PDB-5lw3: Azotobacter vinelandii Mannuronan C-5 epimerase AlgE6 A-module

ID or keywords:

Entry

Database: PDB / ID: 5lw3

Title

Azotobacter vinelandii Mannuronan C-5 epimerase AlgE6 A-module

Components

Poly(beta-D-mannuronate) C5 epimerase 6

Keywords

ISOMERASE / C-5 Epimerase

Function / homology

Function and homology information

mannuronan 5-epimerase / alginic acid biosynthetic process / isomerase activity / calcium ion binding / extracellular region
Similarity search - Function

Biological species

Azotobacter vinelandii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.19 Å

Authors

Rothweiler, U.

Citation

Journal: To Be Published
Title: Azotobacter vinelandii Mannuronan C-5 epimerase AlgE6 A-module
Authors: Rothweiler, U.

History

Deposition	Sep 15, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 25, 2017	Provider: repository / Type: Initial release
Revision 2.0	Jan 17, 2024	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5lw3.cif.gz	177.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5lw3.ent.gz	140.3 KB	Display	PDB format
PDBx/mmJSON format	5lw3.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5lw3_validation.pdf.gz	730.7 KB	Display	wwPDB validaton report
Full document	5lw3_full_validation.pdf.gz	730.9 KB	Display
Data in XML	5lw3_validation.xml.gz	19.3 KB	Display
Data in CIF	5lw3_validation.cif.gz	30.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lw/5lw3 ftp://data.pdbj.org/pub/pdb/validation_reports/lw/5lw3	HTTPS FTP

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Related structure data

Related structure data	2pygS S: Starting model for refinement
Similar structure data	5ike-d 5kt0-d 1s4m-1 2i1l-2 5lv5-d 6ys9-3 3ajb-d 2pyg-2 1g55-d 7mhg-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Poly(beta-D-mannuronate) C5 epimerase 6

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	100.884, 63.672, 73.075
Angle α, β, γ (deg.)	90.00, 97.16, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-728- HOH
2	1	A-845- HOH

#1: Protein	Poly(beta-D-mannuronate) C5 epimerase 6 / Mannuronan epimerase 6 Mass: 40795.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: algE6 / Production host: Escherichia coli (E. coli) / Strain (production host): NEBs ER2566 cells References: UniProt: Q9ZFH0, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₂₆N₂O₆ / Comment: pH buffer*YM
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.85 Å³/Da / Density % sol: 56.9 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 100 mM BisTrisPropane pH 9.5, 15-30% PEG 8000 / Temp details: room temperature

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 1, 2015 / Details: KB mirror
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 1.19→44.617 Å / Num. obs: 146496 / % possible obs: 99.8 % / Redundancy: 4.5 % / R_rim(I) all: 0.063 / Net I/σ(I): 12.31
Reflection shell	Resolution: 1.19→1.23 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.685 / Mean I/σ(I) obs: 1.8 / R_rim(I) all: 0.78 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2pyg

2pyg

Resolution: 1.19→44.617 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.82

	R_factor	Num. reflection	% reflection
R_free	0.1603	7332	5 %
R_work	0.1438	-	-
obs	0.1446	146497	99.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.19→44.617 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2823	0	21	427	3271

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	3040
X-RAY DIFFRACTION	f_angle_d	1.62	4169
X-RAY DIFFRACTION	f_dihedral_angle_d	12.611	1095
X-RAY DIFFRACTION	f_chiral_restr	0.083	461
X-RAY DIFFRACTION	f_plane_restr	0.008	579

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 (%)
1.19-1.2035	0.2407	231	0.2628	4594	X-RAY DIFFRACTION	100
1.2035-1.2177	0.2752	234	0.2512	4688	X-RAY DIFFRACTION	100
1.2177-1.2325	0.2483	236	0.2404	4556	X-RAY DIFFRACTION	100
1.2325-1.2481	0.2265	271	0.2323	4613	X-RAY DIFFRACTION	100
1.2481-1.2646	0.2339	242	0.2151	4619	X-RAY DIFFRACTION	100
1.2646-1.2819	0.2223	246	0.2094	4607	X-RAY DIFFRACTION	100
1.2819-1.3002	0.2112	233	0.1993	4658	X-RAY DIFFRACTION	100
1.3002-1.3196	0.2211	259	0.1992	4603	X-RAY DIFFRACTION	100
1.3196-1.3402	0.2061	224	0.1957	4614	X-RAY DIFFRACTION	100
1.3402-1.3622	0.1868	247	0.1911	4630	X-RAY DIFFRACTION	100
1.3622-1.3857	0.2069	241	0.1814	4648	X-RAY DIFFRACTION	100
1.3857-1.4109	0.1911	224	0.1791	4634	X-RAY DIFFRACTION	100
1.4109-1.438	0.1916	260	0.1696	4612	X-RAY DIFFRACTION	100
1.438-1.4674	0.1909	234	0.1622	4604	X-RAY DIFFRACTION	100
1.4674-1.4993	0.1772	262	0.1528	4632	X-RAY DIFFRACTION	100
1.4993-1.5342	0.1569	245	0.1459	4629	X-RAY DIFFRACTION	100
1.5342-1.5725	0.1707	232	0.139	4661	X-RAY DIFFRACTION	100
1.5725-1.6151	0.1517	229	0.128	4646	X-RAY DIFFRACTION	100
1.6151-1.6626	0.1304	239	0.1291	4654	X-RAY DIFFRACTION	100
1.6626-1.7163	0.1676	244	0.1268	4625	X-RAY DIFFRACTION	100
1.7163-1.7776	0.1577	243	0.1305	4639	X-RAY DIFFRACTION	100
1.7776-1.8488	0.1503	266	0.1276	4595	X-RAY DIFFRACTION	100
1.8488-1.9329	0.1614	254	0.1282	4670	X-RAY DIFFRACTION	100
1.9329-2.0348	0.1503	244	0.1296	4671	X-RAY DIFFRACTION	100
2.0348-2.1623	0.1385	238	0.1324	4629	X-RAY DIFFRACTION	100
2.1623-2.3293	0.1373	252	0.1279	4642	X-RAY DIFFRACTION	100
2.3293-2.5636	0.1664	250	0.1355	4682	X-RAY DIFFRACTION	100
2.5636-2.9345	0.1579	263	0.1438	4653	X-RAY DIFFRACTION	100
2.9345-3.6969	0.1448	238	0.1308	4704	X-RAY DIFFRACTION	100
3.6969-44.6486	0.1342	251	0.1256	4753	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	0.9066	-0.5906	0.3709	1.4268	-0.5046	1.7423	-0.0601	0.0476	0.0443	-0.0057	0.0798	0.049	-0.2115	-0.2174	-0.0222	0.1512	0.044	0.0049	0.1561	0.0234	0.0837	21.0325	19.4811	0.8792
2	0.9497	-0.3373	0.4146	1.2029	-0.5986	1.9198	-0.0643	-0.0501	0.1135	0.1204	0.0647	-0.0598	-0.2784	-0.1459	-0.0334	0.1345	0.0396	0.003	0.1089	0.0078	0.0662	26.7335	16.6304	10.6904
3	2.7526	-0.1953	-0.4113	1.3569	-0.7008	2.1998	-0.03	-0.0084	0.0661	0.0059	-0.0103	-0.1059	-0.1105	-0.016	0.0405	0.097	0.0146	0.0069	0.0863	0.0149	0.0716	30.879	10.4306	8.9937
4	1.0701	-0.3998	0.367	1.3117	-0.4567	2.169	-0.0688	-0.1149	0.0292	0.1389	0.0784	0.0497	-0.2129	-0.2768	0.041	0.106	0.0365	0.0091	0.1352	0.0095	0.0645	24.6137	8.086	17.3468
5	0.6241	-0.2466	0.0155	0.9045	-0.2241	1.3739	-0.0402	-0.03	0.0001	0.0411	0.0468	0.0305	-0.0091	-0.1609	0.0037	0.0795	0.0071	0.0053	0.1113	-0.0044	0.062	28.4306	-1.1188	19.8684
6	2.0445	0.6084	1.0258	2.9631	2.0309	3.8022	-0.0946	-0.1805	0.1303	0.0514	0.0242	0.0536	-0.2007	-0.189	0.0975	0.1041	0.0329	-0.0138	0.0927	0.0358	0.0582	29.3267	-1.2728	29.0611
7	1.2128	-0.4991	-0.0531	0.9928	-0.0137	1.9905	-0.0184	-0.0074	-0.0294	-0.05	0.0312	-0.0094	0.0663	-0.0858	-0.0072	0.0844	-0.0097	0.0029	0.0845	0.0029	0.063	32.8283	-13.0285	26.4214
8	0.8457	0.1954	0.6123	1.4256	0.0998	1.2502	-0.0408	-0.087	-0.0167	0.0597	0.0099	-0.0273	0.0219	-0.1144	0.0295	0.0973	-0.0003	0.0039	0.1073	0.0061	0.0825	36.8141	-12.9193	36.2602
9	1.7452	1.0539	0.936	2.0641	0.9685	1.6926	0.0618	-0.0395	-0.2425	0.0195	0.0716	-0.1124	0.3736	-0.0575	-0.089	0.166	-0.0342	-0.0083	0.1102	0.0295	0.123	33.2205	-26.8264	34.7836

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 46 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 47 through 99 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 100 through 123 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 124 through 168 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 169 through 225 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 226 through 245 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 246 through 301 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 302 through 350 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 351 through 382 )

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