PDB-2w5w: Structure of TAB5 alkaline phosphatase mutant His 135 Asp with Zn...

ID or keywords:

Entry

Database: PDB / ID: 2w5w

Title

Structure of TAB5 alkaline phosphatase mutant His 135 Asp with Zn bound in the M3 site.

Components

ALKALINE PHOSPHATASE

Keywords

HYDROLASE /

PSYCHROPHILES / COLD ADAPTATION /

ALKALINE PHOSPHATASE

Function / homology

Function and homology information

phosphatase activity /

metal ion binding
Similarity search - Function

Biological species

ANTARCTIC BACTERIUM TAB5 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.79 Å

Authors

Koutsioulis, D. / Lyskowski, A. / Maki, S. / Guthrie, E. / Feller, G. / Bouriotis, V. / Heikinheimo, P.

Citation

Journal: Protein Sci. / Year: 2010
Title: Coordination Sphere of the Third Metal Site is Essential to the Activity and Metal Selectivity of Alkaline Phosphatases.
Authors: Koutsioulis, D. / Lyskowski, A. / Maki, S. / Guthrie, E. / Feller, G. / Bouriotis, V. / Heikinheimo, P.

History

Deposition	Dec 15, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 24, 2009	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2w5w.cif.gz	286.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2w5w.ent.gz	242.2 KB	Display	PDB format
PDBx/mmJSON format	2w5w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w5/2w5w ftp://data.pdbj.org/pub/pdb/validation_reports/w5/2w5w	HTTPS FTP

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Related structure data

Related structure data	2w5vC 2w5xC 2iuc C: citing same article (ref.)
Similar structure data	5udk-d 2w5x-d 5y7p-3 4e5y-2 5gk5-4 3ehe-d 6i1f-d 5c1w-d 5y7p-1 4c7x-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
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (1) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: ALKALINE PHOSPHATASE

B: ALKALINE PHOSPHATASE

hetero molecules

81.3 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)	70.110, 173.320, 55.190
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-2083- HOH
2	1	A-2109- HOH
3	1	A-2134- HOH
4	1	A-2243- HOH
5	1	B-2191- HOH

#1: Protein	ALKALINE PHOSPHATASE / / TAB5 ALKALINE PHOSPHATASE MUTANT Mass: 40470.328 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: PHOSPHOSERINE RESIDUE AT POSITION 84. M1, M2, M3 OCCUPIED BY ZN. Source: (gene. exp.) ANTARCTIC BACTERIUM TAB5 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9KWY4, alkaline phosphatase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 971 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, HIS 135 TO ASP ENGINEERED RESIDUE IN CHAIN B, HIS 135 TO ASP

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.74 % / Description: NONE
Crystal grow	Details: 20.00MM TRIS-CL PH8.0, 10.00MM MGCL2, 0.01MM ZNCL2, 23.00% PEG 3350, 0.20MM SODIUM ACETATE, 0.10MM SODIUM CACODYLATE, PH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.28224
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.28224 Å / Relative weight: 1
Reflection	Resolution: 1.69→46.57 Å / Num. obs: 145415 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / B_iso Wilson estimate: 13.5 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 13.3

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.79→43.33 Å / SU ML: 0.16 / σ(F): 0.02 / Phase error: 15.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.17	1861	1.6 %
R_work	0.14	-	-
obs	0.14	118325	96.6 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 54.07 Å² / k_sol: 0.35 e/Å³

Displacement parameters

B_iso mean: 22.46 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.79→43.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5242	0	6	971	6219

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5336
X-RAY DIFFRACTION	f_angle_d	1.147	7218
X-RAY DIFFRACTION	f_dihedral_angle_d	16.944	1868
X-RAY DIFFRACTION	f_chiral_restr	0.088	822
X-RAY DIFFRACTION	f_plane_restr	0.004	932

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 (%)
1.79-1.8384	0.2342	130	0.204	8281	X-RAY DIFFRACTION	89
1.8384-1.8925	0.1957	137	0.1847	8462	X-RAY DIFFRACTION	91
1.8925-1.9536	0.1995	135	0.1703	8662	X-RAY DIFFRACTION	94
1.9536-2.0234	0.1648	147	0.151	8832	X-RAY DIFFRACTION	95
2.0234-2.1044	0.1534	148	0.1402	8921	X-RAY DIFFRACTION	97
2.1044-2.2002	0.1775	143	0.1325	9040	X-RAY DIFFRACTION	97
2.2002-2.3162	0.149	148	0.1324	9070	X-RAY DIFFRACTION	98
2.3162-2.4613	0.1689	143	0.125	9098	X-RAY DIFFRACTION	98
2.4613-2.6513	0.1557	146	0.1301	9189	X-RAY DIFFRACTION	99
2.6513-2.9181	0.1762	140	0.1331	9251	X-RAY DIFFRACTION	99
2.9181-3.3402	0.1749	149	0.1344	9231	X-RAY DIFFRACTION	100
3.3402-4.2077	0.1471	147	0.1208	9205	X-RAY DIFFRACTION	99
4.2077-43.3427	0.1648	148	0.1331	9222	X-RAY DIFFRACTION	100

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	-0.2866	-0.1551	0.6378	0.1277	-0.0961	0.4943	0.0396	0.0166	-0.0649	0.0308	-0.0654	-0.037	0.0147	-0.0194	0.0305	0.0143	0.0125	-0.0134	0.0719	-0.0016	0.1135	-15.1023	27.714	0.8051
2	0.2868	-0.0527	-0.0195	0.4407	0.0415	0.2527	0.0547	-0.0006	-0.0609	-0.0493	-0.0671	-0.0843	0.0194	0.0594	0.015	0.0296	0.0285	-0.0065	0.0791	0.0107	0.1531	-4.4144	17.2943	-3.8573
3	-1.2569	0.0743	-0.2628	0.6338	-0.0542	0.1789	0.0569	0.0226	-0.0673	0.0078	-0.0927	-0.3446	0.1065	0.1596	0.0546	0.0371	0.0342	-0.0158	0.1173	0.04	0.2394	3.5284	12.0306	4.689
4	-0.5101	0.1107	-0.204	0.5901	-0.126	0.2417	-0.0411	-0.0956	-0.0713	0.1421	-0.0666	-0.4121	0.1135	0.1675	0.107	0.0697	0.0282	-0.0495	0.1372	0.0656	0.2902	7.152	10.056	15.7377
5	-0.8196	0.2574	0.1019	0.7812	-0.1988	0.8272	0.0257	-0.0568	-0.0138	0.1352	-0.0479	-0.1314	-0.045	0.0199	0.0272	0.0499	-0.0013	-0.039	0.1151	0.0354	0.156	-0.7432	24.3147	16.4165
6	-0.1441	-0.1643	0.0428	0.4683	0.0198	0.2667	0.0381	-0.0682	-0.0714	0.0468	-0.041	-0.0272	-0.0058	0.0107	0.0001	0.0065	0.002	-0.0127	0.0715	0.0076	0.1157	-12.777	23.7236	5.2057
7	1.1328	-1.4203	0.1015	-0.0807	1.6764	3.3376	-0.3166	0.1186	-0.2567	0.3428	-0.2455	0.5183	0.3666	0.0659	0.5373	0.1403	-0.0685	0.1615	0.1193	-0.0366	0.3057	-45.5784	10.6938	7.8139
8	-0.0825	-0.2531	0.339	0.6397	-0.0276	0.3918	0.0226	0.0598	-0.079	-0.0329	-0.0621	-0.1014	0.0053	0.0848	0.04	0.008	0.0138	-0.0038	0.0515	-0.005	0.1013	-13.3133	23.2311	-6.2922
9	0.283	-0.2693	0.1046	0.1339	-0.015	0.1852	0.0744	0.1562	-0.1123	-0.0696	-0.0028	0.0157	0.0457	-0.0221	-0.065	0.0512	0.0393	-0.0078	0.1242	-0.0233	0.112	-26.3218	24.863	-18.037
10	0.1954	-0.1498	0.1067	0.2817	-0.0825	0.2035	0.053	0.0105	-0.0288	-0.0046	-0.0233	0.0544	-0.0074	-0.0551	-0.0231	0.0104	0.0274	-0.001	0.1033	-0.0115	0.0917	-38.809	32.0079	-11.7763
11	0.0476	0.1482	-0.146	0.032	-0.0472	0.3008	0.0485	0.1638	-0.0086	-0.0718	-0.0035	0.1641	-0.0127	-0.2324	-0.0464	0.0699	0.042	-0.0284	0.2075	-0.0152	0.1909	-50.3129	30.6335	-17.1769
12	-1.2376	0.1165	0.0884	0.388	0.1352	1.1623	0.0647	0.1167	-0.0166	-0.0818	-0.1008	0.2943	0.0544	-0.6385	0.0296	0.0707	0.0307	-0.0576	0.3574	-0.0508	0.2062	-57.7157	25.1247	-24.5251
13	0.7728	-0.3374	0.2907	0.6977	-0.0409	0.2729	0.1562	0.4108	-0.1404	-0.2641	-0.1108	0.0646	0.1027	0.0378	-0.0349	0.104	0.0828	-0.0475	0.2555	-0.0652	0.1131	-42.9646	24.4682	-31.6443
14	0.3909	-0.0461	-0.0219	0.0875	0.0156	0.1055	0.0898	0.1524	-0.1293	-0.0959	-0.058	0.0531	0.0646	-0.0046	-0.0356	0.0529	0.0417	-0.0196	0.1289	-0.0256	0.1124	-32.0953	22.5289	-19.3723
15	0.5528	-0.0748	-0.2133	-0.5793	-0.4383	0.4794	-0.2374	-0.1426	-0.5234	-1.062	-0.0001	-0.0714	0.8208	-0.0454	0.2488	0.3272	-0.0065	0.0646	0.0587	0.0554	0.5253	-21.0901	-6.9633	-2.8215
16	0.1925	-0.1553	0.0346	0.1296	-0.0429	0.1853	0.0478	0.0904	-0.0326	-0.0324	-0.0412	0.0323	-0.0182	-0.0194	-0.0131	0.0241	0.0226	-0.005	0.0772	0.0001	0.1046	-28.2733	29.179	-10.749

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 30:60)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 61:134)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 135:165)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 166:190)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 191:244)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 245:310)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 311:323)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 324:375)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 30:60)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 61:134)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 135:165)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 166:190)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 191:244)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 245:310)
15	X-RAY DIFFRACTION	15	(CHAIN B AND RESID 311:323)
16	X-RAY DIFFRACTION	16	(CHAIN B AND RESID 324:375)

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