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

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Basic information

Entry
Database: PDB / ID: 6bzc
TitleCrystal Structure of Glucose-6-phosphate Isomerase from Elizabethkingia anophelis with bound Glucose-6-phosphate
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / 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
Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. ...Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Glucose-6-phosphate Isomerase from Elizabethkingia anophelis with bound Glucose-6-phosphate
Authors: Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8289
Polymers125,9672
Non-polymers8617
Water9,782543
1
A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5226
Polymers62,9841
Non-polymers5385
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3063
Polymers62,9841
Non-polymers3222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14270 Å2
ΔGint-62 kcal/mol
Surface area35130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.280, 102.140, 153.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 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. Crystal was then soaked with 5 mM glucose-6-phosphate and 20% ...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. Crystal was then soaked with 5 mM glucose-6-phosphate and 20% ethylene glycol for 4 days. Tray: 295124f1, puck: pqf5-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→48.466 Å / Num. obs: 68995 / % possible obs: 99.7 % / Redundancy: 4.004 % / Biso Wilson estimate: 24.64 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.119 / Χ2: 0.98 / Net I/σ(I): 9.51 / Num. measured all: 276270 / Scaling rejects: 29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.14.0580.5082.5720399502950270.7260.587100
2.1-2.164.0690.4173.320116495249440.7820.48199.8
2.16-2.224.0720.3593.7919496479647880.8430.41599.8
2.22-2.294.0850.3234.2818945464746380.8710.37299.8
2.29-2.374.0750.2844.9118425452645220.8980.32899.9
2.37-2.454.0740.2475.7317691434843420.9030.28699.9
2.45-2.544.0710.2176.317145422042120.9390.25199.8
2.54-2.654.060.1897.2516600409840890.9460.21999.8
2.65-2.764.0380.1618.3315854393039260.9610.18699.9
2.76-2.93.9910.1369.5714919374237380.9740.15799.9
2.9-3.063.9860.11411.3314137355435470.9790.13299.8
3.06-3.243.9230.09513.1813304340333910.9830.1199.6
3.24-3.473.9090.0815.6912436319431810.9880.09299.6
3.47-3.743.8690.0717.5911440297229570.9890.08199.5
3.74-4.13.8660.06518.8810659277227570.990.07599.5
4.1-4.583.9140.05920.259667249524700.990.06899
4.58-5.293.9340.05520.168666222322030.9940.06399.1
5.29-6.483.9110.05118.97442190619030.9940.05999.8
6.48-9.173.9010.04120.115816149514910.9970.04799.7
9.17-48.4663.5820.0320.4631138908690.9980.03497.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(dev_2919)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BZB

6bzb


Resolution: 2.05→48.466 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 2075 3.01 %
Rwork0.2069 66919 -
obs0.209 68994 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.27 Å2 / Biso mean: 29.6201 Å2 / Biso min: 9.53 Å2
Refinement stepCycle: final / Resolution: 2.05→48.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8699 0 54 548 9301
Biso mean--35.83 29.51 -
Num. residues----1094
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0499-2.09760.33151450.262144134558100
2.0976-2.15010.32621370.255743704507100
2.1501-2.20820.33471530.254844094562100
2.2082-2.27320.35511280.251744104538100
2.2732-2.34650.32451450.250644194564100
2.3465-2.43040.3161200.240344494569100
2.4304-2.52770.33941470.235844154562100
2.5277-2.64280.35831410.232544194560100
2.6428-2.78210.32571470.22444554602100
2.7821-2.95640.30341550.216144344589100
2.9564-3.18460.30791180.215144974615100
3.1846-3.5050.26061110.19464491460299
3.505-4.01190.23481460.180944834629100
4.0119-5.05380.22091470.16724510465799
5.0538-48.47920.20121350.178347454880100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.7743-1.40920.08813.63550.59731.1261-0.07460.17130.0273-0.48370.147-0.1283-0.1459-0.1334-0.06460.3013-0.03760.05450.31550.04650.150126.972812.5942-44.3986
21.06630.13170.31690.38240.45541.3157-0.11930.13550.1605-0.1192-0.0652-0.0534-0.30740.15980.15170.3214-0.08320.03130.23220.07990.27230.610726.7537-27.0274
30.8143-0.0043-0.3330.47130.1451.32360.0054-0.0891-0.0607-0.00060.0176-0.08070.0720.2067-0.01280.1816-0.0291-0.0130.23880.04610.239732.83487.8501-2.2083
42.72-0.2131.27070.9788-0.41963.0468-0.0285-0.3392-0.14950.16070.10440.12040.0061-0.1777-0.08640.2284-0.01190.04180.22840.05680.211125.154710.42657.6782
50.6815-0.13410.2260.90370.05020.8171-0.00580.07990.1414-0.0296-0.05-0.0473-0.06390.07040.05510.1693-0.04190.02590.1960.04330.180530.32414.0181-19.8884
60.57830.3626-0.09841.0420.26910.41690.01560.0878-0.0814-0.2176-0.0214-0.0004-0.02350.009-0.00360.225-0.01240.02830.2379-0.03170.157224.87350.6955-31.1317
70.76710.33920.06380.55450.15370.5566-0.02020.045-0.0682-0.05390.02130.0238-0.0003-0.02630.00350.17120.0175-0.02050.21840.03430.169815.59953.283-25.2562
80.2015-0.192-0.02921.21540.1650.948-0.04370.0484-0.0595-0.1697-0.00260.2892-0.1482-0.21660.05340.1927-0.0184-0.03090.4070.00390.332-8.96330.5388-26.4454
91.5385-0.60950.07272.968-0.40332.0929-0.03810.0519-0.2567-0.17220.01330.25080.2543-0.15260.00040.278-0.0747-0.02770.2391-0.02750.27912.4937-25.752-26.3626
101.19910.2791-0.31240.7886-0.23550.7935-0.11860.1238-0.1604-0.0357-0.0136-0.14590.28660.06910.1330.31-0.00490.01690.20630.04670.245623.3873-22.6494-13.1092
110.31080.0840.18940.5770.16910.65720.02890.01450.004-0.02090.03110.10350.0445-0.1013-0.04570.1814-0.0010.01030.2510.01230.22536.90170.1834-20.2423
124.1365-1.4203-2.3365.46451.07376.25960.3141-0.09230.6822-0.15990.06180.051-0.4485-0.102-0.32270.2066-0.00210.02450.20530.0190.23555.096331.8516-17.481
130.7043-0.1979-0.19310.6207-0.1620.5089-0.0092-0.015-0.1311-0.1289-0.01140.01260.04320.07890.02480.2099-0.05280.01660.25040.00150.23619.2634-7.9507-29.3232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 59 )A0 - 59
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 116 )A60 - 116
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 212 )A117 - 212
4X-RAY DIFFRACTION4chain 'A' and (resid 213 through 243 )A213 - 243
5X-RAY DIFFRACTION5chain 'A' and (resid 244 through 356 )A244 - 356
6X-RAY DIFFRACTION6chain 'A' and (resid 357 through 432 )A357 - 432
7X-RAY DIFFRACTION7chain 'A' and (resid 433 through 547 )A433 - 547
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 72 )B2 - 72
9X-RAY DIFFRACTION9chain 'B' and (resid 73 through 116 )B73 - 116
10X-RAY DIFFRACTION10chain 'B' and (resid 117 through 305 )B117 - 305
11X-RAY DIFFRACTION11chain 'B' and (resid 306 through 432 )B306 - 432
12X-RAY DIFFRACTION12chain 'B' and (resid 433 through 460 )B433 - 460
13X-RAY DIFFRACTION13chain 'B' and (resid 461 through 547 )B461 - 547

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