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- PDB-1iri: Crystal structure of human autocrine motility factor complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1iri
TitleCrystal structure of human autocrine motility factor complexed with an inhibitor
Componentsautocrine motility factorGlucose-6-phosphate isomerase
KeywordsISOMERASE / cytokine
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / erythrocyte homeostasis / Glycolysis / ciliary membrane ...glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / erythrocyte homeostasis / Glycolysis / ciliary membrane / response to testosterone / humoral immune response / positive regulation of immunoglobulin production / mesoderm formation / response to immobilization stress / response to cadmium ion / response to muscle stretch / positive regulation of endothelial cell migration / response to progesterone / cytokine activity / gluconeogenesis / TP53 Regulates Metabolic Genes / glycolytic process / growth factor activity / glucose homeostasis / response to estradiol / secretory granule lumen / in utero embryonic development / negative regulation of neuron apoptotic process / ficolin-1-rich granule lumen / learning or memory / carbohydrate metabolic process / ubiquitin protein ligase binding / Neutrophil degranulation / extracellular exosome / extracellular region / 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
ERYTHOSE-4-PHOSPHATE / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsTanaka, N. / Haga, A. / Uemura, H. / Akiyama, H. / Funasaka, T. / Nagase, H. / Raz, A. / Nakamura, K.T.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Inhibition mechanism of cytokine activity of human autocrine motility factor examined by crystal structure analyses and site-directed mutagenesis studies.
Authors: Tanaka, N. / Haga, A. / Uemura, H. / Akiyama, H. / Funasaka, T. / Nagase, H. / Raz, A. / Nakamura, K.T.
History
DepositionOct 8, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: autocrine motility factor
B: autocrine motility factor
C: autocrine motility factor
D: autocrine motility factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,7208
Polymers252,9204
Non-polymers8004
Water7,782432
1
A: autocrine motility factor
B: autocrine motility factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8604
Polymers126,4602
Non-polymers4002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-78 kcal/mol
Surface area36730 Å2
MethodPISA
2
C: autocrine motility factor
D: autocrine motility factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8604
Polymers126,4602
Non-polymers4002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-77 kcal/mol
Surface area36820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.651, 107.771, 270.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer. Two dimers exist in an asymmetric unit.

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Components

#1: Protein
autocrine motility factor / Glucose-6-phosphate isomerase / glucose phosphate isomerase


Mass: 63229.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / References: UniProt: P06744, glucose-6-phosphate isomerase
#2: Sugar
ChemComp-E4P / ERYTHOSE-4-PHOSPHATE / Erythrose 4-phosphate


Type: saccharideCarbohydrate / Mass: 200.084 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H9O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 47.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: cacodylate, sodium acetate, PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 47 %
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 mg/mlprotein1drop
20.05 M1dropNaCl
320 %(v/v)glycerol1drop
40.02 MTris1droppH7.5
528 %(w/v)PEG80001reservoir
60.2 Msodium acetate1reservoir
720 %(v/v)glycerol1reservoir
80.1 Msodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. all: 92870 / Num. obs: 92870 / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.3
Reflection shellResolution: 2→2.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 25 Å / % possible obs: 100 % / Num. measured all: 550782 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.357

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1JIQ

1jiq


Resolution: 2.4→25 Å
RfactorNum. reflection% reflection
Rfree0.241 4595 5.205 %
Rwork0.193 --
obs-88274 -
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17780 0 52 432 18264
Refine LS restraintsType: p_bond_d / Dev ideal: 0.013
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor obs: 0.193 / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.528
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.46 Å

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