PDB-4rnl: The crystal structure of a possible galactose mutarotase from Str...

ID or keywords:

Entry

Database: PDB / ID: 4rnl

Title

The crystal structure of a possible galactose mutarotase from Streptomyces platensis subsp. rosaceus

Components

possible galactose mutarotase

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro / Midwest Center for Structural Genomics

Function / homology

Function and homology information

aldose 1-epimerase / aldose 1-epimerase activity / galactose catabolic process via UDP-galactose, Leloir pathway / glucose metabolic process / carbohydrate binding / cytoplasm
Similarity search - Function

Biological species

Streptomyces platensis subsp. rosaceus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Tan, K. / Li, H. / Endres, M. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Citation

Journal: To be Published
Title: The crystal structure of a possible galactose mutarotase from Streptomyces platensis subsp. rosaceus
Authors: Tan, K. / Li, H. / Endres, M. / Phillips Jr., G.N. / Joachimiak, A.

History

Deposition	Oct 24, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 26, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.2	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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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Download

PDBx/mmCIF format	4rnl.cif.gz	537.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4rnl.ent.gz	447.8 KB	Display	PDB format
PDBx/mmJSON format	4rnl.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/rn/4rnl ftp://data.pdbj.org/pub/pdb/validation_reports/rn/4rnl	HTTPS FTP

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Related structure data

Similar structure data	2afo-2 2afx-2 3kys-2 2afw-2 1kw0-d 2ciw-d 2afx-1 5tvo-d 2zyq-3 2afs-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: MCSG-APC109927

Similar structure data

Other databases

TargetTrack: MCSG-APC109927

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (2) #39 - Mar 2003 lac Repressor similarity (2) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1)

Deposited unit

A: possible galactose mutarotase

B: possible galactose mutarotase

C: possible galactose mutarotase

D: possible galactose mutarotase

hetero molecules

146 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: possible galactose mutarotase

hetero molecules

defined by author&software
36.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: possible galactose mutarotase

hetero molecules

defined by author&software
36.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: possible galactose mutarotase

hetero molecules

defined by author&software
36.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: possible galactose mutarotase

hetero molecules

defined by author&software
36.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	47.425, 115.800, 261.345
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	possible galactose mutarotase Mass: 36118.477 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces platensis subsp. rosaceus (bacteria) Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: A0A0B4J187*PLUS
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1365 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.47 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 1M Ammonium phospahte Dibasic, 0.1M Sodium acetate: acetate acid, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2014 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 1.8→43.5 Å / Num. all: 133608 / Num. obs: 135006 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 7 % / B_iso Wilson estimate: 15.339 Å² / R_merge(I) obs: 0.137 / Net I/σ(I): 16.6
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.765 / Mean I/σ(I) obs: 2.52 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELXD	Builder/HKL3000	phasing
MLPHARE	Builder/HKL3000	phasing
DM	Builder/HKL3000	model building
DENZO	Builder/HKL3000	data reduction
SCALEPACK	Builder/HKL3000	data scaling
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM	Builder/HKL3000	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.8→43.333 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 18.53 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1919	6733	4.99 %
R_work	0.1543	-	-
obs	0.1561	134894	98.36 %
all	-	135006	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→43.333 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10086	0	91	1365	11542

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	10655
X-RAY DIFFRACTION	f_angle_d	1.064	14565
X-RAY DIFFRACTION	f_dihedral_angle_d	11.784	3826
X-RAY DIFFRACTION	f_chiral_restr	0.074	1580
X-RAY DIFFRACTION	f_plane_restr	0.005	1975

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 (%)
1.8-1.8091	0.3002	190	0.2545	3324	X-RAY DIFFRACTION	77
1.8091-1.8304	0.2854	247	0.2238	4192	X-RAY DIFFRACTION	98
1.8304-1.8527	0.2576	206	0.2124	4196	X-RAY DIFFRACTION	98
1.8527-1.8762	0.2466	229	0.1994	4247	X-RAY DIFFRACTION	99
1.8762-1.9009	0.2264	229	0.184	4276	X-RAY DIFFRACTION	98
1.9009-1.9269	0.2227	223	0.1797	4180	X-RAY DIFFRACTION	99
1.9269-1.9545	0.2301	208	0.1729	4281	X-RAY DIFFRACTION	99
1.9545-1.9836	0.2152	220	0.1733	4300	X-RAY DIFFRACTION	99
1.9836-2.0146	0.2439	221	0.1701	4181	X-RAY DIFFRACTION	99
2.0146-2.0477	0.201	210	0.1634	4298	X-RAY DIFFRACTION	99
2.0477-2.083	0.2237	203	0.1592	4280	X-RAY DIFFRACTION	99
2.083-2.1208	0.2077	234	0.1593	4235	X-RAY DIFFRACTION	99
2.1208-2.1616	0.2015	234	0.1526	4285	X-RAY DIFFRACTION	99
2.1616-2.2057	0.1813	214	0.1543	4221	X-RAY DIFFRACTION	99
2.2057-2.2537	0.2081	218	0.1542	4325	X-RAY DIFFRACTION	99
2.2537-2.3061	0.195	202	0.1547	4260	X-RAY DIFFRACTION	99
2.3061-2.3638	0.2056	256	0.1523	4319	X-RAY DIFFRACTION	99
2.3638-2.4277	0.206	209	0.154	4248	X-RAY DIFFRACTION	99
2.4277-2.4991	0.2204	229	0.1642	4359	X-RAY DIFFRACTION	99
2.4991-2.5798	0.2267	210	0.1626	4269	X-RAY DIFFRACTION	99
2.5798-2.672	0.2036	243	0.1532	4292	X-RAY DIFFRACTION	99
2.672-2.7789	0.1907	230	0.1565	4369	X-RAY DIFFRACTION	99
2.7789-2.9054	0.1696	238	0.1573	4269	X-RAY DIFFRACTION	100
2.9054-3.0585	0.2182	254	0.1626	4346	X-RAY DIFFRACTION	100
3.0585-3.2501	0.1867	236	0.1537	4341	X-RAY DIFFRACTION	100
3.2501-3.5009	0.1892	218	0.1462	4403	X-RAY DIFFRACTION	100
3.5009-3.8531	0.1735	217	0.1359	4422	X-RAY DIFFRACTION	100
3.8531-4.4101	0.1302	231	0.1211	4414	X-RAY DIFFRACTION	99
4.4101-5.5545	0.1247	237	0.1199	4442	X-RAY DIFFRACTION	99
5.5545-43.3458	0.1845	237	0.1598	4587	X-RAY DIFFRACTION	97

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	2.2271	-1.0421	-1.3827	5.5034	3.6993	5.24	0.0514	-0.0564	-0.1394	0.0704	-0.1237	0.3456	0.034	-0.3664	0.0629	0.0942	-0.0039	-0.0213	0.1362	0.0537	0.178	29.2927	29.3982	180.4024
2	1.5529	-0.923	-0.1801	2.819	-0.1807	1.2612	0.0809	0.0582	-0.0747	-0.182	0.0442	0.3722	-0.0174	-0.0832	-0.0665	0.1182	-0.0152	-0.0218	0.1167	0.0321	0.1479	31.1734	37.3294	171.8118
3	4.8977	0.297	-0.9142	1.0363	0.7405	0.9145	0.0049	-0.0713	-0.0989	-0.0535	0.0851	-0.2427	0.0483	0.0388	-0.1398	0.1263	0.0055	0.0039	0.095	0.0116	0.1699	56.5181	28.1902	168.734
4	6.0054	0.8164	-1.1556	2.0184	0.6938	1.9855	0.0621	0.2721	-0.1078	-0.2298	0.012	-0.0679	0.0258	-0.0139	-0.0276	0.1487	0.0172	-0.0087	0.0554	-0.0114	0.1156	49.8934	26.5309	165.3614
5	4.575	-2.4363	-2.5961	2.5169	1.4983	2.2335	-0.0835	-0.1751	-0.3029	0.0905	0.0523	0.0159	0.1677	0.0281	0.0606	0.1354	0.0059	-0.0249	0.0864	0.0368	0.1478	45.1151	24.2683	181.2504
6	0.6189	0.0898	-0.0196	0.9276	-0.1579	0.4204	0.002	-0.0192	-0.0066	0.0307	-0.0194	-0.0778	-0.0225	0.0275	0.0142	0.1022	0.003	-0.0042	0.0776	0.0197	0.0874	50.7382	44.6226	172.7986
7	7.3336	-2.5032	0.5361	3.5253	-0.5221	0.4204	-0.0718	0.0164	0.2625	0.0396	0.0786	0.083	-0.1107	-0.0422	0.0218	0.129	-0.0019	0.0067	0.0662	0.0168	0.0858	40.1588	50.778	177.541
8	1.3433	0.1048	0.1473	0.7728	0.0734	0.2392	-0.0094	0.0663	-0.0607	-0.0191	0.0175	-0.0779	-0.0112	0.0304	-0.0138	0.1123	0.0021	0.0018	0.0892	0.0203	0.0979	48.0919	38.9728	172.286
9	2.8643	-1.0776	0.5864	4.0122	-3.0758	4.8001	0.0333	-0.1074	0.0065	0.0309	0.1012	0.2552	-0.1175	-0.3677	-0.1309	0.1491	0.0058	-0.0025	0.2261	-0.0244	0.1375	21.7016	72.1324	251.0425
10	1.8023	-0.057	0.5972	0.6797	-0.2541	1.5419	0.0532	-0.3408	-0.1079	0.0388	-0.01	-0.0451	0.0084	-0.0573	-0.0499	0.1524	-0.0144	0.0086	0.1724	0.0149	0.1277	35.8306	61.0492	250.2739
11	5.065	-1.9794	2.0965	1.8027	-0.9247	2.0339	-0.0916	-0.4842	0.2557	0.1444	0.0512	-0.061	-0.2123	0.0918	0.0418	0.1831	-0.0307	0.0058	0.2752	-0.036	0.1387	36.5292	74.4153	255.9984
12	1.3854	-0.0473	0.2764	0.5042	0.2563	1.0066	0.0039	-0.0405	-0.0181	-0.0445	0.0204	-0.0816	-0.0385	0.1245	-0.0389	0.1306	-0.0124	0.009	0.1115	0.0072	0.1403	41.9601	62.7516	236.9906
13	6.2665	-0.6609	2.4677	0.3865	0.6639	3.6178	0.0399	0.1884	-0.2764	-0.1011	0.014	-0.0504	0.0029	0.0089	-0.0399	0.152	-0.0067	0.0114	0.0949	0.0178	0.1305	31.3536	66.6161	230.4313
14	2.6004	0.303	0.054	0.5205	-0.2264	0.7829	0.0004	-0.1833	-0.0637	-0.0072	0.0067	-0.0089	-0.0003	0.0044	0.0053	0.1348	-0.0073	0.0087	0.1171	0.005	0.1174	39.4845	63.271	242.7566
15	3.4684	1.4248	-2.0374	6.5489	-5.4441	6.7463	-0.0248	-0.0538	-0.1068	-0.0391	-0.1213	-0.0803	0.1763	0.2929	0.2222	0.1232	0.0364	0.0024	0.1465	-0.0029	0.1031	53.4539	24.176	205.2543
16	1.9674	0.9827	-0.452	3.9832	0.1364	1.7487	0.0411	-0.0972	0.1628	-0.0421	0.039	-0.1907	-0.1095	0.2147	-0.0353	0.0865	0.0112	0.0064	0.1282	0.0076	0.1111	53.3206	36.0182	210.735
17	5.653	0.1384	-0.0146	0.7673	-0.191	0.4095	-0.0075	-0.2015	0.0412	0.1355	-0.0187	-0.0185	0.0657	0.0923	0.0344	0.1421	0.0017	-0.0049	0.1239	-0.0004	0.09	39.1856	26.5099	218.3396
18	4.192	-0.2703	-1.6577	1.3613	-1.0035	1.6843	0.015	-0.0917	-0.1547	0.0587	0.0656	0.2045	-0.0098	-0.0178	-0.0529	0.1329	0.0004	-0.0066	0.0752	-0.0004	0.1209	27.8925	22.0095	218.6307
19	4.6193	2.0548	-2.1893	1.8177	-1.2038	1.6442	-0.0978	0.2666	-0.1624	-0.1625	-0.002	-0.0284	0.0984	-0.0256	0.1231	0.1475	0.0071	-0.0134	0.126	-0.0134	0.1071	38.037	22.6169	203.2116
20	0.7534	0.1559	-0.1616	0.76	0.1581	0.344	0.0254	0.0101	0.1125	-0.0135	-0.0029	0.0536	-0.0738	-0.0121	-0.0203	0.1176	0.008	0.0053	0.0995	0.0041	0.1148	32.7285	41.4052	215.1732
21	8.3628	2.9503	1.3818	3.0422	1.1311	0.9245	-0.0052	-0.1356	0.3517	-0.0458	-0.0035	-0.0442	-0.1257	0.0032	0.0026	0.1458	-0.0057	0.0333	0.1029	0.0112	0.1445	43.2908	48.1448	211.2424
22	1.9058	0.1496	-0.0149	0.6453	-0.0902	0.26	0.0261	-0.1447	0.0499	0.0339	0.0074	0.0335	-0.0143	0.0032	-0.0413	0.1312	0.005	0.0075	0.1141	-0.0054	0.1053	35.1968	35.7493	214.5382
23	2.6655	0.1542	-0.7361	7.8036	-4.7249	6.075	0.076	-0.3726	0.1493	0.2742	0.0795	0.3851	-0.15	-0.3463	-0.1197	0.1542	0.0224	0.0164	0.2615	-0.0842	0.1151	32.7044	20.4708	256.5039
24	1.38	0.0792	1.1364	1.4681	0.8734	5.7983	-0.0482	-0.1364	0.1149	-0.0656	-0.0462	0.1571	-0.2535	-0.4418	0.0592	0.1011	0.0167	-0.0011	0.142	-0.0235	0.1025	32.234	15.3326	242.6262
25	4.2403	-0.3163	0.0068	0.4546	-0.3022	0.9181	0.035	-0.288	-0.2045	0.0215	-0.0429	-0.0437	0.0455	0.0621	0.0039	0.1505	-0.0011	-0.0037	0.1685	-0.0008	0.0808	53.4154	9.2711	256.0588
26	3.7064	-1.3243	1.5481	1.7093	-0.1088	2.4448	-0.1802	-0.3399	0.2686	0.0858	0.0766	-0.0118	-0.3065	-0.0428	0.1639	0.168	-0.0079	-0.0072	0.1794	-0.0681	0.1066	47.7053	24.2509	255.6404
27	1.11	0.083	0.4433	0.4506	0.2818	0.8984	-0.0094	0.0096	-0.0201	-0.0208	0.0417	-0.0569	-0.0203	0.1271	-0.0297	0.1189	0.0011	0.0033	0.1145	-0.0301	0.0906	53.1405	10.5257	238.136
28	3.2432	2.5418	2.9707	2.1097	2.1544	3.1534	-0.1011	0.2274	-0.1186	-0.1109	0.1497	-0.109	-0.0708	0.0887	-0.0152	0.1302	0.0107	-0.0118	0.1122	-0.013	0.099	42.732	13.8944	231.0819
29	1.6605	0.0766	0.2845	0.0675	-0.0292	0.5707	-0.0292	-0.0805	-0.0539	-0.0177	0.0139	-0.0068	-0.0101	0.0509	0.0187	0.1266	0.006	-0.0002	0.1093	-0.0267	0.082	50.7972	11.8179	243.725

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 73 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 74 through 99 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 100 through 121 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 122 through 156 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 157 through 252 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 253 through 271 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 272 through 340 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid -1 through 41 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 42 through 121 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 122 through 156 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 157 through 252 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 253 through 271 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 272 through 340 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 0 through 25 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 26 through 63 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 64 through 86 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 87 through 121 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 122 through 156 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 157 through 252 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 253 through 271 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 272 through 340 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 2 through 25 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 26 through 63 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 64 through 121 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 122 through 156 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 157 through 252 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 253 through 271 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 272 through 340 )

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