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- PDB-2cxn: Crystal structure of mouse AMF / phosphate complex -

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Basic information

Entry
Database: PDB / ID: 2cxn
TitleCrystal structure of mouse AMF / phosphate complex
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


glycolytic process through glucose-6-phosphate / Gluconeogenesis / Glycolysis / TP53 Regulates Metabolic Genes / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / monosaccharide binding ...glycolytic process through glucose-6-phosphate / Gluconeogenesis / Glycolysis / TP53 Regulates Metabolic Genes / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / erythrocyte homeostasis / positive regulation of immunoglobulin production / ciliary membrane / response to testosterone / response to immobilization stress / mesoderm formation / response to cadmium ion / response to muscle stretch / Neutrophil degranulation / positive regulation of endothelial cell migration / response to progesterone / cytokine activity / glycolytic process / gluconeogenesis / growth factor activity / response to estradiol / glucose homeostasis / myelin sheath / in utero embryonic development / learning or memory / ubiquitin protein ligase binding / negative regulation of apoptotic process / extracellular space / plasma membrane / 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
PHOSPHATE ION / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsTanaka, N. / Haga, A. / Naba, N. / Shiraiwa, K. / Kusakabe, Y. / Hashimoto, K. / Funasaka, T. / Nagase, H. / Raz, A. / Nakamura, K.T.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structures of mouse autocrine motility factor in complex with carbohydrate phosphate inhibitors provide insight into structure-activity relationship of the inhibitors
Authors: Tanaka, N. / Haga, A. / Naba, N. / Shiraiwa, K. / Kusakabe, Y. / Hashimoto, K. / Funasaka, T. / Nagase, H. / Raz, A. / Nakamura, K.T.
History
DepositionJun 30, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)125,8517
Polymers125,3872
Non-polymers4635
Water21,4741192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14320 Å2
ΔGint-83 kcal/mol
Surface area37330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.951, 116.025, 73.208
Angle α, β, γ (deg.)90.00, 101.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 62693.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P06745, glucose-6-phosphate isomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1192 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Cacodylate, PEG8000, NaAcetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. obs: 215161 / % possible obs: 96.1 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.902 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18754 10779 5 %RANDOM
Rwork0.17146 ---
obs0.17228 204350 96.03 %-
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: 14.502 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.03 Å2
2---0.49 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8832 0 29 1192 10053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0219074
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9731.9412274
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.28851112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.21336
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026820
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1790.24576
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0730.2900
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0730.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3641.55536
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.73228916
X-RAY DIFFRACTIONr_scbond_it1.20533538
X-RAY DIFFRACTIONr_scangle_it2.0224.53358
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.252 580
Rwork0.237 11491

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