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- PDB-3qki: Crystal structure of Glucose-6-Phosphate Isomerase (PF14_0341) fr... -

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Basic information

Entry
Database: PDB / ID: 3qki
TitleCrystal structure of Glucose-6-Phosphate Isomerase (PF14_0341) from Plasmodium falciparum 3D7
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


TP53 Regulates Metabolic Genes / Gluconeogenesis / Glycolysis / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / Neutrophil degranulation / glucose 6-phosphate metabolic process / carbohydrate derivative binding / pentose-phosphate shunt / monosaccharide binding ...TP53 Regulates Metabolic Genes / Gluconeogenesis / Glycolysis / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / Neutrophil degranulation / glucose 6-phosphate metabolic process / carbohydrate derivative binding / pentose-phosphate shunt / monosaccharide binding / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. ...Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsGileadi, T. / Wernimont, A.K. / Hutchinson, A. / Weadge, J. / Cossar, D. / Lew, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Gileadi, T. / Wernimont, A.K. / Hutchinson, A. / Weadge, J. / Cossar, D. / Lew, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Hills, T. / Pizarro, J.C. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Glucose-6-Phosphate Isomerase (PF14_0341) from Plasmodium falciparum 3D7
Authors: Gileadi, T. / Wernimont, A.K. / Hills, T. / Hui, R. / Pizarro, J.C.
History
DepositionFeb 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 23, 2013Group: Structure summary
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)208,9673
Polymers208,9673
Non-polymers00
Water29,2921626
1
A: Glucose-6-phosphate isomerase

A: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)139,3122
Polymers139,3122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13570 Å2
ΔGint-70 kcal/mol
Surface area39160 Å2
MethodPISA
2
B: Glucose-6-phosphate isomerase
C: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)139,3122
Polymers139,3122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13290 Å2
ΔGint-75 kcal/mol
Surface area39230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.444, 233.003, 72.794
Angle α, β, γ (deg.)90.000, 91.400, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-641-

HOH

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Components

#1: Protein Glucose-6-phosphate isomerase /


Mass: 69655.797 Da / Num. of mol.: 3 / Fragment: G6PI
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF14_0341 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8ILA4, glucose-6-phosphate isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1626 / 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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 1.2 M Na citrate 0.1 M Na Hepes 5% MPD , pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 174 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.92→40 Å / Num. obs: 172699 / % possible obs: 98.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.169 / Χ2: 1.663 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.92-1.992.70.785164061.576194.3
1.99-2.0730.603168281.656196.6
2.07-2.163.30.553172191.599198.9
2.16-2.283.60.51174112.156199.7
2.28-2.423.70.421174781.6351100
2.42-2.613.80.345174221.6671100
2.61-2.873.90.25174091.5791100
2.87-3.283.90.147174661.5271100
3.28-4.143.90.078174651.824199.9
4.14-403.90.047175951.4121100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52.37 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.53 Å
Translation2.5 Å46.53 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry code 1GZD

1gzd


Resolution: 1.92→39.66 Å / Cor.coef. Fo:Fc: 0.9364 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 7981 5.01 %RANDOM
Rwork0.1737 ---
obs0.1753 159308 --
Displacement parametersBiso max: 122.31 Å2 / Biso mean: 23.6132 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--1.0305 Å20 Å20.8024 Å2
2---5.0656 Å20 Å2
3---6.0961 Å2
Refine analyzeLuzzati coordinate error obs: 0.224 Å
Refinement stepCycle: LAST / Resolution: 1.92→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14024 0 0 1626 15650
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d52362
X-RAY DIFFRACTIONt_trig_c_planes4592
X-RAY DIFFRACTIONt_gen_planes20865
X-RAY DIFFRACTIONt_it1451820
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion18775
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact186004
X-RAY DIFFRACTIONt_bond_d1451820.01
X-RAY DIFFRACTIONt_angle_deg1966021.08
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion17.31
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2999 373 4.81 %
Rwork0.2469 7376 -
all0.2495 7749 -

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