PDB-3i3w: Structure of a phosphoglucosamine mutase from Francisella tularensis

ID or keywords:

Entry

Database: PDB / ID: 3i3w

Title

Structure of a phosphoglucosamine mutase from Francisella tularensis

Components

Phosphoglucosamine mutase

Keywords

ISOMERASE / phosphoglucosamine mutase / CSGID / IDP02164 / Magnesium / Metal-binding / Phosphoprotein / Structural Genomics / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

phosphoglucosamine mutase / phosphoglucosamine mutase activity / carbohydrate metabolic process / magnesium ion binding
Similarity search - Function

Biological species

Francisella tularensis subsp. tularensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Structure of a phosphoglucosamine mutase from Francisella tularensis
Authors: Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jul 1, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 19, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3i3w.cif.gz	176.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3i3w.ent.gz	150.4 KB	Display	PDB format
PDBx/mmJSON format	3i3w.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3i3w_validation.pdf.gz	451.8 KB	Display	wwPDB validaton report
Full document	3i3w_full_validation.pdf.gz	473 KB	Display
Data in XML	3i3w_validation.xml.gz	35.6 KB	Display
Data in CIF	3i3w_validation.cif.gz	49.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i3/3i3w ftp://data.pdbj.org/pub/pdb/validation_reports/i3/3i3w	HTTPS FTP

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Related structure data

Similar structure data	6gyz-d 4p2q-2 1zgl-4 2va0-d 4p2q-1 10733 7dqv-d 4p2r-3 6bga-d 3i6g-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
Other databases	TargetDB: IDP02164

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phosphoglucosamine mutase

B: Phosphoglucosamine mutase

hetero molecules

97.4 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)	104.430, 206.680, 44.760
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Phosphoglucosamine mutase Mass: 48645.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria) Gene: FTT0079, glmM, mrsA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q5NII8, phosphoglucosamine mutase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.48 Å³/Da / Density % sol: 50.45 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Tacsimate 60% pH 7 Frozen in Paratone Oil, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9793 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 20, 2009 / Details: Mirrors
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2.3→30 Å / Num. all: 82357 / Num. obs: 82357 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / B_iso Wilson estimate: 48.7 Å² / R_merge(I) obs: 0.065 / Net I/σ(I): 13.83
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.444 / Mean I/σ(I) obs: 3.03 / Num. unique all: 4095 / % possible all: 97.3

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Processing

Software

Name	Version	Classification
BLU-MAX		data collection
PHENIX		model building
REFMAC	5.2.0019	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.3→29.16 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.939 / SU B: 17.658 / SU ML: 0.208 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23642	2216	5.1 %	RANDOM
R_work	0.19413	-	-	-
obs	0.19631	41648	99.32 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 41.468 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.34 Å²	0 Å²	0 Å²
2-	-	-3.29 Å²	0 Å²
3-	-	-	-4.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→29.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6759	0	2	265	7026

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	6863
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.981	1.962	9268
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.549	5	879
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.386	25.478	314
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.125	15.025	1207
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.471	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	1054
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5148
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	3346
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.316	0.2	4851
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	343
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.217	0.2	67
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.192	0.2	12
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.527	1.5	4457
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.869	2	6965
X-RAY DIFFRACTION	r_scbond_it	1.468	3	2664
X-RAY DIFFRACTION	r_scangle_it	2.299	4.5	2303
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.3→2.359 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.263	165	-
R_work	0.267	3012	-
obs	-	-	98.15 %

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	8.7782	0.3536	4.1442	1.0303	-3.3419	14.0742	0.0721	0.7365	0.5955	-0.1868	-0.8407	-0.2136	-0.5163	1.6725	0.7686	0.0641	-0.2012	0.0281	0.3853	0.0699	0.0826	80.7837	60.3035	28.2564
2	2.2105	-0.1018	1.7671	2.8863	-0.6279	4.3617	0.0459	-0.2079	0.1036	0.067	-0.1267	0.0628	-0.3305	0.1765	0.0809	-0.1122	-0.1653	0.0226	-0.0205	-0.0314	-0.0775	69.1863	62.6588	33.9484
3	3.9771	-2.9444	0.8265	7.796	-1.2295	1.5645	-0.0359	-0.1925	0.8343	0.798	-0.1234	-1.2803	-0.9774	0.9014	0.1593	0.0595	-0.2749	-0.0528	0.4578	0.005	0.0915	79.901	65.4932	40.8218
4	1.2106	-1.087	0.5694	2.9647	-1.6577	2.8293	0.1177	0.1224	-0.0168	-0.2002	-0.0439	0.5034	-0.2166	-0.2018	-0.0738	-0.0223	-0.1723	-0.0134	0.0329	-0.0893	0.018	55.877	68.5174	19.7159
5	3.256	2.4334	3.2698	6.0085	1.7169	5.0571	-0.1015	0.3196	0.1101	-0.1265	-0.094	0.1574	-0.3973	-0.1129	0.1955	0.0889	-0.1433	-0.0287	-0.0241	0.0223	-0.0734	61.3654	85.9564	18.847
6	3.0864	3.269	-0.8568	6.9363	-2.269	14.3795	0.0408	0.0949	0.1643	0.4088	-0.4455	-0.8656	0.1333	0.4061	0.4047	0.065	-0.2401	-0.0901	-0.0161	-0.0539	0.0188	69.6967	92.603	22.517
7	2.9919	0.8335	2.2215	4.6255	-0.326	6.9089	-0.1824	0.0292	0.0359	0.0862	0.0233	0.0935	-0.1204	-0.2507	0.1591	0.0577	-0.13	0.0417	-0.0812	-0.0505	-0.0192	59.6683	83.6938	24.5733
8	7.9492	-0.2533	-2.6409	3.0647	1.139	1.2414	-0.2032	-0.7715	0.2138	0.2332	0.2377	-0.2106	0.6083	-0.1948	-0.0345	0.389	-0.1776	-0.018	0.1108	0.0192	0.1137	82.8452	89.2849	13.6244
9	6.753	-0.0926	0.1192	5.021	-1.0272	6.0618	0.1484	-0.108	-0.3715	-0.05	-0.018	-0.1548	0.4756	-0.0624	-0.1304	0.1827	-0.1685	0.0626	-0.0386	0.0146	0.045	85.4501	94.7191	11.2703
10	8.6381	8.7649	-2.9416	12.468	-6.2577	10.4723	-0.249	-0.3929	-1.0835	-0.3681	-0.5673	-2.8184	0.2316	1.0163	0.8162	0.011	0.0263	-0.0098	0.4647	0.1168	0.2895	81.7842	39.4268	42.7226
11	1.4892	0.4949	-1.4223	2.5938	-1.0544	6.5025	-0.0069	0.1574	-0.1079	-0.1001	-0.125	-0.0258	0.2216	0.4557	0.1319	-0.1764	0.1005	-0.0418	-0.03	-0.0268	-0.0714	70.6611	37.7087	33.1188
12	4.2064	2.0795	-1.5908	4.4455	-1.8733	3.4301	-0.1554	0.1218	-0.5594	-0.2667	-0.0828	-0.3145	0.2843	0.5702	0.2382	-0.0995	0.0965	-0.057	0.1612	-0.0727	-0.1227	69.3682	36.5962	29.0837
13	2.3108	2.2902	-0.0623	5.3531	-0.1231	3.0025	0.1888	-0.3343	0.1809	0.3528	-0.3266	0.5825	0.1254	-0.1128	0.1377	-0.0294	0.0642	0.0275	-0.0428	-0.0887	-0.024	57.2099	28.3215	53.5514
14	4.5566	-3.2117	-0.8818	8.2139	1.5048	7.8654	-0.2158	-0.1456	-0.052	0.3586	0.0716	-0.2045	0.2882	0.3017	0.1443	0.1791	0.1418	0.0435	-0.1235	-0.001	-0.0757	67.0203	9.4709	45.6418
15	2.5254	-1.9666	-1.9056	4.3485	1.128	5.2856	0.0589	-0.0248	0.1729	-0.1844	-0.1506	-0.1023	0.2794	0.0486	0.0917	0.0751	0.0924	-0.054	-0.1283	-0.0469	-0.0534	62.0234	16.3799	42.584
16	8.6358	-3.5246	4.7105	5.9034	-0.3542	3.1202	-0.5139	1.386	0.6106	0.8798	0.2448	-1.8478	-0.7819	0.389	0.2691	0.61	0.0638	-0.2654	0.1897	-0.0048	0.6366	86.1281	10.4539	53.8065
17	7.2781	-5.7649	-2.9024	9.6028	0.9624	8.0972	-0.3953	0.4434	0.0936	0.5336	0.1637	-0.5188	0.0493	-0.0291	0.2317	0.3747	0.1662	-0.2426	-0.0245	-0.0014	0.0752	84.0725	-0.0715	53.5369
18	18.8394	1.4583	-3.2559	6.9188	-3.9554	6.7128	-0.4067	-0.0359	1.0994	1.6402	0.1392	-1.0375	-1.5479	0.1996	0.2675	0.8543	0.1235	-0.5158	-0.0443	-0.1147	0.3946	87.5949	8.4496	58.4083

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 29
2	X-RAY DIFFRACTION	2	A	30 - 115
3	X-RAY DIFFRACTION	3	A	116 - 141
4	X-RAY DIFFRACTION	4	A	142 - 242
5	X-RAY DIFFRACTION	5	A	243 - 283
6	X-RAY DIFFRACTION	6	A	284 - 308
7	X-RAY DIFFRACTION	7	A	309 - 359
8	X-RAY DIFFRACTION	8	A	360 - 385
9	X-RAY DIFFRACTION	9	A	386 - 442
10	X-RAY DIFFRACTION	10	B	6 - 22
11	X-RAY DIFFRACTION	11	B	23 - 118
12	X-RAY DIFFRACTION	12	B	119 - 165
13	X-RAY DIFFRACTION	13	B	166 - 252
14	X-RAY DIFFRACTION	14	B	253 - 306
15	X-RAY DIFFRACTION	15	B	307 - 359
16	X-RAY DIFFRACTION	16	B	360 - 387
17	X-RAY DIFFRACTION	17	B	388 - 406
18	X-RAY DIFFRACTION	18	B	407 - 440

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