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- PDB-4wmj: Colias eurytheme Phosphoglucose isomerase. Homodimer from 4-5(18)... -

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Basic information

Entry
Database: PDB / ID: 4wmj
TitleColias eurytheme Phosphoglucose isomerase. Homodimer from 4-5(18) genotype.
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / Glycolysis
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / 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 speciesColias eurytheme (orange sulphur)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHill, J.A. / Watt, W.B.
CitationJournal: Thesis, Stanford University / Year: 2013
Title: Structure and Function of Phosphoglucose Isomerase In Colias Eurytheme
Authors: Hill, J.A. / Watt, W.B. / Jardetzky, T. / Tuljapurkar, S.
History
DepositionOct 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
C: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)247,7534
Polymers247,7534
Non-polymers00
Water19,6901093
1
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)123,8762
Polymers123,8762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12410 Å2
ΔGint-66 kcal/mol
Surface area36220 Å2
MethodPISA
2
C: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)123,8762
Polymers123,8762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12390 Å2
ΔGint-67 kcal/mol
Surface area36140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.287, 115.495, 135.079
Angle α, β, γ (deg.)90.00, 101.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glucose-6-phosphate isomerase


Mass: 61938.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colias eurytheme (orange sulphur) / Gene: PGI / Production host: Escherichia coli (E. coli) / References: UniProt: G9BZJ0, glucose-6-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1093 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M lithium sulfate, 22% PEG 4000, 0.2M Tris-Cl pH 7.4.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→41.19 Å / Num. obs: 270174 / % possible obs: 77.68 % / Redundancy: 2 % / Net I/σ(I): 8.99

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOLREPphasing
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U0E

1u0e


Resolution: 1.5→41.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.507 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 14357 5 %RANDOM
Rwork0.18315 ---
obs0.1849 270174 77.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.161 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0.01 Å2
2--0.23 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17415 0 0 1093 18508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01917845
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216984
X-RAY DIFFRACTIONr_angle_refined_deg1.91.94224215
X-RAY DIFFRACTIONr_angle_other_deg0.93339058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35952211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28524.909825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.867152974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6541560
X-RAY DIFFRACTIONr_chiral_restr0.1240.22663
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02120410
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024214
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3081.3898856
X-RAY DIFFRACTIONr_mcbond_other1.3081.3898855
X-RAY DIFFRACTIONr_mcangle_it1.8532.0811063
X-RAY DIFFRACTIONr_mcangle_other1.8532.0811064
X-RAY DIFFRACTIONr_scbond_it2.4411.6228989
X-RAY DIFFRACTIONr_scbond_other2.4411.6228990
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6232.32613153
X-RAY DIFFRACTIONr_long_range_B_refined4.4211.76621716
X-RAY DIFFRACTIONr_long_range_B_other4.39911.60621275
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.537 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 294 -
Rwork0.4 5376 -
obs--21.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.08730.03730.07730.06710.0340.16680.02430.0143-0.0026-0.007-0.013-0.00110.01580.0307-0.01140.01650.0072-0.00250.03190.00030.0024-33.7174-2.028722.7841
20.0637-0.00650.04360.13420.00890.1560.0205-0.00670.00050.0093-0.01360.03070.0002-0.0373-0.0070.0095-0.00310.00420.0387-0.00170.008-54.52241.499334.3117
30.05760.0372-0.01080.1674-0.03680.0962-0.0142-0.00740.0073-0.01380.02920.00750.039-0.0261-0.0150.0181-0.0052-0.0070.03480.00250.0028-28.5711-10.770696.8076
40.04790.0044-0.00110.1116-0.0530.1479-0.0076-0.00610.0175-0.0050.0099-0.0286-0.0092-0.018-0.00230.00820.0072-0.00030.0289-0.00160.017-17.13669.136789.6017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 556
2X-RAY DIFFRACTION2B2 - 556
3X-RAY DIFFRACTION3C3 - 556
4X-RAY DIFFRACTION4D4 - 556

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