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- PDB-1x9i: Crystal structure of Crystal structure of phosphoglucose/phosphom... -

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Basic information

Entry
Database: PDB / ID: 1x9i
TitleCrystal structure of Crystal structure of phosphoglucose/phosphomannose phosphoglucose/phosphomannoseisomerase from Pyrobaculum aerophilum in complex with glucose 6-phosphate
Componentsglucose-6-phosphate isomerase
KeywordsISOMERASE / enzyme / crenarchaeon / hyperthermophile / PGI superfamily / glucose 6-phosphate
Function / homology
Function and homology information


mannose-6-phosphate isomerase / mannose-6-phosphate isomerase activity / carbohydrate derivative metabolic process / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / carbohydrate derivative binding / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Bifunctional phosphoglucose/phosphomannose isomerase, SIS domain 1 / Bifunctional glucose-6-phosphate/mannose-6-phosphate isomerase, C-terminal / Bacterial phospho-glucose isomerase C-terminal SIS domain / SIS domain / SIS domain 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 / : / Bifunctional phosphoglucose/phosphomannose isomerase
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / refinement / Resolution: 1.16 Å
AuthorsSwan, M.K. / Hansen, T. / Schoenheit, P. / Davies, C.
Citation
Journal: Biochemistry / Year: 2004
Title: Structural basis for phosphomannose isomerase activity in phosphoglucose isomerase from Pyrobaculum aerophilum: a subtle difference between distantly related enzymes.
Authors: Swan, M.K. / Hansen, T. / Schoenheit, P. / Davies, C.
#1: Journal: To be published
Title: A novel phosphoglucose isomerase/phosphomannose isomerase from the crenarchaeon Pyrobaculum aerophilum is a member of the PGI superfamily: structural evidence at 1.16 A resolution
Authors: Swan, M.K. / Hansen, T. / Schoenheit, P. / Davies, C.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary X-ray diffraction analysis of phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum
Authors: Swan, M.K. / Hansen, T. / Schoenheit, P. / Davies, C.
History
DepositionAug 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Aug 23, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)67,8866
Polymers67,1822
Non-polymers7044
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-7 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.9, 100.8, 56.1
Angle α, β, γ (deg.)90.00, 113.8, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a dimer. The asymmetric unit is a dimer.

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Components

#1: Protein glucose-6-phosphate isomerase


Mass: 33590.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: PAE1610 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: GenBank: 18312750, UniProt: Q8ZWV0*PLUS, glucose-6-phosphate isomerase, mannose-6-phosphate isomerase
#2: Chemical ChemComp-G6Q / GLUCOSE-6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% polyethylene glycol 8000, 0.22M ammonium sulphate, 100mM Tris, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.16→36 Å / Num. all: 176109 / Num. obs: 176109 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 40
Reflection shellResolution: 1.16→1.2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 4 / Num. unique all: 15133 / Rsym value: 0.233 / % possible all: 77.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: refinement
Starting model: pdb entry 1tzb

1tzb


Resolution: 1.16→36 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.886 / SU ML: 0.019 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.164 8871 5 %RANDOM
Rwork0.147 ---
all0.148 176101 --
obs0.148 176101 90.01 %-
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: 12.014 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-0.38 Å2
2--0.26 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.16→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4707 0 44 559 5310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224968
X-RAY DIFFRACTIONr_bond_other_d0.0010.024749
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9816769
X-RAY DIFFRACTIONr_angle_other_deg0.881311053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.325608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95623.365211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85515877
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5841542
X-RAY DIFFRACTIONr_chiral_restr0.0830.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025384
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02958
X-RAY DIFFRACTIONr_nbd_refined0.2140.2991
X-RAY DIFFRACTIONr_nbd_other0.1830.24959
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22475
X-RAY DIFFRACTIONr_nbtor_other0.0830.22838
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2429
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.213
X-RAY DIFFRACTIONr_mcbond_it1.0761.53936
X-RAY DIFFRACTIONr_mcbond_other0.4511.51218
X-RAY DIFFRACTIONr_mcangle_it1.29724993
X-RAY DIFFRACTIONr_scbond_it1.88432208
X-RAY DIFFRACTIONr_scangle_it2.4964.51771
X-RAY DIFFRACTIONr_rigid_bond_restr0.995311539
X-RAY DIFFRACTIONr_sphericity_free3.9743559
X-RAY DIFFRACTIONr_sphericity_bonded2.57539613
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 552 -
Rwork0.176 10278 -
obs-10830 74.82 %

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