	0.0049	0.0957	0.0058	0.1219	-26.544	26.8652	94.0322
4	0.6508	0.0941	-0.0601	0.6344	0.067	0.361	-0.0186	0.0575	-0.0412	-0.0539	0.0229	0.0213	-0.0119	-0.0358	-0.0022	0.0532	-0.0013	-0.0035	0.0819	0.0121	0.0629	-11.1055	26.1017	91.7402
5	0.336	-0.3049	-0.4215	2.5787	-0.4323	0.8271	0.0403	0.1268	-0.1552	-0.0997	-0.0238	0.0855	0.0337	-0.0008	-0.0136	0.1162	0.0363	-0.0444	0.1108	-0.0318	0.0823	18.4047	-1.0693	91.205
6	0.9204	0.1474	0.0307	0.8695	-0.0461	1.5979	-0.0169	-0.1332	-0.0047	0.1077	0.0009	-0.082	-0.1572	0.2081	-0.0245	0.0874	-0.0092	-0.0216	0.1308	0.0195	0.0913	31.0844	6.3176	110.2986
7	1.7192	0.4388	1.0518	0.5223	0.3898	2.199	0.154	-0.0202	-0.0804	0.0545	-0.1061	-0.1321	0.2834	0.0834	-0.0506	0.0991	0.0207	-0.0154	0.0808	-0.0023	0.1192	26.1962	-4.2105	105.2289
8	0.4121	-0.1645	-0.1932	2.3344	-0.9968	1.2388	0.044	0.0609	-0.1622	-0.0071	-0.0274	0.0974	-0.0585	-0.0766	-0.0163	0.055	0.0061	-0.0296	0.0722	-0.0038	0.1245	11.9149	5.9597	98.4262
9	0.9123	-0.4489	0.5204	1.381	-0.8343	1.5463	0.0026	-0.1277	0.0532	0.0755	0.0542	0.0446	-0.0402	0.0206	-0.06	0.0821	0.0014	0.0044	0.0936	-0.0072	0.0758	16.8492	10.7637	111.2486
10	1.2207	0.2983	-0.3611	3.9187	2.3958	2.5638	-0.0045	-0.0063	-0.0116	0.176	-0.1175	0.2996	0.0373	-0.1914	0.1222	0.0672	0.0035	-0.0131	0.1276	0.0274	0.1168	8.1116	4.0337	112.7567
11	0.9038	0.0363	-0.2546	1.4308	-0.1852	0.7244	0.0343	0.0597	-0.0596	0.0229	-0.0312	0.2045	-0.0263	-0.1378	0.0029	0.0417	0.005	-0.0192	0.0981	-0.0018	0.0947	2.4712	11.2107	104.0615
12	0.9801	-0.3944	-0.1561	1.1147	-0.1739	0.5754	0.0582	0.0293	0.0994	0.0048	-0.0553	-0.0193	-0.0044	-0.0689	0.0033	0.0928	-0.0104	-0.0182	0.0525	0.014	0.0584	15.675	16.0888	101.6461
13	1.1071	0.3442	1.1535	0.4152	0.2784	2.8254	-0.0594	-0.0315	-0.1102	0.1292	0.0073	0.0485	0.1127	0.0843	0.0505	0.1081	0.0158	-0.0018	0.0979	0.0156	0.0894	18.5847	-1.2939	108.076

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 25 through 58 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 187 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 188 through 204 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 205 through 257 )	A
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 25 through 44 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 45 through 75 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 76 through 102 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 103 through 119 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 120 through 167 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 168 through 179 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 180 through 213 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 214 through 232 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 233 through 257 )	B

-
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://pdbjlc1.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