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- PDB-2gc1: The crystal structure of phosphoglucose isomerase from Pyrococcus... -

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Basic information

Entry
Database: PDB / ID: 2gc1
TitleThe crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with sorbitol 6-phosphate and zinc
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / cupin / phosphoglucose isomerase / sorbitol 6-phosphate
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glycolytic process / gluconeogenesis / iron ion binding / cytoplasm
Similarity search - Function
Glucose-6-phosphate isomerase, prokaryote / Glucose-6-phosphate isomerase, archaea/bacteria / Glucose-6-phosphate isomerase (GPI) / : / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
D-SORBITOL-6-PHOSPHATE / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBerrisford, J.M. / Rice, D.W. / Baker, P.J.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Evidence Supporting a cis-enediol-based Mechanism for Pyrococcus furiosus Phosphoglucose Isomerase
Authors: Berrisford, J.M. / Hounslow, A.M. / Akerboom, J. / Hagen, W.R. / Brouns, S.J. / van der Oost, J. / Murray, I.A. / Michael Blackburn, G. / Waltho, J.P. / Rice, D.W. / Baker, P.J.
History
DepositionMar 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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

Downloads & links

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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)43,4777
Polymers42,7572
Non-polymers7215
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-136 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.311, 72.857, 71.640
Angle α, β, γ (deg.)90.00, 103.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 21378.273 Da / Num. of mol.: 2 / Fragment: phosphoglucose isomerase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: pgiA / Plasmid: pLUW557 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P83194, glucose-6-phosphate isomerase
#2: Sugar ChemComp-S6P / D-SORBITOL-6-PHOSPHATE / 1-O-PHOSPHONO-D-GLUCITOL / D-GLUCITOL-6-PHOSPHATE


Type: D-saccharide / Mass: 262.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H15O9P
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.05 M ammonium sulphate, 0.1 M sodium acetate pH 4.6, 20% PEG monoethyl ether 2000, 5 mM D-sorbitol 6-phosphate, 5mM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2005 / Details: Osmic Varimax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→69.673 Å / Num. all: 28380 / Num. obs: 28380 / % possible obs: 92.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 9.6
Reflection shellResolution: 1.95→2.06 Å / % possible obs: 88.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2 / Num. measured all: 17653 / Num. unique obs: 3961 / Rsym value: 0.379 / % possible all: 88.2

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X8E

1x8e


Resolution: 1.95→19.92 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.163 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1436 5.1 %RANDOM
Rwork0.198 ---
all0.201 28346 --
obs0.201 28346 91.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.979 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.09 Å2
2--0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 35 307 3369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223145
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9664268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66124.43149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42415525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6981512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022400
X-RAY DIFFRACTIONr_nbd_refined0.1870.21472
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22064
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2294
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.210
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1060.21
X-RAY DIFFRACTIONr_mcbond_it0.651.51934
X-RAY DIFFRACTIONr_mcangle_it1.10223010
X-RAY DIFFRACTIONr_scbond_it1.45531421
X-RAY DIFFRACTIONr_scangle_it2.234.51251
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 104 -
Rwork0.252 1875 -
obs-1979 87.8 %

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