PDB-3ifs: 2.0 Angstrom Resolution Crystal Structure of Glucose-6-phosphate ...

ID or keywords:

Entry

Database: PDB / ID: 3ifs

Title

2.0 Angstrom Resolution Crystal Structure of Glucose-6-phosphate Isomerase (pgi) from Bacillus anthracis.

Components

Glucose-6-phosphate isomerase

Keywords

ISOMERASE /

glucose-6-phosphate isomerase / idp01650 / pgi family /

Gluconeogenesis /

Glycolysis /

Phosphoprotein /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

glucose-6-phosphate isomerase /

glucose-6-phosphate isomerase activity /

gluconeogenesis / glycolytic process /

cytoplasm
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.004 Å

Authors

Minasov, G. / Wawrzak, Z. / Onopriyenko, O. / Gordon, E. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: 2.0 Angstrom Resolution Crystal Structure of Glucose-6-phosphate Isomerase (pgi) from Bacillus anthracis.
Authors: Minasov, G. / Wawrzak, Z. / Onopriyenko, O. / Gordon, E. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jul 24, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 11, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software / Item: _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ifs.cif.gz	581.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3ifs.ent.gz	498.7 KB	Display	PDB format
PDBx/mmJSON format	3ifs.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/if/3ifs ftp://data.pdbj.org/pub/pdb/validation_reports/if/3ifs	HTTPS FTP

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Related structure data

Similar structure data	1c7q-1 1c7r-1 3ff1-3 6eev-1 3l94-d 3q7f-d 4i64-d 4i6w-d 1ogy-2 3src-d 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) 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: idp01650

Similar structure data

Other databases

TargetDB: idp01650

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (10) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (9)

Deposited unit

A: Glucose-6-phosphate isomerase

B: Glucose-6-phosphate isomerase

C: Glucose-6-phosphate isomerase

D: Glucose-6-phosphate isomerase

E: Glucose-6-phosphate isomerase

F: Glucose-6-phosphate isomerase

hetero molecules

307 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glucose-6-phosphate isomerase

B: Glucose-6-phosphate isomerase

hetero molecules

defined by author&software
103 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Glucose-6-phosphate isomerase

D: Glucose-6-phosphate isomerase

hetero molecules

defined by author&software
102 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Glucose-6-phosphate isomerase

F: Glucose-6-phosphate isomerase

hetero molecules

defined by author&software
102 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

A: Glucose-6-phosphate isomerase

B: Glucose-6-phosphate isomerase

C: Glucose-6-phosphate isomerase

D: Glucose-6-phosphate isomerase

hetero molecules

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

5

E: Glucose-6-phosphate isomerase

F: Glucose-6-phosphate isomerase

hetero molecules

E: Glucose-6-phosphate isomerase

F: Glucose-6-phosphate isomerase

hetero molecules

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

Unit cell

Length a, b, c (Å)	111.802, 303.640, 72.087
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	E-762- HOH

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	Glucose-6-phosphate isomerase / / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI Mass: 51096.043 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS4767, BA_5130, GBAA_5130, pgi / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q81K75, glucose-6-phosphate isomerase

#1: Protein

Glucose-6-phosphate isomerase /

/ GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI

Mass: 51096.043 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS4767, BA_5130, GBAA_5130, pgi / Plasmid: pMCSG / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q81K75,

glucose-6-phosphate isomerase

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Non-polymers , 5 types, 2363 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-LI / LITHIUM ION / Lithium Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2356 / 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 Å³/Da / Density % sol: 38.36 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein solution: 0.3M NaCl, 10mM HEPES (pH 7.5); Screen solution: 20% PEG 3350,0.1M Na Formate, 0.1M Li Sulfate, 0.1M Bis-Tris (pH 6.5)., VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2009 / Details: Beryllium lenses
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.004→30 Å / Num. all: 163392 / Num. obs: 163392 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / B_iso Wilson estimate: 20.6 Å² / R_merge(I) obs: 0.101 / Net I/σ(I): 13.9
Reflection shell	Resolution: 2.004→2.03 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.411 / Mean I/σ(I) obs: 3.7 / Num. unique all: 8095 / % possible all: 100

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
CRANK		phasing
REFMAC	5.5.0051	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.004→29.87 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.943 / SU B: 7.829 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic, individual / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19022	8207	5 %	RANDOM
R_work	0.13996	-	-	-
all	0.14251	155079	-	-
obs	0.14251	155079	98.69 %	-

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: 14.085 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.3 Å²	0 Å²	0 Å²
2-	-	0.76 Å²	0 Å²
3-	-	-	-1.07 Å²

Refinement step

Cycle: LAST / Resolution: 2.004→29.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21260	0	32	2356	23648

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	22299
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	15099
X-RAY DIFFRACTION	r_angle_refined_deg	1.406	1.968	30195
X-RAY DIFFRACTION	r_angle_other_deg	0.853	3	36928
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.481	5	2799
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.815	24.94	1075
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.49	15	3913
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.116	15	98
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	3261
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	25275
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4554
X-RAY DIFFRACTION	r_mcbond_it	0.895	1.5	13655
X-RAY DIFFRACTION	r_mcbond_other	0.289	1.5	5644
X-RAY DIFFRACTION	r_mcangle_it	1.562	2	21960
X-RAY DIFFRACTION	r_scbond_it	2.919	3	8644
X-RAY DIFFRACTION	r_scangle_it	4.503	4.5	8235

LS refinement shell

Resolution: 2.004→2.055 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.224	575	-
R_work	0.165	10654	-
obs	-	10654	93.3 %

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	0.3387	-0.0802	0.0378	0.9264	0.0928	0.2622	-0.0231	0.0581	0.0173	-0.1118	0.028	-0.0243	-0.0373	-0.0058	-0.005	0.0214	-0.0053	-0.0025	0.0339	-0.0039	0.0086	79.8383	77.9646	27.7665
2	0.5597	-0.0086	0.0472	0.7633	0.008	0.6981	-0.0178	0.0189	-0.0922	-0.0121	0.0028	-0.043	0.0657	0.0368	0.015	0.0074	0.0039	0.0046	0.0124	-0.0138	0.0322	84.2423	59.2426	35.2534
3	0.4909	-0.0773	-0.1737	0.3937	0.0684	0.4352	-0.0171	-0.0084	-0.0088	-0.0154	-0.0066	0.039	0.0109	-0.0497	0.0237	0.0056	-0.0014	-0.0062	0.0079	-0.0016	0.0108	72.4305	84.9387	41.0624
4	4.2756	0.2071	0.5559	3.7198	-0.1544	2.0627	0.0333	-0.09	-0.1138	-0.0415	-0.1365	-0.357	0.0799	0.22	0.1032	0.0059	0.009	0.0108	0.0683	0.0081	0.0566	107.8964	72.0751	48.9251
5	0.6592	0.2421	-0.0194	0.3667	0.1498	0.203	0.0136	-0.0648	-0.0534	0.1001	-0.0337	-0.0368	0.0616	0.0085	0.0201	0.034	-0.0003	-0.0049	0.0307	0.0093	0.0125	77.441	72.6349	68.6595
6	0.5257	0.2686	-0.0003	0.6112	0.0943	0.3453	0.0244	-0.0681	-0.0206	0.0934	-0.0444	0.0598	0.0664	-0.0744	0.02	0.0252	-0.0107	0.0122	0.0365	-0.001	0.0165	66.0626	71.6455	65.4833
7	0.4335	0.0069	-0.1962	0.2974	0.1998	0.5957	0.0118	0.0203	-0.044	0.0132	-0.0232	-0.032	0.0662	0.0065	0.0114	0.0139	0.0047	-0.0038	0.0129	0	0.0134	88.9735	75.9795	57.25
8	6.4642	1.2882	2.1056	1.7837	1.1075	3.9067	-0.0546	-0.1048	0.362	-0.0501	-0.1188	0.2292	-0.0815	-0.2628	0.1734	0.0039	0.0091	-0.0067	0.0376	-0.0298	0.0534	55.1639	93.2858	50.9174
9	0.901	0.4451	0.1028	0.5734	-0.0611	0.2461	0.029	-0.1616	0.1025	0.0736	-0.0754	0.0678	-0.0546	-0.013	0.0464	0.0193	-0.0021	-0.0054	0.0492	-0.0372	0.0412	96.042	119.7669	73.3879
10	0.8436	0.3245	0.0404	0.7798	0.0395	0.9865	-0.0411	-0.0276	0.1021	-0.0542	-0.0226	-0.0016	-0.119	0.1111	0.0637	0.0252	-0.0175	-0.0198	0.0304	-0.0046	0.0615	113.5522	130.3768	65.0751
11	0.769	0.2339	0.2262	0.9074	0.018	0.508	-0.0301	-0.0448	0.1943	-0.0666	-0.0338	0.1752	-0.0799	-0.0409	0.0639	0.0183	0.0104	-0.0212	0.0163	-0.0309	0.0879	86.401	119.7281	61.5286
12	3.9715	-0.1444	-0.2137	3.613	1.1259	5.4757	-0.0633	0.003	-0.2209	0.0631	0.1235	-0.1964	0.207	0.3629	-0.0602	0.0111	0.0209	-0.0054	0.0466	-0.0233	0.0528	121.0177	104.1793	52.8287
13	0.5829	0.1763	0.3628	0.7029	0.3422	0.4824	-0.1859	0.1187	0.0829	-0.3383	0.102	0.0452	-0.2	0.0829	0.0839	0.1894	-0.071	-0.0383	0.0451	0.027	0.0258	97.7145	122.6806	31.5684
14	0.6082	0.0772	-0.0978	1.3479	0.3029	0.7715	-0.1711	0.0615	0.2119	-0.4228	0.0525	0.2446	-0.2542	-0.015	0.1186	0.2342	-0.0278	-0.1714	0.0082	0.0281	0.1485	90.5078	138.9755	37.2138
15	0.636	0.0931	0.3294	0.6986	0.1803	0.5772	-0.0994	0.0342	0.0351	-0.1788	0.0785	-0.0459	-0.1063	0.0959	0.0209	0.0566	-0.0269	0.0058	0.0205	-0.0014	0.0063	103.6603	113.2406	42.7679
16	4.3445	1.0035	-1.2573	5.0887	0.8602	4.9052	-0.1268	-0.0107	0.5166	-0.2366	-0.005	1.0438	-0.0234	-0.3325	0.1318	0.0682	0.0156	-0.1566	0.0342	-0.0286	0.429	67.6483	124.9796	50.0043
17	0.6268	0.1181	0.0175	0.2667	0.015	0.5133	0.0145	-0.1279	-0.0983	0.0598	0.0113	-0.0177	0.0206	-0.0527	-0.0257	0.0479	0.0058	0.009	0.0402	0.0284	0.0462	42.041	131.0159	105.2948
18	0.7653	0.2066	0.1095	0.7029	0.0868	1.2426	0.0007	-0.0744	-0.071	0.0319	0.0185	0.0904	0.0553	-0.2963	-0.0192	0.0136	-0.0044	0.0203	0.0925	0.0304	0.0514	21.8932	127.827	98.3785
19	0.6993	-0.0337	-0.1002	0.5233	0.0796	0.606	-0.0191	-0.0144	-0.1076	0.0017	0.0133	-0.0141	0.047	0.0161	0.0058	0.0072	0.0002	-0.001	0.0013	0.0028	0.0207	52.2958	130.5192	95.0407
20	3.921	0.8985	0.9159	3.3972	0.3799	3.1972	-0.0971	-0.0201	0.3191	-0.0032	0.0401	0.3784	-0.3077	-0.1852	0.057	0.0839	0.0438	0.0014	0.0365	-0.0032	0.076	22.7541	153.8524	86.2033
21	0.2846	-0.0495	-0.0977	0.4867	-0.1028	0.3451	-0.0398	0.1003	-0.0274	-0.1237	0.0648	0.026	0.0561	-0.0155	-0.025	0.0617	-0.0382	-0.0089	0.0702	-0.0163	0.0331	41.5834	131.3684	64.7619
22	0.6717	0.129	0.0985	0.8033	-0.1784	0.9729	-0.0117	0.1026	-0.1762	-0.0826	0.0566	0.0164	0.2205	0.0187	-0.0448	0.0894	-0.0191	0.0085	0.0351	-0.0471	0.082	44.5509	113.0429	70.4524
23	0.6641	-0.1521	-0.1543	0.6449	0.0025	0.6216	-0.0366	0.0279	-0.0017	-0.0155	0.045	0.0674	0.0046	-0.0706	-0.0084	0.0132	-0.0154	-0.0043	0.027	0.0083	0.0077	37.5452	141.5326	75.909
24	4.394	-0.5292	0.4848	3.6992	0.0569	3.7947	-0.034	-0.0458	-0.0075	0.1388	0.0977	-0.3459	-0.046	0.3266	-0.0637	0.0422	0.0128	0.0111	0.0685	-0.0343	0.0756	69.6434	121.5718	84.0748

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 95
2	X-RAY DIFFRACTION	2	A	96 - 239
3	X-RAY DIFFRACTION	3	A	240 - 421
4	X-RAY DIFFRACTION	4	A	422 - 450
5	X-RAY DIFFRACTION	5	B	1 - 116
6	X-RAY DIFFRACTION	6	B	117 - 264
7	X-RAY DIFFRACTION	7	B	265 - 420
8	X-RAY DIFFRACTION	8	B	421 - 450
9	X-RAY DIFFRACTION	9	C	1 - 96
10	X-RAY DIFFRACTION	10	C	97 - 227
11	X-RAY DIFFRACTION	11	C	228 - 422
12	X-RAY DIFFRACTION	12	C	423 - 450
13	X-RAY DIFFRACTION	13	D	1 - 105
14	X-RAY DIFFRACTION	14	D	106 - 241
15	X-RAY DIFFRACTION	15	D	242 - 420
16	X-RAY DIFFRACTION	16	D	421 - 450
17	X-RAY DIFFRACTION	17	E	1 - 105
18	X-RAY DIFFRACTION	18	E	106 - 227
19	X-RAY DIFFRACTION	19	E	228 - 420
20	X-RAY DIFFRACTION	20	E	421 - 450
21	X-RAY DIFFRACTION	21	F	1 - 105
22	X-RAY DIFFRACTION	22	F	106 - 239
23	X-RAY DIFFRACTION	23	F	240 - 420
24	X-RAY DIFFRACTION	24	F	421 - 450

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Protein , 1 types, 6 molecules ABCDEF

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Non-polymers , 5 types, 2363 molecules

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