PDB-6bzb: Crystal Structure of Glucose-6-phosphate Isomerase from Elizabeth...

ID or keywords:

Entry

Database: PDB / ID: 6bzb

Title

Crystal Structure of Glucose-6-phosphate Isomerase from Elizabethkingia anophelis

Components

Glucose-6-phosphate isomerase

Keywords

ISOMERASE / gluconeogenesis / carbohydrate biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / glycolytic process / gluconeogenesis / cytosol
Similarity search - Function

Biological species

Elizabethkingia anophelis NUHP1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.6 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of Glucose-6-phosphate Isomerase from Elizabethkingia anophelis
Authors: Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Dec 22, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 10, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6bzb.cif.gz	472 KB	Display	PDBx/mmCIF format
PDB format	pdb6bzb.ent.gz	383.8 KB	Display	PDB format
PDBx/mmJSON format	6bzb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6bzb_validation.pdf.gz	429.2 KB	Display	wwPDB validaton report
Full document	6bzb_full_validation.pdf.gz	430.6 KB	Display
Data in XML	6bzb_validation.xml.gz	51.1 KB	Display
Data in CIF	6bzb_validation.cif.gz	79.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bz/6bzb ftp://data.pdbj.org/pub/pdb/validation_reports/bz/6bzb	HTTPS FTP

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Related structure data

Related structure data	3hjbS S: Starting model for refinement
Similar structure data	6bzc-2 6bzc-1 1gzd-d 2wu8-d 6l9c-d 1q50-d 2cfk-d 1iat-d 1nuh-d 1t10-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-ElanA.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

A: Glucose-6-phosphate isomerase

B: Glucose-6-phosphate isomerase

126 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glucose-6-phosphate isomerase

defined by author
Evidence: gel filtration
63 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glucose-6-phosphate isomerase

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	69.950, 104.750, 152.650
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Glucose-6-phosphate isomerase / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI Mass: 62983.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria) Gene: pgi, BD94_3890 / Plasmid: ElanA.17127.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A077EQ93, glucose-6-phosphate isomerase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1347 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Glucose-6-phosphate isomerase / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI

Mass: 62983.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Elizabethkingia anophelis NUHP1 (bacteria)
Gene: pgi, BD94_3890 / Plasmid: ElanA.17127.a.B1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A077EQ93, glucose-6-phosphate isomerase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1347 / 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: 2.22 Å³/Da / Density % sol: 44.59 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: ElanA.17127.a.B1.PS38341 at 26.1 mg/ml was mixed 1:1 with MCSG1(f1): 0.1 M Bis-Tris:HCl, pH=6.5, 20% (w/v) PEG MME 5000, 20% ethylene glycol cryo. Tray: 295124f1, puck: hay3-9

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97876 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2017 / Details: Beryllium Lenses

Radiation

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

Radiation wavelength

Wavelength: 0.97876 Å / Relative weight: 1

Reflection

Resolution: 1.6→43.185 Å / Num. obs: 147843 / % possible obs: 99.8 % / Redundancy: 5.971 % / B_iso Wilson estimate: 16.2 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.064 / R_rim(I) all: 0.07 / Χ²: 1.067 / Net I/σ(I): 17.46 / Num. measured all: 882722 / Scaling rejects: 16

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.6-1.64	6.151	0.545	3.37	10823	0.881	0.593	99.9
1.64-1.69	6.159	0.454	4.01	10576	0.914	0.494	99.9
1.69-1.74	6.147	0.381	4.88	10272	0.937	0.415	99.9
1.74-1.79	6.152	0.315	5.93	9989	0.955	0.344	99.9
1.79-1.85	6.139	0.253	7.46	9689	0.969	0.276	99.9
1.85-1.91	6.101	0.203	9.21	9374	0.979	0.222	99.9
1.91-1.98	6.03	0.158	11.65	9066	0.986	0.173	99.8
1.98-2.07	5.947	0.124	14.51	8718	0.991	0.136	99.8
2.07-2.16	5.87	0.098	17.63	8366	0.994	0.107	99.8
2.16-2.26	5.781	0.081	20.6	8012	0.995	0.089	99.7
2.26-2.39	5.772	0.073	22.59	7625	0.996	0.08	99.6
2.39-2.53	5.753	0.063	25.11	7226	0.996	0.07	99.7
2.53-2.7	5.732	0.056	27.52	6817	0.997	0.062	99.7
2.7-2.92	5.733	0.049	30.31	6364	0.998	0.054	99.8
2.92-3.2	5.772	0.044	33.6	5861	0.998	0.048	99.8
3.2-3.58	5.859	0.038	37.33	5318	0.998	0.041	99.8
3.58-4.13	5.996	0.033	39.94	4736	0.999	0.036	99.8
4.13-5.06	6.051	0.029	41.69	4041	0.999	0.032	100
5.06-7.16	5.967	0.028	40.48	3168	0.999	0.031	99.8
7.16-43.185	5.509	0.026	40.97	1802	0.999	0.028	97.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	(dev_2919)	refinement
PDB_EXTRACT	3.24	data extraction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3HJB

3hjb

Resolution: 1.6→43.185 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.77

	R_factor	Num. reflection	% reflection
R_free	0.1768	1933	1.31 %
R_work	0.1488	-	-
obs	0.1492	147818	99.79 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 75.89 Å² / B_iso mean: 21.5199 Å² / B_iso min: 8.14 Å²

Refinement step

Cycle: final / Resolution: 1.6→43.185 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8666	0	0	1361	10027
B_iso mean	-	-	-	32.2	-
Num. residues	-	-	-	-	1093

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.64	0.2439	138	0.1914	10295	10433	100
1.64-1.6844	0.2142	137	0.1825	10347	10484	100
1.6844-1.7339	0.227	139	0.1757	10313	10452	100
1.7339-1.7899	0.2112	144	0.1716	10336	10480	100
1.7899-1.8539	0.1914	127	0.1641	10368	10495	100
1.8539-1.9281	0.1984	137	0.1712	10350	10487	100
1.9281-2.0159	0.2054	157	0.1638	10318	10475	100
2.0159-2.1221	0.2167	140	0.1635	10396	10536	100
2.1221-2.2551	0.1843	135	0.1543	10399	10534	100
2.2551-2.4292	0.2077	135	0.1564	10384	10519	100
2.4292-2.6736	0.1797	142	0.1525	10416	10558	100
2.6736-3.0604	0.1713	134	0.1453	10499	10633	100
3.0604-3.8554	0.1351	129	0.1285	10569	10698	100
3.8554-43.2009	0.142	139	0.1275	10895	11034	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	1.3923	-1.0467	0.0316	2.3955	0.3401	1.0763	0.0118	0.3578	0.0496	-0.3932	-0.0335	-0.0104	-0.1107	0.076	0.0218	0.2078	-0.0747	0.0006	0.249	0.0475	0.1131	27.5069	12.8271	-44.8812
2	0.6323	0.2074	0.3381	0.4833	0.327	1.0464	-0.0863	0.0673	0.1568	-0.1	0.0431	0.005	-0.2446	0.1496	0.064	0.1443	-0.0409	-0.0012	0.1201	0.0221	0.1516	34.0241	23.4794	-22.7237
3	1.0765	0.0483	-0.0214	0.4884	0.4088	1.3015	0.04	-0.0659	-0.1069	0.1351	-0.0096	-0.0438	0.135	0.043	-0.0336	0.143	-0.0137	-0.0203	0.0992	0.0068	0.1197	31.3275	3.9957	-2.3874
4	2.1635	-0.1271	0.8327	1.8373	-0.1196	1.855	0.0612	-0.2016	0.044	0.1747	-0.0743	0.0709	0.0478	-0.0807	0.0102	0.1277	-0.0375	0.0119	0.1252	-0.0327	0.0912	26.0076	13.7291	5.9193
5	0.4571	0.1617	0.1397	0.5379	0.2717	0.6625	-0.012	0.0861	0.0155	-0.0457	0.0205	-0.0202	-0.0438	0.0676	-0.0092	0.0794	-0.0063	0	0.112	0.0006	0.0937	28.9495	8.7373	-25.509
6	3.4566	-1.1944	-1.0907	4.3339	2.5999	5.3851	-0.1332	0.1464	-0.4463	0.1921	0.0702	0.034	0.4235	0.1747	0.0536	0.1913	0.0077	-0.0012	0.2124	-0.067	0.1572	17.3697	-20.4264	-47.6974
7	0.4698	0.0675	0.2461	0.58	0.2646	0.6025	-0.0265	-0.0368	0.0592	0.0253	-0.0369	0.0828	-0.0294	-0.0901	0.0346	0.0938	-0.0015	-0.012	0.0955	-0.013	0.1027	16.1272	11.1765	-18.2822
8	1.0031	-0.0028	-0.0354	1.2369	0.6963	1.1888	0.012	0.04	0.0563	-0.1302	-0.2184	0.3748	-0.1242	-0.3674	0.1906	0.1391	0.0122	-0.0461	0.2895	-0.0927	0.2904	-8.3274	1.7421	-25.7131
9	0.671	-0.0242	0.1141	0.7429	0.2576	0.7867	0.0394	0.0088	-0.1677	0.1065	-0.1178	0.1745	0.2908	-0.2212	0.0173	0.2275	-0.0937	0.034	0.1961	-0.0599	0.2247	3.3542	-21.0035	-21.5646
10	1.2825	0.0042	-0.2208	0.6288	-0.0936	0.5915	0.0552	-0.1109	-0.1223	0.239	-0.0087	-0.0938	0.2151	0.0317	-0.0256	0.2381	-0.0012	-0.0477	0.1061	0.0034	0.1484	28.0174	-15.7595	-8.4804
11	1.5135	0.0055	0.137	1.0826	-0.1943	2.2028	0.0184	0.0035	-0.2238	0.2073	0.0055	-0.2377	0.2869	-0.0224	-0.065	0.2471	0.0299	-0.048	0.1058	-0.0292	0.2163	33.6199	-21.9953	-17.1612
12	1.1113	-0.071	0.0151	0.6033	-0.1158	0.4624	0.0688	0.0535	-0.3842	0.1237	0.0201	-0.1691	0.3635	0.0379	-0.0143	0.3281	0.0251	-0.0537	0.1183	-0.038	0.2769	26.521	-28.2988	-16.7417
13	0.4508	0.0625	0.0438	0.669	0.3919	0.7266	0.0151	0.0033	-0.029	0.0542	-0.108	0.1206	0.0969	-0.1803	0.0477	0.0931	-0.0318	0.0173	0.1457	-0.0333	0.1301	7.2662	-3.1511	-18.4201
14	0.4932	-0.5776	-0.8517	3.4939	0.8407	2.5356	0.2603	0.0897	0.0254	-0.0306	-0.1217	-0.1138	-0.1938	0.0168	-0.1133	0.1725	0.064	-0.0072	0.1719	-0.0243	0.1758	4.5342	32.8193	-17.0631
15	0.3985	0.0909	0.1573	0.5872	0.2118	0.5532	0.0152	0.0699	-0.1093	-0.0031	-0.0201	0.0031	0.0908	-0.0039	0.0259	0.1213	-0	-0.0077	0.1343	-0.0399	0.1249	18.7741	-5.8708	-28.2489

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 52 )	A	1 - 52
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 53 through 136 )	A	53 - 136
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 137 through 197 )	A	137 - 197
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 198 through 252 )	A	198 - 252
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 253 through 432 )	A	253 - 432
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 433 through 460 )	A	433 - 460
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 461 through 547 )	A	461 - 547
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 52 )	B	2 - 52
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 53 through 135 )	B	53 - 135
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 136 through 197 )	B	136 - 197
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 198 through 226 )	B	198 - 226
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 227 through 274 )	B	227 - 274
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 275 through 432 )	B	275 - 432
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 433 through 456 )	B	433 - 456
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 457 through 547 )	B	457 - 547

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