PDB-4uek: Galactitol-1-phosphate 5-dehydrogenase from E. coli with Tris wit...

ID or keywords:

Entry

Database: PDB / ID: 4uek

Title

Galactitol-1-phosphate 5-dehydrogenase from E. coli with Tris within the active site.

Components

GALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE

Keywords

OXIDOREDUCTASE

Function / homology

Function and homology information

galactitol-1-phosphate 5-dehydrogenase /

galactitol-1-phosphate 5-dehydrogenase activity / galactitol catabolic process / protein homodimerization activity / zinc ion binding / identical protein binding /

cytosol
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Benavente, R. / Esteban-Torres, M. / Kohring, G.W. / Cortes-Cabrera, A. / Gago, F. / Acebron, I. / de las Rivas, B. / Munoz, R. / Mancheno, J.M.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Enantioselective Oxidation of Galactitol 1-Phosphate by Galactitol-1-Phosphate 5-Dehydrogenase from Escherichia Coli
Authors: Benavente, R. / Esteban-Torres, M. / Kohring, G.W. / Cortes-Cabrera, A. / Sanchez-Murcia, P.A. / Gago, F. / Acebron, I. / De Las Rivas, B. / Munoz, R. / Mancheno, J.M.

History

Deposition	Dec 18, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 15, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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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PDBx/mmCIF format	4uek.cif.gz	284 KB	Display	PDBx/mmCIF format
PDB format	pdb4uek.ent.gz	229.8 KB	Display	PDB format
PDBx/mmJSON format	4uek.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ue/4uek ftp://data.pdbj.org/pub/pdb/validation_reports/ue/4uek	HTTPS FTP

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Related structure data

Related structure data	4uejC 4ueoC 4a2cS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2dq4-d 4uej-d 4cpd-2 6dkj-1 2ejv-d 6ddr-d 2vwp-1 5cdt-d 1mg0-1 4oaq-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	#13 - Jan 2001 Alcohol Dehydrogenase similarity (9) #32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: GALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE

B: GALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE

hetero molecules

75.4 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)	65.568, 78.896, 68.572
Angle α, β, γ (deg.)	90.00, 94.59, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	GALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE / Mass: 37430.066 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P0A9S3, galactitol-1-phosphate 5-dehydrogenase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.2 Å³/Da / Density % sol: 45 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.2814
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2814 Å / Relative weight: 1
Reflection	Resolution: 1.9→45.45 Å / Num. obs: 49264 / % possible obs: 89.7 % / Redundancy: 6.1 % / B_iso Wilson estimate: 18.04 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 7.9
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / % possible all: 89.7

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A2C

4a2c

Resolution: 1.9→45.455 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 32.11 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2577	2487	5.1 %
R_work	0.2018	-	-
obs	0.2047	49078	89.31 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.9→45.455 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5254	0	21	471	5746

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5396
X-RAY DIFFRACTION	f_angle_d	1.159	7322
X-RAY DIFFRACTION	f_dihedral_angle_d	13.869	1970
X-RAY DIFFRACTION	f_chiral_restr	0.046	840
X-RAY DIFFRACTION	f_plane_restr	0.006	944

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 (%)
1.9-1.9365	0.2824	77	0.2337	1363	X-RAY DIFFRACTION	47
1.9365-1.9761	0.2911	77	0.2367	1610	X-RAY DIFFRACTION	56
1.9761-2.019	0.3166	97	0.2396	1852	X-RAY DIFFRACTION	65
2.019-2.066	0.3008	115	0.2429	2095	X-RAY DIFFRACTION	73
2.066-2.1177	0.2618	120	0.2333	2399	X-RAY DIFFRACTION	83
2.1177-2.1749	0.328	140	0.222	2651	X-RAY DIFFRACTION	92
2.1749-2.2389	0.2644	136	0.2077	2862	X-RAY DIFFRACTION	100
2.2389-2.3112	0.2755	155	0.2007	2876	X-RAY DIFFRACTION	100
2.3112-2.3938	0.2389	136	0.2042	2917	X-RAY DIFFRACTION	99
2.3938-2.4896	0.2646	146	0.2151	2832	X-RAY DIFFRACTION	99
2.4896-2.6029	0.2724	162	0.2126	2881	X-RAY DIFFRACTION	99
2.6029-2.7401	0.2769	173	0.2146	2897	X-RAY DIFFRACTION	100
2.7401-2.9118	0.2777	153	0.2183	2858	X-RAY DIFFRACTION	100
2.9118-3.1366	0.3158	148	0.2173	2891	X-RAY DIFFRACTION	99
3.1366-3.4521	0.2206	170	0.201	2876	X-RAY DIFFRACTION	100
3.4521-3.9514	0.2572	152	0.1819	2887	X-RAY DIFFRACTION	99
3.9514-4.9774	0.2145	151	0.1601	2914	X-RAY DIFFRACTION	100
4.9774-45.4677	0.2204	179	0.1904	2930	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	0.6828	-0.8801	0.9568	3.1267	-2.0154	3.0831	0.0626	0.0692	-0.2352	-0.2256	0.0522	0.2185	0.3749	0.0588	-0.1297	0.1307	0.0162	0.0279	0.1455	-0.0044	0.1577	28.5982	-6.6928	2.022
2	2.5648	-0.4324	-0.4021	0.553	0.0748	1.4838	0.0447	-0.0644	0.0303	0.0392	-0.0442	0.0583	-0.0406	0.0406	-0.0157	0.1234	0.0022	-0.0056	0.1201	0.0073	0.072	21.0808	3.5765	5.0837
3	0.6272	0.36	-0.0766	0.099	0.1188	2.8992	0.0183	-0.0548	0.0345	-0.0406	-0.0222	0.0228	-0.079	0.1279	0.0023	0.0838	0.0289	0.0073	0.1015	0.0172	0.1213	25.8043	4.1196	18.2105
4	5.9788	4.5733	-1.4818	6.8187	-4.3222	5.2865	0.1571	-0.2859	-0.4137	0.0864	-0.1315	0.0162	0.0243	0.2769	-0.0052	0.1175	0.0671	0.0111	0.3196	0.0474	0.1798	32.9043	-4.6318	36.5299
5	2.5151	0.4056	0.0578	2.3122	0.6075	1.6548	0.0678	-0.2173	-0.3097	0.1165	-0.0369	-0.0261	0.1583	0.0751	-0.0422	0.1027	0.021	0.0032	0.1605	0.039	0.1492	15.4131	-4.5171	36.3605
6	3.0632	-0.908	-0.367	2.7695	0.8412	2.4699	-0.0299	0.1195	0.1312	-0.003	-0.0737	-0.0954	-0.1369	0.1065	0.0817	0.1192	0.0102	0.0231	0.1655	0.0093	0.0543	28.5373	7.2225	17.3733
7	7.8286	-0.0642	0.8627	5.6986	0.2195	1.8017	0.083	-0.1637	-0.6597	0.4111	-0.0004	-0.2976	0.3869	-0.0031	0.0668	0.2151	0.0483	-0.0077	0.1799	0.0156	0.2013	35.8953	-12.0712	13.0152
8	1.0104	1.3202	1.3174	4.0741	1.2607	2.0503	0.0872	-0.2344	-0.3439	0.2421	0.1262	-0.1472	0.1093	-0.1337	-0.2048	0.1487	-0.0092	0.0098	0.2865	0.0656	0.2205	-12.6728	-6.7249	59.3775
9	3.177	0.3928	0.5999	0.7334	-0.0768	1.503	-0.0161	-0.2483	0.0456	0.0038	0.0759	0.0012	-0.1058	-0.0839	-0.0656	0.1609	0.0109	0.0047	0.1995	0.0119	0.095	-5.1141	3.4553	56.1757
10	2.83	0.7225	-0.1139	2.9607	-0.8304	3.2286	0.1083	-0.5407	-0.1259	-0.0626	-0.0191	-0.2385	-0.117	-0.1645	-0.0689	0.1459	0.0058	0.0352	0.2188	-0.0274	0.11	-8.9426	3.0638	56.5342
11	1.9664	-1.0562	-0.5357	1.0337	0.6391	4.8178	0.0039	0.1125	0.0433	-0.0214	-0.055	0.0167	-0.113	-0.3539	0.0376	0.0896	-0.011	0.0006	0.1047	-0.0015	0.106	-10.3893	4.2683	33.9382
12	7.7882	-6.1092	-2.7699	6.4153	4.845	5.5026	0.2115	0.5397	-0.4772	0.0012	-0.4035	0.0422	0.2777	-0.5564	0.1428	0.1082	-0.036	-0.0068	0.3273	-0.0686	0.1725	-16.5003	-4.5464	24.2978
13	2.2085	-0.4394	-0.0045	2.4852	-0.1168	2.1614	0.1031	0.1736	-0.2811	-0.0577	-0.0179	0.0321	0.1683	-0.1173	-0.083	0.0927	-0.0013	-0.0061	0.1351	-0.0303	0.1524	0.7861	-4.5255	24.6773
14	1.3304	-0.089	0.473	3.6907	-1.1772	2.557	-0.0724	-0.2433	0.1201	0.062	0.0795	0.0053	-0.241	-0.2073	-0.0339	0.1263	-0.0051	0.0195	0.1392	0.0147	0.0557	-12.3602	6.9114	43.8262
15	3.4022	2.0453	2.6289	4.6585	-1.4992	7.5261	0.116	-0.3628	-0.6449	-0.6426	-0.0577	-0.313	0.7458	-0.2892	-0.0556	0.2366	-0.0735	-0.022	0.2552	0.1027	0.3276	-19.8795	-12.2567	48.2572

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1 THROUGH 46 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 47 THROUGH 102 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 103 THROUGH 194 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 195 THROUGH 216 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 217 THROUGH 285 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 286 THROUGH 322 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 323 THROUGH 346 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 1 THROUGH 46 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 47 THROUGH 102 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 103 THROUGH 136 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 137 THROUGH 195 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 196 THROUGH 216 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 217 THROUGH 285 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 286 THROUGH 322 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 323 THROUGH 346 )

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