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- PDB-2q8n: Crystal structure of Glucose-6-phosphate isomerase (EC 5.3.1.9) (... -

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Basic information

Entry
Database: PDB / ID: 2q8n
TitleCrystal structure of Glucose-6-phosphate isomerase (EC 5.3.1.9) (TM1385) from Thermotoga maritima at 1.82 A resolution
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / TM1385 / Glucose-6-phosphate isomerase (EC 5.3.1.9) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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 / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Glucose-6-phosphate isomerase (EC 5.3.1.9) (TM1385) from Thermotoga maritima at 1.82 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.6Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE.

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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
C: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,98816
Polymers156,0273
Non-polymers1,96213
Water11,043613
1
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
C: Glucose-6-phosphate isomerase
hetero molecules

A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
C: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,97732
Polymers312,0546
Non-polymers3,92326
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_566x,-y+1,-z+3/21
Unit cell
Length a, b, c (Å)117.506, 125.867, 245.476
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-545-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 2 / Auth seq-ID: 1 - 447 / Label seq-ID: 13 - 459

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Glucose-6-phosphate isomerase / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI


Mass: 52008.930 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Species: Thermotoga maritima / Strain: MSB8, DSM 3109, JCM 10099 / Gene: TM1385, pgi / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9X1A5, glucose-6-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 0.23M Li Sulfate, 0.10M Tris-HCl, 0.031M HCl, 43% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 31, 2005 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→45.932 Å / Num. obs: 161864 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 35.51 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 19.96
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.82-1.890.6662.1697191719699.9
1.89-1.960.5452.7648581482599.8
1.96-2.050.3924.41001281619799.9
2.05-2.160.2476.41005161632599.9
2.16-2.290.2691222561548899.9
2.29-2.470.23311.91609811647499.9
2.47-2.720.155171680831625099.8
2.72-3.110.08925.31655471605899.7
3.11-3.910.04544.41657791622799.8
3.91-45.9320.02873.51637811682499.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1B0Z

1b0z


Resolution: 1.82→45.932 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.633 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. PEG 400, SULFATE, CHLORIDE ARE MODELED DUE TO THEIR PRESENCE IN DENSITY AND CRYSTALLIZATION SOLVENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 8195 5.1 %RANDOM
Rwork0.197 ---
obs0.199 161863 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.431 Å2
Baniso -1Baniso -2Baniso -3
1-4.31 Å20 Å20 Å2
2---1.89 Å20 Å2
3----2.42 Å2
Refinement stepCycle: LAST / Resolution: 1.82→45.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10624 0 100 613 11337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02210941
X-RAY DIFFRACTIONr_bond_other_d0.0020.027414
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.97414826
X-RAY DIFFRACTIONr_angle_other_deg0.994318083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94551374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45324.217498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.371151860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1511569
X-RAY DIFFRACTIONr_chiral_restr0.0970.21650
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212166
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022224
X-RAY DIFFRACTIONr_nbd_refined0.2140.22113
X-RAY DIFFRACTIONr_nbd_other0.1970.28105
X-RAY DIFFRACTIONr_nbtor_refined0.1860.25458
X-RAY DIFFRACTIONr_nbtor_other0.090.25835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2624
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.2145
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.244
X-RAY DIFFRACTIONr_mcbond_it1.96236911
X-RAY DIFFRACTIONr_mcbond_other0.40632757
X-RAY DIFFRACTIONr_mcangle_it2.989510855
X-RAY DIFFRACTIONr_scbond_it5.18284567
X-RAY DIFFRACTIONr_scangle_it7.229113957
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2606TIGHT POSITIONAL0.040.05
2B2606TIGHT POSITIONAL0.040.05
3C2606TIGHT POSITIONAL0.040.05
1A3084MEDIUM POSITIONAL0.280.5
2B3084MEDIUM POSITIONAL0.230.5
3C3084MEDIUM POSITIONAL0.280.5
1A2606TIGHT THERMAL0.340.5
2B2606TIGHT THERMAL0.250.5
3C2606TIGHT THERMAL0.330.5
1A3084MEDIUM THERMAL1.512
2B3084MEDIUM THERMAL1.232
3C3084MEDIUM THERMAL1.492
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 598 -
Rwork0.381 11269 -
obs-11867 99.89 %

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