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

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Basic information

Entry
Database: PDB / ID: 6bzb
TitleCrystal Structure of Glucose-6-phosphate Isomerase from Elizabethkingia anophelis
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 / carbohydrate derivative binding / gluconeogenesis / glycolytic process / cytoplasm
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
Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: 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
DepositionDec 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)125,9672
Polymers125,9672
Non-polymers00
Water24,2661347
1
A: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)62,9841
Polymers62,9841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)62,9841
Polymers62,9841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12160 Å2
ΔGint-65 kcal/mol
Surface area35620 Å2
MethodPISA
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 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1347 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
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, 20% ethylene glycol cryo. Tray: 295124f1, puck: hay3-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97876 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 1.6→43.185 Å / Num. obs: 147843 / % possible obs: 99.8 % / Redundancy: 5.971 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(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 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.646.1510.5453.37108230.8810.59399.9
1.64-1.696.1590.4544.01105760.9140.49499.9
1.69-1.746.1470.3814.88102720.9370.41599.9
1.74-1.796.1520.3155.9399890.9550.34499.9
1.79-1.856.1390.2537.4696890.9690.27699.9
1.85-1.916.1010.2039.2193740.9790.22299.9
1.91-1.986.030.15811.6590660.9860.17399.8
1.98-2.075.9470.12414.5187180.9910.13699.8
2.07-2.165.870.09817.6383660.9940.10799.8
2.16-2.265.7810.08120.680120.9950.08999.7
2.26-2.395.7720.07322.5976250.9960.0899.6
2.39-2.535.7530.06325.1172260.9960.0799.7
2.53-2.75.7320.05627.5268170.9970.06299.7
2.7-2.925.7330.04930.3163640.9980.05499.8
2.92-3.25.7720.04433.658610.9980.04899.8
3.2-3.585.8590.03837.3353180.9980.04199.8
3.58-4.135.9960.03339.9447360.9990.03699.8
4.13-5.066.0510.02941.6940410.9990.032100
5.06-7.165.9670.02840.4831680.9990.03199.8
7.16-43.1855.5090.02640.9718020.9990.02897.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_2919)refinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1768 1933 1.31 %
Rwork0.1488 --
obs0.1492 147818 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.89 Å2 / Biso mean: 21.5199 Å2 / Biso min: 8.14 Å2
Refinement stepCycle: final / Resolution: 1.6→43.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8666 0 0 1361 10027
Biso mean---32.2 -
Num. residues----1093
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.24391380.19141029510433100
1.64-1.68440.21421370.18251034710484100
1.6844-1.73390.2271390.17571031310452100
1.7339-1.78990.21121440.17161033610480100
1.7899-1.85390.19141270.16411036810495100
1.8539-1.92810.19841370.17121035010487100
1.9281-2.01590.20541570.16381031810475100
2.0159-2.12210.21671400.16351039610536100
2.1221-2.25510.18431350.15431039910534100
2.2551-2.42920.20771350.15641038410519100
2.4292-2.67360.17971420.15251041610558100
2.6736-3.06040.17131340.14531049910633100
3.0604-3.85540.13511290.12851056910698100
3.8554-43.20090.1421390.1275108951103499
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)
11.3923-1.04670.03162.39550.34011.07630.01180.35780.0496-0.3932-0.0335-0.0104-0.11070.0760.02180.2078-0.07470.00060.2490.04750.113127.506912.8271-44.8812
20.63230.20740.33810.48330.3271.0464-0.08630.06730.1568-0.10.04310.005-0.24460.14960.0640.1443-0.0409-0.00120.12010.02210.151634.024123.4794-22.7237
31.07650.0483-0.02140.48840.40881.30150.04-0.0659-0.10690.1351-0.0096-0.04380.1350.043-0.03360.143-0.0137-0.02030.09920.00680.119731.32753.9957-2.3874
42.1635-0.12710.83271.8373-0.11961.8550.0612-0.20160.0440.1747-0.07430.07090.0478-0.08070.01020.1277-0.03750.01190.1252-0.03270.091226.007613.72915.9193
50.45710.16170.13970.53790.27170.6625-0.0120.08610.0155-0.04570.0205-0.0202-0.04380.0676-0.00920.0794-0.006300.1120.00060.093728.94958.7373-25.509
63.4566-1.1944-1.09074.33392.59995.3851-0.13320.1464-0.44630.19210.07020.0340.42350.17470.05360.19130.0077-0.00120.2124-0.0670.157217.3697-20.4264-47.6974
70.46980.06750.24610.580.26460.6025-0.0265-0.03680.05920.0253-0.03690.0828-0.0294-0.09010.03460.0938-0.0015-0.0120.0955-0.0130.102716.127211.1765-18.2822
81.0031-0.0028-0.03541.23690.69631.18880.0120.040.0563-0.1302-0.21840.3748-0.1242-0.36740.19060.13910.0122-0.04610.2895-0.09270.2904-8.32741.7421-25.7131
90.671-0.02420.11410.74290.25760.78670.03940.0088-0.16770.1065-0.11780.17450.2908-0.22120.01730.2275-0.09370.0340.1961-0.05990.22473.3542-21.0035-21.5646
101.28250.0042-0.22080.6288-0.09360.59150.0552-0.1109-0.12230.239-0.0087-0.09380.21510.0317-0.02560.2381-0.0012-0.04770.10610.00340.148428.0174-15.7595-8.4804
111.51350.00550.1371.0826-0.19432.20280.01840.0035-0.22380.20730.0055-0.23770.2869-0.0224-0.0650.24710.0299-0.0480.1058-0.02920.216333.6199-21.9953-17.1612
121.1113-0.0710.01510.6033-0.11580.46240.06880.0535-0.38420.12370.0201-0.16910.36350.0379-0.01430.32810.0251-0.05370.1183-0.0380.276926.521-28.2988-16.7417
130.45080.06250.04380.6690.39190.72660.01510.0033-0.0290.0542-0.1080.12060.0969-0.18030.04770.0931-0.03180.01730.1457-0.03330.13017.2662-3.1511-18.4201
140.4932-0.5776-0.85173.49390.84072.53560.26030.08970.0254-0.0306-0.1217-0.1138-0.19380.0168-0.11330.17250.064-0.00720.1719-0.02430.17584.534232.8193-17.0631
150.39850.09090.15730.58720.21180.55320.01520.0699-0.1093-0.0031-0.02010.00310.0908-0.00390.02590.1213-0-0.00770.1343-0.03990.124918.7741-5.8708-28.2489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 52 )A1 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 136 )A53 - 136
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 197 )A137 - 197
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 252 )A198 - 252
5X-RAY DIFFRACTION5chain 'A' and (resid 253 through 432 )A253 - 432
6X-RAY DIFFRACTION6chain 'A' and (resid 433 through 460 )A433 - 460
7X-RAY DIFFRACTION7chain 'A' and (resid 461 through 547 )A461 - 547
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 52 )B2 - 52
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 135 )B53 - 135
10X-RAY DIFFRACTION10chain 'B' and (resid 136 through 197 )B136 - 197
11X-RAY DIFFRACTION11chain 'B' and (resid 198 through 226 )B198 - 226
12X-RAY DIFFRACTION12chain 'B' and (resid 227 through 274 )B227 - 274
13X-RAY DIFFRACTION13chain 'B' and (resid 275 through 432 )B275 - 432
14X-RAY DIFFRACTION14chain 'B' and (resid 433 through 456 )B433 - 456
15X-RAY DIFFRACTION15chain 'B' and (resid 457 through 547 )B457 - 547

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