PDB-5flw: Crystal structure of putative exo-beta-1,3-galactanase from Bifid...

ID or keywords:

Entry

Database: PDB / ID: 5flw

Title

Crystal structure of putative exo-beta-1,3-galactanase from Bifidobacterium bifidum s17

Components

EXO-BETA-1,3-GALACTANASE

Keywords

HYDROLASE / GALACTANASE / BIFIDOBACTERIUM / GH43 / FAMILY 43

Function / homology

Function and homology information

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

Biological species

BIFIDOBACTERIUM BIFIDUM (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.401 Å

Authors

Godoy, A.S. / de Lima, M.Z.T. / Ramia, M.P. / Camilo, C.M. / Muniz, J.R.C. / Polikarpov, I.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Crystal structure of a putative exo-beta-1,3-galactanase from Bifidobacterium bifidum S17.
Authors: Godoy, A.S. / de Lima, M.Z. / Camilo, C.M. / Polikarpov, I.

History

Deposition	Oct 28, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 23, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 30, 2016	Group: Database references / Structure summary
Revision 1.2	Apr 13, 2016	Group: Database references
Revision 1.3	Apr 20, 2016	Group: Database references
Revision 1.4	May 10, 2017	Group: Database references
Revision 1.5	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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	5flw.cif.gz	275.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5flw.ent.gz	225.9 KB	Display	PDB format
PDBx/mmJSON format	5flw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5flw_validation.pdf.gz	430 KB	Display	wwPDB validaton report
Full document	5flw_full_validation.pdf.gz	430.8 KB	Display
Data in XML	5flw_validation.xml.gz	36.3 KB	Display
Data in CIF	5flw_validation.cif.gz	59.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fl/5flw ftp://data.pdbj.org/pub/pdb/validation_reports/fl/5flw	HTTPS FTP

-
Related structure data

Related structure data	3nqhS S: Starting model for refinement
Similar structure data	4blv-1 5xfe-d 4ch2-2 1shh-2 1z8j-d 6zf3-d 2fp9-2 5d9b-d 1nro-d 1hai-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: EXO-BETA-1,3-GALACTANASE

B: EXO-BETA-1,3-GALACTANASE

hetero molecules

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

1

A: EXO-BETA-1,3-GALACTANASE

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

2

B: EXO-BETA-1,3-GALACTANASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.926, 67.343, 202.126
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	EXO-BETA-1,3-GALACTANASE Mass: 34045.355 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 73-376 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BIFIDOBACTERIUM BIFIDUM (bacteria) / Strain: S17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA References: UniProt: E4VCC5, UniProt: E3END6*PLUS, galactan 1,3-beta-galactosidase
#2: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1261 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 3.24 Å³/Da / Density % sol: 62 % / Description: NONE
Crystal grow	Details: 0.05 M CALCIUM CHLORIDE DEHYDRATE, 0.1 M BIS-TRIS PH 6.5 AND 30% (V/V) POLYETHYLENE GLYCOL MONOMETHYL 550

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 1.1
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection twin	Operator: K,H,-L / Fraction: 0.06
Reflection	Resolution: 1.4→47.6 Å / Num. obs: 174550 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8 % / R_merge(I) obs: 0.06 / Net I/σ(I): 16.6
Reflection shell	Resolution: 1.4→1.42 Å / Redundancy: 7.8 % / R_merge(I) obs: 1.02 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NQH

3nqh

Resolution: 1.401→19.939 Å / σ(F): 1.34 / Phase error: 19.32 / Stereochemistry target values: TWIN_LSQ_F / Details: LIGAND IS NOT MODEL IN CHAIN A

	R_factor	Num. reflection	% reflection
R_free	0.1834	1773	1 %
R_work	0.1619	-	-
obs	0.1618	174374	99.96 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.401→19.939 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4788	0	14	1261	6063

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	5042
X-RAY DIFFRACTION	f_angle_d	1.088	6907
X-RAY DIFFRACTION	f_dihedral_angle_d	16.022	1759
X-RAY DIFFRACTION	f_chiral_restr	0.1	720
X-RAY DIFFRACTION	f_plane_restr	0.007	908

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.4013-1.4425	0.3426	143	0.3304	14230	X-RAY DIFFRACTION	99
1.4425-1.489	0.3112	150	0.2854	14159	X-RAY DIFFRACTION	99
1.489-1.5421	0.2717	186	0.2625	14202	X-RAY DIFFRACTION	99
1.5421-1.6037	0.2503	141	0.2322	14225	X-RAY DIFFRACTION	99
1.6037-1.6765	0.1826	122	0.2137	14252	X-RAY DIFFRACTION	99
1.6765-1.7647	0.203	130	0.199	14313	X-RAY DIFFRACTION	99
1.7647-1.8749	0.2113	141	0.1808	14287	X-RAY DIFFRACTION	99
1.8749-2.0191	0.1649	137	0.1684	14328	X-RAY DIFFRACTION	99
2.0191-2.2212	0.191	163	0.1647	14334	X-RAY DIFFRACTION	99
2.2212-2.5402	0.1812	130	0.1555	14431	X-RAY DIFFRACTION	99
2.5402-3.1912	0.1676	159	0.1357	14533	X-RAY DIFFRACTION	99
3.1912-12.3403	0.1456	136	0.1156	14929	X-RAY DIFFRACTION	99

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	1.2288	0.9485	0.6677	1.5941	-0.5774	2.5603	-0.0969	-0.0034	0.1241	-0.0386	0.0664	0.0902	-0.2129	-0.0845	0.0436	0.1651	0.0191	-0.0156	0.0762	-0.0032	0.128	26.9588	11.1193	-52.932
2	2.7218	-0.9355	-0.621	1.9435	0.3611	2.3982	-0.0275	0.0002	0.1447	0.0902	0.0226	0.0419	-0.2093	-0.1499	-0.0289	0.1417	0.005	-0.0153	0.0552	0.0131	0.0966	30.2298	6.797	-43.2712
3	0.5375	-0.0185	0.2897	0.482	-0.5878	1.2615	-0.0195	-0.0247	0.0732	0.0734	0.008	0.0083	-0.1753	-0.0643	0.0102	0.1458	0.0048	-0.0093	0.0791	-0.006	0.1108	32.4278	4.8466	-38.7868
4	1.393	-0.706	-0.1176	2.4156	-0.3914	1.3423	-0.0252	-0.0145	0.0452	-0.0563	0.0098	-0.0534	-0.1486	-0.023	0.0229	0.1204	-0.0081	-0.016	0.0793	0.002	0.0899	35.3178	-2.0118	-34.307
5	1.0886	0.0024	0.5031	1.3481	-0.7391	1.1735	-0.0164	-0.1525	-0.0294	0.019	0.0871	0.1669	0.0382	-0.2656	-0.0563	0.0948	-0.0049	-0.0055	0.1501	0.0217	0.1287	21.7948	-8.5587	-33.7434
6	0.7055	0.0874	0.2966	0.6933	-0.6374	1.0569	-0.0017	-0.0475	-0.036	-0.0822	0.1018	0.1854	0.1248	-0.3811	-0.0503	0.1023	-0.0205	-0.0187	0.1781	0.0342	0.1684	17.4385	-8.1416	-40.3875
7	0.9517	0.1055	-0.5446	0.8399	-0.545	1.9239	-0.0214	-0.0977	0.0272	-0.1047	0.1612	0.3074	0.0141	-0.5534	-0.0569	0.0954	-0.0027	-0.0358	0.2823	0.0595	0.2201	10.966	-1.9788	-44.347
8	2.19	0.4783	0.4697	1.4558	-0.8908	1.412	-0.0383	0.0898	-0.0887	-0.2383	0.0804	0.0005	0.1622	-0.1185	-0.0378	0.1666	-0.0107	-0.026	0.0738	0.006	0.1227	26.4397	0.951	-54.5352
9	2.1022	0.7441	-0.6365	1.3866	-0.3643	1.2757	-0.0275	0.036	0.0831	-0.2129	0.2244	0.3719	0.0295	-0.4853	-0.1152	0.1344	-0.0076	-0.066	0.2404	0.0739	0.2155	12.9514	4.2615	-55.8006
10	1.9834	-0.1698	-0.1542	1.6501	-1.2082	1.4661	0.0413	-0.177	-0.3267	0.1363	0.059	0.0341	0.2956	-0.0704	-0.0616	0.2358	-0.0086	-0.0116	0.1262	0.0432	0.1694	41.9249	-32.2666	-4.5508
11	0.7787	0.0859	0.4036	0.5682	-0.0636	2.8029	0.0395	-0.0767	-0.0838	-0.015	0.0308	0.0671	0.2372	-0.082	-0.0755	0.1421	-0.0104	-0.0011	0.1033	0.0275	0.1317	34.7945	-25.5539	-12.834
12	0.9563	-0.602	-0.4699	2.1113	0.944	2.5116	-0.0158	-0.0601	0.0118	0.0701	0.0019	0.1262	0.0262	-0.1661	0.0346	0.1079	-0.004	0.0025	0.1288	0.0144	0.1237	33.81	-14.2299	-14.6454
13	0.7133	0.1554	0.2048	0.5531	-0.1104	1.2759	-0.0175	-0.042	0.0269	0.0032	0.0157	0.0512	0.0166	0.0007	0.0024	0.1037	0.0084	-0.0055	0.1	0.0072	0.1071	39.5522	-12.1815	-20.6255
14	1.0393	-0.3349	0.4042	0.8416	-0.2596	1.2351	-0.0317	0.0439	0.0058	0.0298	-0.0075	-0.0943	0.0009	0.1353	0.0363	0.1014	-0.0039	-0.0069	0.124	0.0004	0.1148	50.1328	-11.0331	-15.7402
15	0.8508	-0.036	0.3267	1.6872	-0.4784	1.1818	-0.0075	-0.0597	0.0352	0.1018	-0.0414	-0.0935	-0.0171	0.1265	0.0453	0.1068	0.0057	-0.0239	0.1256	-0.0045	0.112	53.2317	-12.6188	-6.3357
16	1.7527	1.2432	1.312	3.1261	0.542	2.4798	0.0603	0.1171	-0.243	-0.1153	0.06	-0.131	0.445	0.212	-0.1222	0.184	0.0361	-0.0071	0.1164	0.0167	0.1412	48.6664	-29.4158	-12.1909
17	1.5869	0.6825	0.9819	3.1003	-0.0131	1.7592	0.108	-0.0129	-0.1749	0.0865	-0.0384	-0.1593	0.2614	0.09	-0.0656	0.1643	0.0374	-0.0244	0.1459	0.0203	0.1373	55.874	-24.6753	-1.5658

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 3 THROUGH 23 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 24 THROUGH 47 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 48 THROUGH 102 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 103 THROUGH 129 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 130 THROUGH 164 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 165 THROUGH 215 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 216 THROUGH 260 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 261 THROUGH 276 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 277 THROUGH 304 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 3 THROUGH 23 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 24 THROUGH 82 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 83 THROUGH 102 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 103 THROUGH 164 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 165 THROUGH 215 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 216 THROUGH 260 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 261 THROUGH 276 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 277 THROUGH 304 )

-
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