PDB-4f66: The crystal structure of 6-phospho-beta-glucosidase from Streptoc...

ID or keywords:

Entry

Database: PDB / ID: 4f66

Title

The crystal structure of 6-phospho-beta-glucosidase from Streptococcus mutans UA159 in complex with beta-D-glucose-6-phosphate.

Components

Putative phospho-beta-glucosidase

Keywords

HYDROLASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG

Function / homology

Function and homology information

6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase activity / : / carbohydrate metabolic process
Similarity search - Function

Biological species

Streptococcus mutans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.479 Å

Authors

Tan, K. / Michalska, K. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: GH1-family 6-P-beta-glucosidases from human microbiome lactic acid bacteria.
Authors: Michalska, K. / Tan, K. / Li, H. / Hatzos-Skintges, C. / Bearden, J. / Babnigg, G. / Joachimiak, A.

History

Deposition	May 14, 2012	Deposition site: RCSB / Processing site: RCSB
Supersession	Jun 13, 2012	ID: 4DDE
Revision 1.0	Jun 13, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jul 29, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4f66.cif.gz	420.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4f66.ent.gz	342.6 KB	Display	PDB format
PDBx/mmJSON format	4f66.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4f66_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4f66_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4f66_validation.xml.gz	46.1 KB	Display
Data in CIF	4f66_validation.cif.gz	71 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f6/4f66 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/4f66	HTTPS FTP

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Related structure data

Related structure data	3qomC 4f79C 4gpnC 4gzeC 3pn8S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3qom-1 5okq-d 2xhy-1 5bwf-d 4gpn-d 5okk-d 4gze-1 4rsc-d 4f79-1 4gze-3 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: MCSG-APC100193

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative phospho-beta-glucosidase

B: Putative phospho-beta-glucosidase

hetero molecules

112 kDa, 2 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)	58.665, 92.449, 94.351
Angle α, β, γ (deg.)	90.00, 101.32, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

Experimentally unknown. It is predicted that the molecule is monomeric.

#1: Protein

Putative phospho-beta-glucosidase

Mass: 55475.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptococcus mutans (bacteria) / Strain: UA159 / Gene: bgl, SMU_1601 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q8DT00, 6-phospho-beta-glucosidase

#2: Sugar

ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose

Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₃O₉P

#3: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂

#4: Chemical

ChemComp-FMT / FORMIC ACID

Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1145 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.6 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M Sodium format, 20% (w/v) PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2011 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.48→25.2 Å / Num. all: 163713 / Num. obs: 163713 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / R_merge(I) obs: 0.067 / Net I/σ(I): 27.1
Reflection shell	Resolution: 1.48→1.51 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.589 / Mean I/σ(I) obs: 1.92 / Num. unique all: 7937 / % possible all: 96.5

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry: 3PN8

3pn8

Resolution: 1.479→25.077 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 17.37 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1853	8214	5.02 %	random
R_work	0.1617	-	-	-
obs	0.1629	163661	99.61 %	-
all	-	163661	-	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 45.185 Å² / k_sol: 0.369 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.3277 Å²	-0 Å²	1.7011 Å²
2-	-	-1.3678 Å²	0 Å²
3-	-	-	-1.9599 Å²

Refinement step

Cycle: LAST / Resolution: 1.479→25.077 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7804	0	54	1145	9003

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	8233
X-RAY DIFFRACTION	f_angle_d	1.06	11173
X-RAY DIFFRACTION	f_dihedral_angle_d	13.091	2999
X-RAY DIFFRACTION	f_chiral_restr	0.076	1120
X-RAY DIFFRACTION	f_plane_restr	0.005	1456

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 (%)
1.4791-1.4959	0.3208	266	0.2813	4719	X-RAY DIFFRACTION	92
1.4959-1.5135	0.2673	274	0.2615	5098	X-RAY DIFFRACTION	99
1.5135-1.5319	0.2608	295	0.2494	5150	X-RAY DIFFRACTION	100
1.5319-1.5513	0.2959	271	0.2442	5250	X-RAY DIFFRACTION	100
1.5513-1.5717	0.2346	277	0.2246	5165	X-RAY DIFFRACTION	100
1.5717-1.5933	0.2631	271	0.2186	5190	X-RAY DIFFRACTION	100
1.5933-1.616	0.2446	293	0.1994	5123	X-RAY DIFFRACTION	100
1.616-1.6401	0.2186	286	0.1924	5175	X-RAY DIFFRACTION	100
1.6401-1.6658	0.2389	282	0.184	5158	X-RAY DIFFRACTION	100
1.6658-1.6931	0.2016	281	0.1764	5197	X-RAY DIFFRACTION	100
1.6931-1.7222	0.2115	250	0.1733	5225	X-RAY DIFFRACTION	100
1.7222-1.7536	0.1808	305	0.1655	5146	X-RAY DIFFRACTION	100
1.7536-1.7873	0.194	276	0.1588	5188	X-RAY DIFFRACTION	100
1.7873-1.8237	0.1911	271	0.1591	5226	X-RAY DIFFRACTION	100
1.8237-1.8634	0.1845	285	0.1582	5161	X-RAY DIFFRACTION	100
1.8634-1.9067	0.1828	250	0.1525	5206	X-RAY DIFFRACTION	100
1.9067-1.9544	0.1821	301	0.1503	5188	X-RAY DIFFRACTION	100
1.9544-2.0072	0.1825	239	0.1535	5220	X-RAY DIFFRACTION	100
2.0072-2.0662	0.1939	264	0.1538	5190	X-RAY DIFFRACTION	100
2.0662-2.1329	0.1792	278	0.1526	5207	X-RAY DIFFRACTION	100
2.1329-2.2091	0.1824	247	0.1484	5218	X-RAY DIFFRACTION	100
2.2091-2.2975	0.1784	275	0.1508	5199	X-RAY DIFFRACTION	100
2.2975-2.402	0.1746	272	0.1512	5214	X-RAY DIFFRACTION	100
2.402-2.5285	0.1818	260	0.1482	5240	X-RAY DIFFRACTION	100
2.5285-2.6867	0.1844	278	0.1578	5222	X-RAY DIFFRACTION	100
2.6867-2.8939	0.188	285	0.1609	5185	X-RAY DIFFRACTION	100
2.8939-3.1846	0.1819	224	0.1586	5266	X-RAY DIFFRACTION	100
3.1846-3.6442	0.1693	282	0.1567	5251	X-RAY DIFFRACTION	100
3.6442-4.5867	0.153	279	0.1341	5239	X-RAY DIFFRACTION	100
4.5867-25.0805	0.1627	297	0.1656	5231	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	2.3084	-0.0719	0.2793	0.8966	-0.1282	1.0499	0.0323	0.1368	0.1376	-0.1905	0.034	0.0672	0.0401	-0.1442	-0.0527	0.1344	-0.0343	-0.0023	0.1191	0.0038	0.086	-2.3207	0.9515	22.2931
2	1.8677	-0.5399	-0.1163	1.9353	0.0977	1.0943	0.0391	0.5847	0.0512	-0.3773	-0.0286	0.1826	0.0582	-0.2577	-0.0283	0.2128	-0.0446	-0.0322	0.2477	0.0339	0.1096	-4.0656	-1.1968	12.2396
3	1.4532	0.067	-0.335	0.6436	-0.034	0.5629	-0.1181	0.2281	-0.2317	-0.1675	0.0537	0.1151	0.1364	-0.1744	0.0567	0.1838	-0.0554	-0.0201	0.1764	-0.0383	0.1294	-8.5312	-11.2921	21.05
4	0.8617	0.0694	-0.4079	0.5704	-0.0931	0.5666	-0.0268	0.127	-0.0698	-0.0922	0.0121	0.0793	0.0705	-0.1293	0.011	0.0709	-0.0333	-0.0287	0.0978	-0.0081	0.0936	-11.254	-6.0567	30.9735
5	0.5951	0.2411	0.0484	0.4042	0.1717	0.2957	-0.0229	0.036	0.0427	-0.0332	0.0105	0.0712	-0.0167	-0.0517	0.0112	0.0737	-0.0072	-0.0061	0.0913	0.0064	0.1072	-4.9939	4.6853	41.2201
6	1.1015	0.2853	-0.1368	0.8778	0.2734	0.5211	-0.0106	-0.1328	0.0648	0.0623	-0.0296	0.1707	0.0846	-0.0697	0.0308	0.0719	-0.0095	-0.0052	0.0944	-0.0063	0.1	-6.5398	1.9852	47.3617
7	0.2356	0.0891	-0.2717	0.5802	0.2031	0.7104	0.0001	0.027	0.0849	-0.0631	0.0392	0.0136	-0.0525	-0.0319	-0.0433	0.0656	0.0001	-0.0125	0.0929	0.0013	0.1097	7.3706	10.765	39.884
8	0.4233	-0.0608	-0.273	0.5633	-0.2675	1.9736	0.0559	0.1337	0.0583	-0.234	-0.0114	-0.088	0.0197	0.158	-0.0079	0.1399	-0.0201	0.0361	0.1161	-0.0004	0.0992	16.2999	4.2866	21.0508
9	1.1519	-0.1431	0.2808	0.8357	-0.0912	1.0993	0.0315	0.2411	0.1054	-0.2495	-0.0008	0.0452	-0.0405	-0.0137	-0.0449	0.1529	-0.0137	0.0141	0.1289	0.0096	0.0936	5.0991	3.1547	18.9004
10	0.7265	-0.0332	-0.2148	1.8225	-0.8706	2.1185	-0.0645	0.1574	-0.0874	-0.2065	-0.0332	-0.2827	0.1177	0.2789	0.1182	0.1757	0.0006	0.062	0.1414	-0.0221	0.1264	17.7283	-5.024	18.0929
11	0.8947	-0.6038	-0.2779	1.6808	0.542	1.366	-0.0402	-0.1853	0.0123	0.2719	0.0682	-0.1293	0.1222	0.2262	-0.0179	0.1759	0.0509	-0.0113	0.1533	0.02	0.077	18.4654	-2.5921	81.4585
12	0.3164	-0.1407	-0.1486	0.4504	-0.2812	0.851	-0.0498	-0.0749	-0.0481	0.0196	0.0024	-0.0458	0.1399	0.1865	0.002	0.1085	0.0403	0.0028	0.1252	-0.0023	0.107	19.9965	-4.94	59.8059
13	0.349	0.1541	-0.1318	0.455	0.0694	1.1926	0.0412	-0.1103	0.0661	0.1415	0.0317	-0.0776	-0.1502	0.1591	-0.0478	0.1263	0.0177	-0.0116	0.1189	-0.0303	0.1243	14.7074	14.1193	70.5254

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 0:50)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 51:79)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 80:120)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 121:181)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 182:272)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 273:318)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 319:375)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 376:411)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 412:456)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 457:477)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 0:181)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 182:318)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 319:477)

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