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- PDB-1tzb: Crystal structure of native phosphoglucose/phosphomannose isomera... -

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Basic information

Entry
Database: PDB / ID: 1tzb
TitleCrystal structure of native phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum
Componentsglucose-6-phosphate isomerase, conjectural
KeywordsISOMERASE / enzyme / crenarchaeon / hyperthermophile / PGI family
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
Bifunctional phosphoglucose/phosphomannose isomerase
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.16 Å
AuthorsSwan, M.K. / Hansen, T. / Schoenheit, P. / Davies, C.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: A novel phosphoglucose/phosphomannose isomease 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.
#1: Journal: To be Published
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
DepositionJul 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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, conjectural
B: glucose-6-phosphate isomerase, conjectural
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,13412
Polymers67,1822
Non-polymers95310
Water11,259625
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-111 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.100, 100.800, 55.800
Angle α, β, γ (deg.)90.00, 113.20, 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, conjectural


Mass: 33590.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Strain: str. IM2 / Gene: PAE1610 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q8ZWV0, glucose-6-phosphate isomerase, mannose-6-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#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.: 625 / 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: 168938 / Num. obs: 168938 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 9.6 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 38.6
Reflection shellResolution: 1.16→1.2 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3.3 / Num. unique all: 11874 / Rsym value: 0.347 / % possible all: 61.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.16→36 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.503 / SU ML: 0.023 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.165 8508 5 %RANDOM
Rwork0.149 ---
all0.15 168938 --
obs0.15 168938 87.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.659 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0.39 Å2
2---0.27 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.16→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4707 0 52 625 5384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225005
X-RAY DIFFRACTIONr_bond_other_d0.0020.024780
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9746818
X-RAY DIFFRACTIONr_angle_other_deg0.847311124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4015607
X-RAY DIFFRACTIONr_chiral_restr0.0740.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025394
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02967
X-RAY DIFFRACTIONr_nbd_refined0.230.21007
X-RAY DIFFRACTIONr_nbd_other0.2370.25824
X-RAY DIFFRACTIONr_nbtor_other0.0820.22839
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2472
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.230
X-RAY DIFFRACTIONr_mcbond_it0.5581.53048
X-RAY DIFFRACTIONr_mcangle_it0.91225005
X-RAY DIFFRACTIONr_scbond_it1.11931957
X-RAY DIFFRACTIONr_scangle_it1.7934.51808
X-RAY DIFFRACTIONr_rigid_bond_restr0.57925005
X-RAY DIFFRACTIONr_sphericity_free1.2692624
X-RAY DIFFRACTIONr_sphericity_bonded1.15924909
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.231 465
Rwork0.229 8072
obs-8537

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