PDB-5kbp: The crystal structure of an alpha-mannosidase from Enterococcus f...

ID or keywords:

Entry

Database: PDB / ID: 5kbp

Title

The crystal structure of an alpha-mannosidase from Enterococcus faecalis V583

Components

Glycosyl hydrolase, family 38

Keywords

HYDROLASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

alpha-mannosidase activity / mannose metabolic process / carbohydrate binding / metal ion binding
Similarity search - Function

Biological species

Enterococcus faecalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.4 Å

Authors

Tan, K. / Chhor, G. / Jedrzejczak, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The crystal structure of an alpha-mannosidase from Enterococcus faecalis V583
Authors: Tan, K. / Chhor, G. / Jedrzejczak, R. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Jun 3, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 13, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5kbp.cif.gz	715.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5kbp.ent.gz	591.2 KB	Display	PDB format
PDBx/mmJSON format	5kbp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5kbp_validation.pdf.gz	456.8 KB	Display	wwPDB validaton report
Full document	5kbp_full_validation.pdf.gz	466.3 KB	Display
Data in XML	5kbp_validation.xml.gz	60.2 KB	Display
Data in CIF	5kbp_validation.cif.gz	83 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kb/5kbp ftp://data.pdbj.org/pub/pdb/validation_reports/kb/5kbp	HTTPS FTP

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Related structure data

Similar structure data	2wyi-d 4nca-d 5gq9-d 20553 3hvr-d 5xq2-d 6pzk-d 4ncb-d 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: CSGID-IDP56691

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (14) #198 - Jun 2016 Beta-galactosidase similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Glycosyl hydrolase, family 38

B: Glycosyl hydrolase, family 38

hetero molecules

208 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)	127.834, 127.834, 223.716
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-1091- HOH

#1: Protein	Glycosyl hydrolase, family 38 Mass: 102659.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria) Strain: ATCC 700802 / V583 / Gene: EF_1707 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q834E8
#2: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.57 Å³/Da / Density % sol: 52.16 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 Li2SO4, 0.1M Tris:HCl, 2.0M (NH4)2SO4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2013
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97924 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. obs: 83104 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / R_merge(I) obs: 0.077 / Net I/σ(I): 26.1
Reflection shell	Resolution: 2.4→2.44 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.704 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	dev_2386	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Resolution: 2.4→50 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.51

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2315	4144	4.99 %	random
R_work	0.1867	-	-	-
obs	0.1889	83021	99.51 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.4→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14105	0	120	265	14490

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	14556
X-RAY DIFFRACTION	f_angle_d	0.465	19822
X-RAY DIFFRACTION	f_dihedral_angle_d	16.775	8606
X-RAY DIFFRACTION	f_chiral_restr	0.041	2154
X-RAY DIFFRACTION	f_plane_restr	0.003	2581

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 (%)
2.4-2.4258	0.3692	146	0.2866	2573	X-RAY DIFFRACTION	100
2.4258-2.4543	0.366	124	0.284	2640	X-RAY DIFFRACTION	100
2.4543-2.4843	0.3518	111	0.2772	2603	X-RAY DIFFRACTION	100
2.4843-2.5157	0.3236	152	0.2821	2615	X-RAY DIFFRACTION	100
2.5157-2.5488	0.3744	142	0.2769	2624	X-RAY DIFFRACTION	100
2.5488-2.5837	0.3072	109	0.2603	2622	X-RAY DIFFRACTION	100
2.5837-2.6206	0.3149	112	0.2595	2628	X-RAY DIFFRACTION	100
2.6206-2.6598	0.3839	127	0.2567	2626	X-RAY DIFFRACTION	100
2.6598-2.7013	0.3067	134	0.2545	2603	X-RAY DIFFRACTION	100
2.7013-2.7456	0.306	148	0.2492	2602	X-RAY DIFFRACTION	100
2.7456-2.7929	0.3263	157	0.2524	2633	X-RAY DIFFRACTION	100
2.7929-2.8437	0.3495	127	0.2533	2628	X-RAY DIFFRACTION	100
2.8437-2.8984	0.3172	137	0.2534	2618	X-RAY DIFFRACTION	100
2.8984-2.9576	0.318	139	0.2503	2614	X-RAY DIFFRACTION	100
2.9576-3.0219	0.3203	160	0.2529	2589	X-RAY DIFFRACTION	100
3.0219-3.0921	0.2983	134	0.2557	2614	X-RAY DIFFRACTION	100
3.0921-3.1695	0.2982	148	0.2407	2634	X-RAY DIFFRACTION	100
3.1695-3.2551	0.2881	134	0.2255	2617	X-RAY DIFFRACTION	100
3.2551-3.3509	0.2661	142	0.2035	2674	X-RAY DIFFRACTION	100
3.3509-3.459	0.2521	132	0.1935	2586	X-RAY DIFFRACTION	99
3.459-3.5826	0.25	146	0.1788	2637	X-RAY DIFFRACTION	100
3.5826-3.726	0.2176	140	0.1696	2618	X-RAY DIFFRACTION	99
3.726-3.8956	0.1851	144	0.1503	2646	X-RAY DIFFRACTION	100
3.8956-4.1008	0.1745	139	0.1404	2629	X-RAY DIFFRACTION	99
4.1008-4.3576	0.159	138	0.134	2614	X-RAY DIFFRACTION	99
4.3576-4.6939	0.1638	146	0.128	2623	X-RAY DIFFRACTION	99
4.6939-5.1658	0.1472	139	0.1277	2657	X-RAY DIFFRACTION	99
5.1658-5.9123	0.2042	126	0.1533	2695	X-RAY DIFFRACTION	99
5.9123-7.4449	0.1771	177	0.1759	2695	X-RAY DIFFRACTION	100
7.4449-50	0.2015	134	0.1624	2720	X-RAY DIFFRACTION	95

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	1.6868	0.6458	-0.2458	1.9246	0.1133	1.8248	-0.0026	-0.2193	-0.0783	0.0203	-0.0105	-0.0441	0.1413	0.1566	0.0043	0.4153	0.0373	-0.0206	0.3365	0.0142	0.3218	52.2905	-7.9748	45.789
2	3.4445	1.5364	4.4019	1.7417	1.766	7.2251	0.0281	-0.4389	-0.0332	0.2016	-0.1179	0.2729	0.1055	-0.5512	0.0718	0.5057	0.0142	0.0604	0.3406	0.0183	0.4059	38.8554	-11.9851	58.0298
3	0.5309	0.1441	0.1927	1.0047	0.001	0.6933	0.0171	0.143	-0.0282	-0.2769	-0.0128	0.2651	0.0495	-0.1264	-0.0022	0.474	0.0393	-0.1397	0.3733	-0.0121	0.4068	30.7129	4.5771	22.7187
4	2.9264	0.8297	0.4392	2.5793	0.6018	0.6955	-0.0126	0.2758	-0.3558	-0.2473	0.1508	-0.0764	0.1147	0.1441	-0.1192	0.6307	0.0702	-0.0492	0.4142	-0.0327	0.3628	67.9342	-3.644	17.5806
5	2.0415	0.5389	0.7081	2.4214	1.1728	2.1288	-0.059	0.7647	-0.2054	-0.6897	0.2774	-0.3721	-0.0403	0.2357	-0.2138	0.7338	0.0972	0.0824	0.6818	-0.0823	0.4475	81.0441	3.3461	9.8994
6	1.5359	0.2132	0.5291	1.6434	-0.1326	1.4748	0.1303	0.2192	0.012	-0.1468	-0.0764	-0.0337	0.0634	0.1222	-0.0522	0.4587	0.0696	-0.0078	0.3329	0.0003	0.3106	67.218	14.2671	33.218
7	2.6086	-0.0106	-0.3963	1.0527	0.003	0.3944	-0.0493	-0.3408	0.1285	0.2088	0.0746	0.0276	0.0379	-0.1275	-0.0203	0.665	-0.0009	-0.0642	0.4644	0.0385	0.2875	61.4782	24.8678	60.1566
8	1.0378	0.1576	0.6784	1.6774	0.7787	1.1266	-0.0337	0.1233	0.1193	-0.1479	-0.0066	-0.0776	-0.0547	-0.0403	0.0416	0.4562	0.0333	0.0287	0.3384	0.0794	0.2595	66.3126	36.9177	25.1462
9	1.0432	-0.0303	-0.0568	1.0724	-0.3969	1.2799	0.0329	-0.0335	0.0219	0.0765	-0.0621	-0.2518	-0.1104	0.1137	0.0262	0.4176	-0.0045	-0.0808	0.2931	-0.0216	0.3167	83.6703	18.7488	41.8486

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 114 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 115 through 279 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 280 through 895 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 3 through 96 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 97 through 279 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 280 through 390 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 391 through 508 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 509 through 768 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 769 through 895 )

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