PDB-2w5v: Structure of TAB5 alkaline phosphatase mutant His 135 Asp with Mg...

ID or keywords:

Entry

Database: PDB / ID: 2w5v

Title

Structure of TAB5 alkaline phosphatase mutant His 135 Asp with Mg 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 / OTHER / Resolution: 1.78 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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Download

PDBx/mmCIF format	2w5v.cif.gz	279.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2w5v.ent.gz	236.4 KB	Display	PDB format
PDBx/mmJSON format	2w5v.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/w5/2w5v ftp://data.pdbj.org/pub/pdb/validation_reports/w5/2w5v	HTTPS FTP

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Related structure data

Related structure data	2w5wC 2w5xC 2iuc C: citing same article (ref.)
Similar structure data	2w5x-d 4xug-d 4hpx-d 1tjp-d 1c29-d 1c8v-d 2clk-d 2bu1-d 1afs-d 5y7p-4 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)	70.320, 173.020, 54.970
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-2054- HOH
2	1	A-2055- 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 OCCUPIED BY ZN, M3 BY MG. 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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.07 Å³/Da / Density % sol: 40.57 % / 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: 1.2869
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2869 Å / Relative weight: 1
Reflection	Resolution: 1.78→46.37 Å / Num. obs: 121795 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 7 % / B_iso Wilson estimate: 17.69 Å² / R_merge(I) obs: 0.13 / Net I/σ(I): 10.7

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Processing

Software

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

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 1.78→46.4 Å / SU ML: 0.22 / σ(F): 0.01 / Phase error: 20.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.199	3577	3.2 %
R_work	0.159	-	-
obs	0.161	111690	90.4 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 54.59 Å² / k_sol: 0.36 e/Å³

Displacement parameters

B_iso mean: 26.74 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.8882 Å²	-0 Å²	0 Å²
2-	-	-1.3827 Å²	-0 Å²
3-	-	-	5.0578 Å²

Refinement step

Cycle: LAST / Resolution: 1.78→46.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5242	0	8	589	5839

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5336
X-RAY DIFFRACTION	f_angle_d	1.021	7218
X-RAY DIFFRACTION	f_dihedral_angle_d	16.693	1868
X-RAY DIFFRACTION	f_chiral_restr	0.075	822
X-RAY DIFFRACTION	f_plane_restr	0.003	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 (%)
1.7828-1.8062	0.299	79	0.3778	2445	X-RAY DIFFRACTION	53
1.8062-1.831	0.3842	112	0.3289	3445	X-RAY DIFFRACTION	74
1.831-1.8571	0.3358	123	0.3069	3507	X-RAY DIFFRACTION	77
1.8571-1.8849	0.3363	132	0.2829	3633	X-RAY DIFFRACTION	79
1.8849-1.9143	0.2791	126	0.254	3750	X-RAY DIFFRACTION	82
1.9143-1.9457	0.2913	134	0.237	3952	X-RAY DIFFRACTION	84
1.9457-1.9792	0.261	126	0.2232	3876	X-RAY DIFFRACTION	85
1.9792-2.0152	0.2481	128	0.2126	4023	X-RAY DIFFRACTION	88
2.0152-2.054	0.2538	148	0.199	4106	X-RAY DIFFRACTION	90
2.054-2.0959	0.2177	138	0.1884	4156	X-RAY DIFFRACTION	90
2.0959-2.1415	0.1976	143	0.174	4243	X-RAY DIFFRACTION	92
2.1415-2.1913	0.2255	140	0.1659	4347	X-RAY DIFFRACTION	94
2.1913-2.2461	0.2117	145	0.1577	4288	X-RAY DIFFRACTION	94
2.2461-2.3068	0.1777	140	0.1567	4331	X-RAY DIFFRACTION	94
2.3068-2.3747	0.2316	139	0.1495	4402	X-RAY DIFFRACTION	96
2.3747-2.4514	0.2079	144	0.1546	4370	X-RAY DIFFRACTION	96
2.4514-2.539	0.1648	148	0.1536	4447	X-RAY DIFFRACTION	96
2.539-2.6406	0.2283	152	0.152	4490	X-RAY DIFFRACTION	97
2.6406-2.7608	0.2191	141	0.154	4492	X-RAY DIFFRACTION	97
2.7608-2.9063	0.2018	146	0.16	4530	X-RAY DIFFRACTION	98
2.9063-3.0884	0.221	149	0.1568	4519	X-RAY DIFFRACTION	98
3.0884-3.3268	0.1591	153	0.1477	4539	X-RAY DIFFRACTION	99
3.3268-3.6614	0.1617	152	0.1215	4589	X-RAY DIFFRACTION	99
3.6614-4.191	0.1532	144	0.1092	4491	X-RAY DIFFRACTION	98
4.191-5.279	0.1214	148	0.1016	4589	X-RAY DIFFRACTION	100
5.279-46.4116	0.1473	147	0.1386	4553	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	0.7867	-0.0322	0.0193	0.269	-0.1415	0.2782	-0.0142	0.1473	-0.0902	0.0299	-0.0582	-0.0163	-0.0452	0.0027	0.0298	0.1294	0.0136	-0.0363	0.1128	0.0022	0.1254	-15.144	27.6228	0.7994
2	0.4679	-0.029	0.0109	0.3329	0.0335	0.3602	0.0612	0.0361	-0.0424	-0.0775	-0.0702	-0.0574	0.0113	0.0624	0.0126	0.1277	0.0359	-0.0095	0.1099	0.0019	0.1546	-4.4301	17.2385	-3.887
3	0.1571	-0.2434	0.0507	0.6261	-0.0468	0.2676	0.057	0.0661	-0.1243	-0.0481	-0.053	-0.2124	0.0974	0.1019	-0.0042	0.1542	0.0246	-0.0206	0.1578	0.0234	0.2317	3.5452	11.9717	4.6763
4	0.7629	-0.1646	0.0812	0.47	-0.0597	0.4621	-0.0599	-0.147	-0.2183	0.1313	0.089	-0.2399	0.1038	0.1163	-0.0131	0.1923	0.0199	-0.0656	0.2032	0.0275	0.2781	7.1703	10.0117	15.7381
5	0.3475	0.0929	0.3383	0.4243	0.0579	0.4532	0.007	-0.1007	-0.0584	0.1769	-0.046	-0.127	-0.0582	-0.0234	0.0274	0.1512	-0.0065	-0.0446	0.1494	0.0209	0.1568	-0.7224	24.2619	16.4004
6	0.2862	-0.1238	0.0986	0.1893	0.1438	0.3506	0.0194	-0.0559	-0.0814	0.048	-0.0292	-0.016	-0.0306	-0.0043	0.0106	0.127	0.0074	-0.0275	0.1053	-0.0016	0.1418	-12.7948	23.6359	5.1912
7	0.2913	-0.2898	-0.0636	0.1041	-0.0521	0.6645	-0.1229	-0.1052	-0.276	0.113	-0.1222	0.3266	0.4369	0.1351	0.1509	0.2134	-0.0381	0.09	0.1416	0.0189	0.3538	-45.4973	10.6009	7.6637
8	0.5352	-0.3271	0.4038	0.3089	0.068	0.4502	0.032	0.1059	-0.0333	-0.008	-0.0359	-0.022	0.0222	0.0585	0.0016	0.1375	0.0303	-0.0035	0.1135	-0.0096	0.1305	-13.3501	23.1593	-6.3119
9	0.4066	-0.1065	0.0703	0.1497	-0.0757	0.1696	0.0918	0.1548	-0.0777	-0.1427	-0.034	0.0611	0.0346	-0.042	-0.0201	0.1769	0.0641	-0.0281	0.1733	-0.0337	0.12	-26.4191	24.7657	-18.0404
10	0.3095	-0.1773	0.0637	0.3668	-0.0827	0.3011	0.1005	0.0751	-0.0082	-0.0484	-0.0494	0.0729	-0.0122	-0.0729	-0.0301	0.1107	0.0452	-0.0143	0.1291	-0.0196	0.1021	-38.9241	31.8857	-11.7516
11	0.5681	-0.118	0.0144	0.2302	-0.2087	0.2617	0.0576	0.2469	-0.1776	-0.1184	-0.0052	0.1452	0.0582	-0.2488	-0.0494	0.1443	0.0508	-0.0439	0.2348	-0.0239	0.1678	-50.4473	30.5423	-17.1119
12	0.1944	-0.104	0.4097	0.4091	0.0543	0.8789	0.1136	0.1714	-0.0553	-0.2107	-0.065	0.1366	0.1165	-0.608	-0.0044	0.1689	0.0606	-0.0967	0.4712	-0.0817	0.1811	-57.8723	25.2337	-24.5201
13	1.0853	-0.1909	0.1583	0.8153	0.4282	0.1425	0.2325	0.5468	-0.2048	-0.3778	-0.2028	0.1199	0.0811	-0.0276	0.0104	0.2222	0.1306	-0.0893	0.3465	-0.0992	0.1355	-43.1264	24.3859	-31.6351
14	0.7108	-0.1067	-0.129	0.2382	0.1127	-0.1116	0.1037	0.258	-0.1015	-0.1373	-0.0702	0.0218	0.0176	-0.0113	-0.0267	0.1779	0.0588	-0.0377	0.2018	-0.0384	0.1276	-32.2078	22.4375	-19.3966
15	0.2132	0.0004	-0.0057	-0.0721	-0.0496	0.044	-0.3303	-0.1215	-0.4407	-0.1563	0.1027	0.173	0.4315	0.024	0.2152	0.3398	0.0218	0.1035	0.0776	0.0495	0.4933	-21.0406	-7.1858	-3.1078
16	0.4569	0.0274	-0.0274	0.0976	-0.095	0.1943	0.08	0.1204	-0.0591	-0.0256	-0.0631	0.0337	-0.0258	-0.036	-0.0216	0.1352	0.036	-0.0187	0.117	-0.0207	0.1211	-28.3584	29.0707	-10.7545

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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