PDB-4eam: 1.70A resolution structure of apo beta-glycosidase (W33G) from su...

ID or keywords:

Entry

Database: PDB / ID: 4eam

Title

1.70A resolution structure of apo beta-glycosidase (W33G) from sulfolobus solfataricus

Components

Beta-galactosidase

Keywords

HYDROLASE / GLYCOSIDE HYDROLASE / Chemical biology / allosteric activation / switchable enzyme / chemical rescue

Function / homology

Function and homology information

beta-galactosidase / carbohydrate catabolic process / beta-galactosidase activity / beta-glucosidase activity / cytosol
Similarity search - Function

Biological species

Sulfolobus solfataricus P2 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.7 Å

Authors

Lovell, S. / Battaile, K.P. / Deckert, K. / Brunner, L.C. / Budiardjo, S.J. / Karanicolas, J.

Citation

Journal: J.Am.Chem.Soc. / Year: 2012
Title: Designing allosteric control into enzymes by chemical rescue of structure.
Authors: Deckert, K. / Budiardjo, S.J. / Brunner, L.C. / Lovell, S. / Karanicolas, J.

History

Deposition	Mar 22, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 13, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 21, 2012	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 13, 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 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4eam.cif.gz	411.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4eam.ent.gz	337.8 KB	Display	PDB format
PDBx/mmJSON format	4eam.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4eam_validation.pdf.gz	464.9 KB	Display	wwPDB validaton report
Full document	4eam_full_validation.pdf.gz	469 KB	Display
Data in XML	4eam_validation.xml.gz	41.8 KB	Display
Data in CIF	4eam_validation.cif.gz	63 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ea/4eam ftp://data.pdbj.org/pub/pdb/validation_reports/ea/4eam	HTTPS FTP

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Related structure data

Related structure data	4eanC 2ceqS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4ean-1 2cer-2 2ceq-1 6kdc-d 4yj6-d 4ean-2 2ceq-2 3wq8-8 4ha4-d 6zcw-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) 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

Related structure data

4eanC

2ceqS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Beta-galactosidase

B: Beta-galactosidase

hetero molecules

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

1

A: Beta-galactosidase

hetero molecules

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

2

B: Beta-galactosidase

hetero molecules

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

3

A: Beta-galactosidase

hetero molecules

A: Beta-galactosidase

hetero molecules

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

4

B: Beta-galactosidase

hetero molecules

B: Beta-galactosidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	167.700, 167.700, 96.398
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-899- HOH
2	1	B-963- HOH

#1: Protein	Beta-galactosidase / Lactase Mass: 56630.230 Da / Num. of mol.: 2 / Mutation: W33G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: lacS, SSO3019 / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P22498, beta-galactosidase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 717 / 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: 3.45 Å³/Da / Density % sol: 64.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 45% MPD, 100 mM Bis-Tris, 200 mM Calcium Chloride, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 17-ID / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2012

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. all: 170417 / Num. obs: 170417 / % possible obs: 99.89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.75 % / R_merge(I) obs: 0.088 / Net I/σ(I): 12.6094

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique all	Diffraction-ID	% possible all
1.7-1.79	7.11	0.63	175867	24747	1	100
1.79-1.9	6.88	0.43	161234	23433	1	99.99
1.9-2.03	6.87	0.26	151564	22050	1	99.99
2.03-2.19	6.95	0.17	142970	20577	1	100
2.19-2.4	6.61	0.12	125078	18924	1	99.98
2.4-2.69	6.75	0.09	115820	17167	1	99.95
2.69-3.1	6.79	0.07	102761	15131	1	99.97
3.1-3.8	5.96	0.06	76381	12805	1	99.53
3.8-5.38	6.53	0.04	65473	10033	1	99.88
5.38-50	6.09	0.04	33818	5550	1	98.41

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	48.41 Å
Translation	2.5 Å	48.41 Å

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Processing

Software

Name	Version	Classification
SCALA	CCP4_3.3.20	data scaling
PHASER	2.3.0	phasing
PHENIX	dev_1011	refinement
PDB_EXTRACT	3.1	data extraction
JDirector		data collection
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2CEQ

2ceq

Resolution: 1.7→34.156 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.14 / Phase error: 18.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.186	8526	5.01 %	RANDOM
R_work	0.168	-	-	-
obs	0.1689	170140	99.74 %	-

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 41.775 Å² / k_sol: 0.338 e/Å³

Displacement parameters

B_iso max: 84.6 Å² / B_iso mean: 21.6055 Å² / B_iso min: 8.97 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.2431 Å²	0 Å²	0 Å²
2-	-	-2.2431 Å²	0 Å²
3-	-	-	4.4863 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→34.156 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7826	0	70	717	8613

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	8305
X-RAY DIFFRACTION	f_angle_d	1.227	11361
X-RAY DIFFRACTION	f_chiral_restr	0.079	1152
X-RAY DIFFRACTION	f_plane_restr	0.007	1472
X-RAY DIFFRACTION	f_dihedral_angle_d	12.524	3008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7-1.7193	0.3116	283	0.333	5352	5635	100
1.7193-1.7396	0.3458	272	0.3198	5374	5646	100
1.7396-1.7608	0.3066	286	0.287	5380	5666	100
1.7608-1.7831	0.3105	247	0.2773	5357	5604	100
1.7831-1.8065	0.2507	297	0.2542	5366	5663	100
1.8065-1.8313	0.2587	269	0.2501	5349	5618	100
1.8313-1.8574	0.2577	298	0.2456	5374	5672	100
1.8574-1.8852	0.2724	299	0.2392	5332	5631	100
1.8852-1.9146	0.2007	280	0.1835	5395	5675	100
1.9146-1.946	0.2071	298	0.1782	5336	5634	100
1.946-1.9796	0.2222	272	0.1856	5378	5650	100
1.9796-2.0155	0.1768	300	0.1478	5403	5703	100
2.0155-2.0543	0.176	262	0.1437	5385	5647	100
2.0543-2.0962	0.1638	227	0.1445	5417	5644	100
2.0962-2.1418	0.1743	276	0.1423	5391	5667	100
2.1418-2.1916	0.1734	293	0.1426	5338	5631	100
2.1916-2.2464	0.1694	301	0.1423	5368	5669	100
2.2464-2.3071	0.1729	293	0.1461	5369	5662	100
2.3071-2.375	0.1918	272	0.1695	5372	5644	100
2.375-2.4517	0.1525	279	0.1356	5391	5670	100
2.4517-2.5393	0.1556	279	0.1445	5388	5667	100
2.5393-2.6409	0.1557	303	0.1292	5400	5703	100
2.6409-2.761	0.1586	298	0.1394	5381	5679	100
2.761-2.9065	0.1571	251	0.1422	5434	5685	100
2.9065-3.0885	0.1642	298	0.1513	5388	5686	100
3.0885-3.3268	0.2189	307	0.186	5373	5680	99
3.3268-3.6612	0.1664	327	0.1736	5375	5702	99
3.6612-4.1902	0.1749	300	0.1371	5417	5717	99
4.1902-5.2761	0.1517	279	0.1347	5487	5766	100
5.2761-34.1634	0.2145	280	0.2283	5544	5824	98

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	0.8984	0.2353	-0.2178	1.0863	-0.0985	0.4636	0.0691	0.0594	0.173	0.0985	0.0145	0.0926	-0.0496	-0.0476	-0.0925	0.0963	0.005	0.0394	0.1524	0.017	0.1233	6.7385	-55.9794	24.8743
2	0.6236	-0.4714	0.027	0.5501	0.3644	1.2313	0.0337	0.0715	-0.1064	-0.0043	-0.1024	0.1227	0.1078	-0.3172	0.0878	0.1286	0.0031	0.0256	0.2412	0.0095	0.1867	-9.851	-62.0469	19.6982
3	3.2437	2.1469	-0.9584	1.8553	-0.2986	0.9719	0.1313	-0.0824	0.2861	0.0531	-0.0599	0.116	-0.0642	-0.0674	-0.0747	0.15	0.0536	0.0663	0.1973	0.0255	0.2396	-12.6405	-51.1128	26.0043
4	0.8035	-0.7296	0.024	1.2604	-0.0285	0.1223	0.0227	0.1178	0.0184	0.0537	-0.0029	0.0573	-0.0396	-0.0706	-0.0282	0.1183	-0.0023	0.0253	0.2142	0.0203	0.1387	-4.3247	-66.1052	19.4533
5	0.925	-0.2386	-0.2237	0.9803	0.2129	0.4486	0.0123	0.2996	-0.0532	-0.0797	0.0419	0.0805	-0.0022	-0.0947	-0.0606	0.109	0.0048	-0.007	0.2502	0.0218	0.097	-2.4456	-66.4418	7.2743
6	5.6997	-0.7495	-0.1131	1.7467	0.044	1.5635	0.0649	0.7032	-0.5372	-0.2013	-0.0162	0.0356	0.0992	-0.1869	-0.015	0.1912	-0.0344	-0.014	0.3257	-0.0427	0.1244	-0.5872	-70.5781	-1.6552
7	3.0136	-0.1467	0.2395	0.7298	-0.1969	0.4013	0.1637	0.2462	-0.4663	-0.1781	-0.0119	-0.0073	0.0964	-0.0676	-0.1293	0.1681	0.0032	-0.0035	0.2113	-0.0165	0.1636	10.618	-67.9181	3.9238
8	0.6929	0.2417	-0.1531	0.3413	0.0387	0.1072	0.0242	0.1531	0.0758	-0.0257	0.0215	-0.001	-0.0273	-0.0368	-0.042	0.1247	0.0075	0.0404	0.1775	0.0382	0.129	14.6933	-55.4497	11.0722
9	2.7347	-0.8713	-0.0565	1.0988	0.5717	0.641	0.0556	0.1301	0.0829	-0.0701	-0.0309	0.0311	-0.0716	-0.0232	-0.0302	0.1261	-0.018	0.0541	0.1527	0.0577	0.1674	23.3197	-45.9209	9.1025
10	0.8935	0.3055	0.136	0.7593	-0.0981	0.4595	-0.011	-0.009	-0.1514	0.0433	-0.0096	-0.1756	-0.0051	0.087	0.0078	0.0986	-0.0083	0.0016	0.1443	0.0215	0.1318	70.5466	-74.4102	15.5403
11	1.316	-0.1569	-0.3825	0.158	-0.2337	1.4995	0.0301	0.0824	0.0526	-0.0996	-0.0829	-0.3255	-0.1934	0.309	0.0852	0.14	-0.0095	0.0351	0.192	0.0268	0.2391	84.0005	-69.8493	4.0583
12	3.8105	1.6595	-0.6377	0.9258	0.0505	1.305	0.0093	-0.005	-0.1253	0.0002	-0.0683	-0.4642	0.0822	0.3644	0.0445	0.1179	0.0449	0.0099	0.2733	0.0841	0.3888	89.0767	-79.7027	11.2268
13	0.487	-0.214	-0.2729	1.8616	-0.0882	0.3063	-0.009	0.0163	-0.0416	-0.0118	-0.0303	-0.2449	0.009	0.0848	0.0361	0.1059	-0.0074	0.0057	0.1734	0.0167	0.1623	78.7713	-65.934	4.9301
14	1.523	0.0739	-0.2787	1.1246	-0.2405	0.5231	-0.0272	0.244	0.0392	-0.1755	0.0284	-0.0841	0.008	0.0094	-0.0029	0.1556	-0.0123	0.0359	0.1668	-0.0055	0.0896	69.3776	-66.8163	-7.4621
15	1.5394	-0.1414	-0.6634	0.6232	0.0168	0.8106	0.1036	0.1767	0.1706	-0.1757	0.0114	-0.085	-0.0811	-0.0377	-0.1089	0.1596	-0.0118	0.024	0.1354	0.01	0.1205	61.0209	-66.6214	-4.8499
16	0.5126	0.261	-0.1147	0.5111	-0.2774	0.4564	-0.0491	0.0492	-0.088	-0.078	0.0068	-0.0869	0.0364	-0.0075	0.0463	0.1136	-0.0056	0.0045	0.1198	-0.0217	0.1255	57.5115	-80.8254	6.2676

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:72 )	A	1 - 72
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 73:111 )	A	73 - 111
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 112:140 )	A	112 - 140
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 141:228 )	A	141 - 228
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 229:274 )	A	229 - 274
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 275:309 )	A	275 - 309
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 310:346 )	A	310 - 346
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 347:456 )	A	347 - 456
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 457:489 )	A	457 - 489
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 1:72 )	B	1 - 72
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 73:111 )	B	73 - 111
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 112:140 )	B	112 - 140
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 141:228 )	B	141 - 228
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 229:285 )	B	229 - 285
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 286:364 )	B	286 - 364
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 365:489 )	B	365 - 489

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