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- PDB-1x9h: Crystal structure of phosphoglucose/phosphomannose isomerase from... -

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Basic information

Entry
Database: PDB / ID: 1x9h
TitleCrystal structure of phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum in complex with fructose 6-phosphate
Componentsglucose-6-phosphate isomerase
KeywordsISOMERASE / enzyme / crenarchaeon / hyperthermophile / PGI superfamily / fructose 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
FRUCTOSE -6-PHOSPHATE / : / Bifunctional phosphoglucose/phosphomannose isomerase
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFINEMENT / Resolution: 1.5 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: Structure summary / Category: audit_author / Item: _audit_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)68,55113
Polymers67,1822
Non-polymers1,36911
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9000 Å2
ΔGint-66 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.2, 100.8, 55.9
Angle α, β, γ (deg.)90.00, 113.4, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-F6R / FRUCTOSE -6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O9P
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 403 / 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: 1.5→36 Å / Num. all: 86757 / Num. obs: 86757 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 19.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 1.7 / Num. unique all: 7410 / Rsym value: 0.391 / % possible all: 82.8

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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: 1.5→36 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.157 / SU ML: 0.064 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18 4290 5 %RANDOM
Rwork0.152 ---
all0.153 87508 --
obs0.153 86508 96.38 %-
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: 16.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å2-0.48 Å2
2---0.42 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4716 0 81 403 5200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225039
X-RAY DIFFRACTIONr_bond_other_d0.0010.024833
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9876850
X-RAY DIFFRACTIONr_angle_other_deg1.128311228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1245606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62623.226217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5215894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1251545
X-RAY DIFFRACTIONr_chiral_restr0.0750.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025403
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02970
X-RAY DIFFRACTIONr_nbd_refined0.2120.21049
X-RAY DIFFRACTIONr_nbd_other0.1820.25103
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22493
X-RAY DIFFRACTIONr_nbtor_other0.0820.22924
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2336
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.214
X-RAY DIFFRACTIONr_mcbond_it0.9911.53937
X-RAY DIFFRACTIONr_mcbond_other0.2681.51218
X-RAY DIFFRACTIONr_mcangle_it1.19224990
X-RAY DIFFRACTIONr_scbond_it2.29732287
X-RAY DIFFRACTIONr_scangle_it2.8544.51860
X-RAY DIFFRACTIONr_rigid_bond_restr3.275311722
X-RAY DIFFRACTIONr_sphericity_free3.8863403
X-RAY DIFFRACTIONr_sphericity_bonded1.46639783
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 257 -
Rwork0.264 5022 -
obs-5279 79.8 %

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