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- PDB-2gc0: The crystal structure of phosphoglucose isomerase from Pyrococcus... -

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Basic information

Entry
Database: PDB / ID: 2gc0
TitleThe crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with 5-phospho-D-arabinonohydroxamate and zinc
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / cupin / phosphoglucose isomerase / 5-phospho-D-arabinonohydroxamate
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / gluconeogenesis / glycolytic process / 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
5-PHOSPHO-D-ARABINOHYDROXAMIC ACID / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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

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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)43,4106
Polymers42,7572
Non-polymers6534
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-119 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.149, 73.112, 74.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PAN / 5-PHOSPHO-D-ARABINOHYDROXAMIC ACID


Mass: 261.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12NO9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M tri sodium citrate pH 6.5, 30% polyethylene glycol 4000 and 10% isopropanol, 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 30, 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: 2→74.159 Å / Num. all: 25249 / Num. obs: 25249 / % possible obs: 99.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 5.6
Reflection shellResolution: 2→2.11 Å / % possible obs: 99.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / Num. measured all: 16233 / Num. unique all: 3597 / Num. unique obs: 3597 / Rsym value: 0.42 / % possible all: 99.4

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Phasing

Phasing MRRfactor: 0.439 / Cor.coef. Fo:Fc: 0.561
Highest resolutionLowest resolution
Rotation3 Å17.41 Å
Translation3 Å17.41 Å

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Processing

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

1x8e


Resolution: 2→17.41 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.427 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1289 5.1 %RANDOM
Rwork0.166 ---
all0.169 25249 --
obs0.169 25249 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.189 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→17.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3020 0 34 336 3390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223134
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9644242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6525374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76124.459148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36615524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9761512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022398
X-RAY DIFFRACTIONr_nbd_refined0.1840.21473
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22059
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2311
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.220
X-RAY DIFFRACTIONr_mcbond_it6.52321930
X-RAY DIFFRACTIONr_mcangle_it7.28633008
X-RAY DIFFRACTIONr_scbond_it8.30521409
X-RAY DIFFRACTIONr_scangle_it10.56731234
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 92 -
Rwork0.209 1696 -
obs-1788 99.11 %

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