PDB-4em6: The structure of Glucose-6-phosphate isomerase (GPI) from Brucell...

ID or keywords:

Entry

Database: PDB / ID: 4em6

Title

The structure of Glucose-6-phosphate isomerase (GPI) from Brucella melitensis

Components

Glucose-6-phosphate isomerase

Keywords

ISOMERASE / Glucose-6-phosphate isomerase / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI / SSGCID / Seattle Structural Genomics Center for Infectious Disease / NIAID / National Institute of Allergy and Infectious Diseases

Function / homology

Function and homology information

glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
Similarity search - Function

Biological species

Brucella melitensis bv. 1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: The structure of Glucose-6-phosphate isomerase (GPI) from Brucella melitensis
Authors: Clifton, M.C. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

History

Deposition	Apr 11, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 2, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_ref_seq_dif.details / _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	4em6.cif.gz	841.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4em6.ent.gz	694.3 KB	Display	PDB format
PDBx/mmJSON format	4em6.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/em/4em6 ftp://data.pdbj.org/pub/pdb/validation_reports/em/4em6	HTTPS FTP

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Related structure data

Related structure data	2wu8S S: Starting model for refinement
Similar structure data	6xuh-2 2cxt-d 2o2d-1 1xtb-d 2o2c-2 1hox-d 6bzb-d 1iri-2 1g98-d 1nuh-1 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: BrmeA.17127.a

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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

D: Glucose-6-phosphate isomerase

A: Glucose-6-phosphate isomerase

B: Glucose-6-phosphate isomerase

C: Glucose-6-phosphate isomerase

hetero molecules

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

1

D: Glucose-6-phosphate isomerase

B: Glucose-6-phosphate isomerase

hetero molecules

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

2

A: Glucose-6-phosphate isomerase

C: Glucose-6-phosphate isomerase

hetero molecules

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

Unit cell

Length a, b, c (Å)	71.590, 72.730, 115.250
Angle α, β, γ (deg.)	95.420, 91.540, 110.060
Int Tables number	1
Space group name H-M	P1

#1: Protein	Glucose-6-phosphate isomerase / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI Mass: 60018.328 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis bv. 1 (bacteria) / Strain: 16M / Gene: pgi, BMEI1636 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YF86, glucose-6-phosphate isomerase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2587 / 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: 2.33 Å³/Da / Density % sol: 47.27 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 39.92 mg/ml BrmeA.17127.a PW34214, 0.2M calcium chloride dihydrate, 20% PEG3350. Cryoprotection 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2012

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.9→95.066 Å / Num. obs: 162585 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 16.591 Å² / R_merge(I) obs: 0.026 / Net I/σ(I): 27.06

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
1.9-1.95		0.059	13.44	23954	10203	80.3
1.95-2		0.052	15.48	27898	11760	95.5
2-2.06		0.045	17.48	27166	11447	95.4
2.06-2.12		0.041	19.57	26310	11108	95.4
2.12-2.19		0.036	21.45	25676	10834	95.8
2.19-2.27		0.034	22.81	24844	10484	95.9
2.27-2.36		0.032	24.31	24093	10145	96
2.36-2.45		0.03	25.69	23087	9740	96.3
2.45-2.56		0.028	26.96	22100	9340	96.1
2.56-2.69		0.027	28.78	21330	8980	96.6
2.69-2.83		0.025	30.72	20117	8508	96.6
2.83-3		0.023	32.95	19104	8074	96.6
3-3.21		0.022	35.19	17985	7602	96.9
3.21-3.47		0.021	38.1	16926	7149	97.2
3.47-3.8		0.019	40.09	15370	6504	96.9
3.8-4.25		0.019	41.04	13925	5895	97.1
4.25-4.91		0.019	41.63	12343	5221	97
4.91-6.01		0.019	40.54	10382	4401	97.4
6.01-8.5		0.018	40.99	8062	3411	97.9
	8.5	0.017	44.44	4114	1779	92.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2WU8

2wu8

Resolution: 1.9→95.066 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.941 / WR_factor R_free: 0.1738 / WR_factor R_work: 0.1353 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.923 / SU B: 4.723 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1282 / SU R_free: 0.1172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1689	8159	5 %	RANDOM
R_work	0.1308	-	-	-
obs	0.1327	162585	95.07 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 48.68 Å² / B_iso mean: 9.9259 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.33 Å²	0.21 Å²	0.55 Å²
2-	-	0.25 Å²	0.95 Å²
3-	-	-	0.44 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→95.066 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16590	0	21	2587	19198

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	17033
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	11316
X-RAY DIFFRACTION	r_angle_refined_deg	1.313	1.948	23180
X-RAY DIFFRACTION	r_angle_other_deg	0.919	3	27514
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.671	5	2202
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.914	23.289	745
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.482	15	2675
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.359	15	128
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	2609
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	19330
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3518
X-RAY DIFFRACTION	r_mcbond_it	0.565	1.5	10862
X-RAY DIFFRACTION	r_mcbond_other	0.166	1.5	4452
X-RAY DIFFRACTION	r_mcangle_it	0.98	2	17345
X-RAY DIFFRACTION	r_scbond_it	1.697	3	6171
X-RAY DIFFRACTION	r_scangle_it	2.683	4.5	5823

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.218	453	-
R_work	0.158	9722	-
all	-	10175	-
obs	-	-	80.3 %

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	0.2846	0.0264	-0.083	0.3279	-0.178	0.7748	-0.0099	0.0597	-0.0491	-0.0446	0.0539	0.0746	0.1033	-0.0749	-0.044	0.0245	-0.028	-0.0185	0.0489	0.0104	0.0523	-75.54	4.891	80.18
2	0.5516	-0.0431	-0.229	0.0772	0.0554	0.5399	0.0081	-0.0561	0.06	0.017	0.0055	0.0028	-0.0464	0.009	-0.0136	0.037	-0.0001	0.009	0.0263	-0.0002	0.0356	-58.347	21.862	106.397
3	0.5362	0.1694	0.1677	0.3487	0.0186	0.4308	0.0143	-0.0467	-0.0281	0.0316	0.0035	0.0036	0.0106	-0.0072	-0.0178	0.0239	0.0003	0.0106	0.0264	0.0076	0.0172	-60.9	12.353	105.952
4	0.2458	0.0121	-0.056	0.1618	-0.0724	0.259	-0.0018	0.0319	0.0163	-0.0174	0.0183	0.0084	0.0071	-0.0386	-0.0164	0.0199	-0.0026	-0.0071	0.0317	0.0032	0.0205	-63.643	17.712	77.26
5	1.7036	1.4525	-0.2436	3.2194	1.6058	1.8953	0.0425	-0.1803	-0.1424	0.2822	0.0445	-0.2792	0.2289	0.2001	-0.0871	0.0545	0.0378	-0.0254	0.0625	0.0184	0.0935	-28.11	5.216	90.033
6	3.5843	0.2322	-1.273	1.1744	-1.1312	3.36	0.0075	0.0279	0.1236	0.0351	-0.0695	-0.1323	-0.0663	0.1688	0.062	0.0083	0	-0.0222	0.0591	0.0005	0.0733	5.5263	45.4858	151.1099
7	0.254	0.0359	0.1173	0.1804	0.0057	0.2993	-0.0128	0.0059	0.0328	-0.0268	-0.0023	0.0204	-0.0253	-0.0164	0.0151	0.0229	0.0074	-0.0001	0.0177	0.0035	0.0404	-25.231	53.1739	130.9037
8	12.9684	0.7668	-2.9388	0.0569	-0.3309	6.6678	0.0714	-0.0323	0.8557	-0.0058	-0.0161	0.0594	-0.5379	-0.2209	-0.0554	0.1363	0.0495	-0.0275	0.0299	-0.0141	0.1263	-32.4653	62.7104	137.1371
9	0.2909	-0.005	-0.0451	0.2881	-0.0727	0.2821	-0.0046	-0.0457	0.0017	0.0229	-0.0083	-0.0091	0	0.0086	0.0129	0.0111	0.0015	-0.0075	0.0318	-0.001	0.0252	-17.1757	42.9958	149.1479
10	2.1879	0.8279	-0.1818	2.4501	-0.87	0.7263	-0.0682	0.2884	-0.0048	-0.2948	0.0346	0.0717	0.0753	-0.0071	0.0336	0.0866	0.015	0.006	0.096	-0.02	0.0279	-18.4403	23.2774	114.1067
11	0.3433	-0.1612	0.0845	0.7827	-0.242	0.3855	0.012	0.0748	-0.0359	-0.1406	-0.0309	0.0025	0.076	0.05	0.0189	0.039	0.009	0.0184	0.0416	-0.001	0.0287	-35.2452	12.541	66.3529
12	0.6541	-0.0761	-0.0161	0.4251	0.1245	0.2618	0.0038	0.004	0.0884	0.0031	0.0056	-0.0222	-0.0694	0.0106	-0.0094	0.0364	-0.0043	0.0013	0.0152	0.0059	0.0329	-46.7414	43.1918	84.8519
13	0.1907	0.0148	-0.0192	0.3935	-0.1137	0.3214	0.0011	0.0039	0.0085	-0.0232	-0.0037	-0.0219	0.0193	0.0166	0.0026	0.0177	0.0064	0.0046	0.0301	0.0025	0.0283	-42.0618	16.2775	78.8621
14	2.8074	1.6505	-0.7931	4.8446	-1.8522	2.2851	-0.0188	-0.0761	-0.2678	0.0673	0.02	0.0539	0.1316	-0.1541	-0.0011	0.0564	0.0082	-0.0023	0.0297	0.008	0.066	-49.7198	-14.996	90.3934
15	0.1909	0.0198	-0.0393	0.139	-0.0911	0.1759	-0.0038	0.0269	0.0226	-0.022	0.0193	0.022	-0.0058	-0.0325	-0.0155	0.0225	0.0059	-0.0043	0.0308	0.0051	0.0184	-54.2299	22.7578	74.8864
16	3.4784	0.0649	-0.3982	1.4155	-1.6423	5.0509	-0.0469	-0.3388	-0.2663	-0.0003	-0.0005	-0.0773	0.1745	0.2333	0.0474	0.0451	0.0497	-0.0083	0.0794	0.0101	0.0813	0.1735	13.3253	141.8909
17	0.414	-0.0402	-0.1376	0.1103	0.0262	0.2073	-0.0303	-0.0187	-0.0869	0.0054	-0.0019	0.0237	0.0547	-0.0216	0.0321	0.0343	-0.0037	0.0082	0.0116	0.0039	0.0423	-29.4141	15.5302	140.8131
18	0.6755	-0.1566	-0.2223	0.4834	0.1118	0.2035	-0.0246	-0.0162	0.0004	0.0053	0.0163	0.0302	0.0169	-0.0313	0.0082	0.0167	-0.005	-0.0067	0.0458	0.0101	0.0211	-45.3656	30.1491	151.8189
19	3.0886	-1.8993	0.1593	2.1305	-0.0768	0.4614	-0.0325	0.046	-0.2803	-0.0355	0.0209	0.134	0.0887	-0.0333	0.0116	0.0443	-0.0196	0.0179	0.0237	-0.0073	0.0378	-33.5498	11.7889	137.2356
20	0.2476	-0.0037	-0.0203	0.2657	0.066	0.2182	-0.0083	-0.0179	-0.0027	-0.0108	-0.0049	-0.0135	0.0011	0.0159	0.0132	0.0112	0.0061	0.0015	0.0189	0.0023	0.0239	-17.9146	29.9186	138.0194

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 119
2	X-RAY DIFFRACTION	2	A	120 - 196
3	X-RAY DIFFRACTION	3	A	197 - 309
4	X-RAY DIFFRACTION	4	A	310 - 522
5	X-RAY DIFFRACTION	5	A	523 - 548
6	X-RAY DIFFRACTION	6	B	3 - 25
7	X-RAY DIFFRACTION	7	B	26 - 285
8	X-RAY DIFFRACTION	8	B	286 - 290
9	X-RAY DIFFRACTION	9	B	291 - 512
10	X-RAY DIFFRACTION	10	B	513 - 548
11	X-RAY DIFFRACTION	11	C	7 - 96
12	X-RAY DIFFRACTION	12	C	97 - 288
13	X-RAY DIFFRACTION	13	C	289 - 431
14	X-RAY DIFFRACTION	14	C	432 - 455
15	X-RAY DIFFRACTION	15	C	456 - 548
16	X-RAY DIFFRACTION	16	D	3 - 25
17	X-RAY DIFFRACTION	17	D	26 - 172
18	X-RAY DIFFRACTION	18	D	173 - 278
19	X-RAY DIFFRACTION	19	D	279 - 309
20	X-RAY DIFFRACTION	20	D	310 - 548

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